3839 lines (3838 with data), 263.2 kB
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 27/28\n",
"\n",
" To enable shared memory capabilities, try: install.extras('\n",
"NMF\n",
"')\n",
"\n",
"Loading required package: mclust\n",
"\n",
"Package 'mclust' version 5.4.6\n",
"Type 'citation(\"mclust\")' for citing this R package in publications.\n",
"\n",
"Loading required package: ade4\n",
"\n",
"\n",
"Attaching package: ‘ade4’\n",
"\n",
"\n",
"The following object is masked from ‘package:BiocGenerics’:\n",
"\n",
" score\n",
"\n",
"\n",
"\n",
"Attaching package: ‘GPArotation’\n",
"\n",
"\n",
"The following object is masked from ‘package:NMF’:\n",
"\n",
" entropy\n",
"\n",
"\n",
"\n",
"Attaching package: ‘MOFAtools’\n",
"\n",
"\n",
"The following objects are masked from ‘package:NMF’:\n",
"\n",
" featureNames, featureNames<-, predict, sampleNames, sampleNames<-\n",
"\n",
"\n",
"The following objects are masked from ‘package:Biobase’:\n",
"\n",
" featureNames, featureNames<-, sampleNames, sampleNames<-\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" predict\n",
"\n",
"\n",
"Loading required package: JADE\n",
"\n",
"Loading required package: lattice\n",
"\n",
"Loading required package: caTools\n",
"\n",
"Loading required package: gdata\n",
"\n",
"gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.\n",
"\n",
"\n",
"\n",
"gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.\n",
"\n",
"\n",
"Attaching package: ‘gdata’\n",
"\n",
"\n",
"The following object is masked from ‘package:Biobase’:\n",
"\n",
" combine\n",
"\n",
"\n",
"The following object is masked from ‘package:BiocGenerics’:\n",
"\n",
" combine\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" nobs\n",
"\n",
"\n",
"The following object is masked from ‘package:utils’:\n",
"\n",
" object.size\n",
"\n",
"\n",
"The following object is masked from ‘package:base’:\n",
"\n",
" startsWith\n",
"\n",
"\n",
"Loading required package: gtools\n",
"\n",
"\n",
"Attaching package: ‘gtools’\n",
"\n",
"\n",
"The following object is masked from ‘package:InterSIM’:\n",
"\n",
" logit\n",
"\n",
"\n",
"Loading required package: gplots\n",
"\n",
"\n",
"Attaching package: ‘gplots’\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" lowess\n",
"\n",
"\n"
]
}
],
"source": [
"library(\"InterSIM\", quietly = TRUE)\n",
"source(\"runfactorization.R\")"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1] \"../data/\"\n",
"[1] \"20210329212141\"\n",
"[1] \"../data/simulations_20210329212141/\"\n",
"[1] \"../results20210329212141/\"\n"
]
}
],
"source": [
"# Base folder for data\n",
"data_folder <- \"../data/\"\n",
"# Label to identify current run\n",
"tag <- format(Sys.time(), \"%Y%m%d%H%M%S\")\n",
"# Folder containing simulated data\n",
"simul_folder <- paste0(data_folder, \"simulations_\", tag, \"/\") \n",
"# Folder for comparison results\n",
"results_folder <- paste0(\"../results\", tag, \"/\")\n",
"print(data_folder)\n",
"print(tag)\n",
"print(simul_folder)\n",
"print(results_folder)\n",
"dir.create(data_folder, showWarnings = FALSE)\n",
"dir.create(simul_folder, showWarnings = FALSE)\n",
"dir.create(results_folder, showWarnings = FALSE)\n"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [],
"source": [
"list_clusters <- seq(5,15,5)\n",
"list_distrib <- c(\"heterogeneous\",\"equal\")\n",
"\n",
"# For a given number of clusters\n",
"for(size in list_distrib) {\n",
" thisdir1 <- paste(simul_folder,size, sep=\"\")\n",
" dir.create(thisdir1, showWarnings = FALSE)\n",
" # Data distribution among clusters will either be heterogeneous or equal \n",
" for (num.clusters in list_clusters) {\n",
" thisdir2 <- paste(thisdir1,\"/\",num.clusters, sep=\"\")\n",
" dir.create(thisdir2, showWarnings = FALSE)\n",
" }\n",
" }\n",
" "
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [],
"source": [
"## Simulate data\n",
"## INPUTS:\n",
"# folder = location where the simulated data should be saved\n",
"# num.clusters = number of clusters to be imposed on the data\n",
"# size = heterogeneous for heterogeneous clusters, equal for equally-sized clusters\n",
"## OUPUTS: matrices of simulated data are saved to file in folder\n",
"##模拟数据\n",
"##输入：\n",
"#folder=应保存模拟数据的位置\n",
"#num.clusters =要施加在数据上的集群数\n",
"#size =对于异构集群，heterogeneous，对于相等大小的集群，equal\n",
"## OUPUTS：模拟数据矩阵保存到文件夹中的文件中\n",
"simulated_data_generation <- function(out.folder, num.clusters, size=\"heterogeneous\", predefined=TRUE) {\n",
" \n",
" # Number of clusters\n",
" num.clusters <- as.numeric(num.clusters)\n",
" # Size of the effect\n",
" effect <- 2.5\n",
" # Sample proportions per clusters defined here are those used for the paper\n",
" #此处定义的每类样本比例是本文使用的比例\n",
" prop_predefined <- list(\n",
" \"heterogeneous\" = list(\n",
" \"5\" = c(0.35, 0.13, 0.19, 0.08, 0.25),\n",
" \"10\" = c(0.20, 0.10, 0.07, 0.10, 0.15, 0.13, 0.10, 0.08, 0.05, 0.02),\n",
" \"15\" = c(0.10,0.08,0.04,0.03,0.12,0.03,0.10,0.03,0.05,0.02,0.1,0.2,0.03,0.02,0.05)\n",
" ),\n",
" \"equal\" = list(\n",
" \"5\" = c(0.25,0.2,0.2,0.2,0.15),\n",
" \"10\" = c(0.15,0.1,0.1,0.1,0.1,0.1,0.05,0.1,0.1,0.1),\n",
" \"15\" = c(0.07,0.07,0.07,0.06,0.07,0.07,0.07,0.06,0.07,0.06,0.07,0.06,0.07,0.06,0.07)\n",
" )\n",
" )\n",
"\n",
" # Check provided parameter (size) against allowed values\n",
" if(! size %in% names(prop_predefined)) {\n",
" print(paste0(\"ERROR: size can only assume value : \", \n",
" paste0(names(prop_predefined), collapse=\",\"),\n",
" \" found : \", size))\n",
" }\n",
"\n",
" # If article proportions are to be used\n",
" if(predefined) {\n",
" # Check provided parameter (number of clusters) against allowed values\n",
" if(! as.character(num.clusters) %in% names(prop_predefined[[size]])) {\n",
" print(paste0(\"ERROR: num.clusters can only assume value : \", \n",
" paste0(names(prop_predefined[[size]]), collapse=\",\"),\n",
" \" found : \",\n",
" num.clusters))\n",
" }\n",
" prop <- prop_predefined[[size]][[as.character(num.clusters)]]\n",
" prop[1] <- 1-sum(prop[-1])\n",
" }\n",
" # Otherwise\n",
" else {\n",
" if(size == \"equal\") {\n",
" # Could be simplified! Only necessary because InterSIM is \"easily offended\" :\n",
" # ensure same object type as in the heterogeneous case, and that not all \n",
" # values are exactly the same (should not impact the number of samples per group)\n",
" # - same type\n",
" equals <- rep(1, num.clusters)\n",
" prop <- equals/sum(equals)\n",
" # - slightly imbalanced\n",
" delta <- 0.05*prop[1]\n",
" prop[1] <- prop[1]+delta\n",
" prop[num.clusters] <- prop[num.clusters]-delta\n",
" # - sum is 1\n",
" prop <- round(prop, digits = 10)\n",
" prop[1] <- 1-sum(prop[-1])\n",
" }\n",
" else {\n",
" random <- runif(n = num.clusters, min = 0, max = 1)\n",
" prop <- random/sum(random)\n",
" }\n",
" }\n",
"\n",
" # Simulate data based on provided parameters\n",
" print(prop)\n",
" print(sum(prop))\n",
" print(sum(prop)==1)\n",
" sim.D <- InterSIM(n.sample=100, cluster.sample.prop=prop, \n",
" delta.methyl=effect, delta.expr=effect, delta.protein=effect, \n",
" p.DMP=0.25, p.DEG=NULL, p.DEP=NULL,\n",
" do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)\n",
" \n",
" \n",
" thisdir <- paste(out.folder,size,\"/\",num.clusters, sep=\"\")\n",
" print(thisdir)\n",
" #dir.create(paste(out.folder,size,num.clusters, sep=\"/\"), showWarnings = FALSE)\n",
" #dir.create(paste(out.folder,size,num.clusters, sep=\"/\"), showWarnings = FALSE)\n",
" #dir.create(paste(out.folder,size,num.clusters, sep=\"/\"), showWarnings = FALSE)\n",
"\n",
" \n",
"\n",
" # Export simulations as tables\n",
" write.table(sim.D$clustering.assignment, paste(thisdir, \"clusters.txt\", sep=\"/\"), sep=\"\\t\")\n",
" write_table_with_index_header(t(sim.D$dat.methyl), paste(thisdir, \"omics1.txt\", sep=\"/\"))\n",
" write_table_with_index_header(t(sim.D$dat.expr), paste(thisdir, \"omics2.txt\", sep=\"/\"))\n",
" write_table_with_index_header(t(sim.D$dat.protein), paste(thisdir, \"omics3.txt\", sep=\"/\"))\n",
"\n",
" return(\"data saved in folder\")\n",
"}\n",
"\n",
"## Support function\n",
"write_table_with_index_header <- function(data, file, sep=\"\\t\") {\n",
" write.table(cbind(probe=row.names(data),data), file, sep = sep, \n",
" append = FALSE, quote = FALSE, row.names = FALSE, col.names = TRUE)\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1] \"##########\"\n",
"[1] \"-> Distribution: heterogeneous, Nb clusters: 5\"\n",
"[1] \"-> Simulating data...\"\n",
"[1] 0.35 0.13 0.19 0.08 0.25\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/heterogeneous/5\"\n",
"[1] \"-> Done.\"\n",
"[1] \"##########\"\n",
"[1] \"-> Distribution: equal, Nb clusters: 5\"\n",
"[1] \"-> Simulating data...\"\n",
"[1] 0.25 0.20 0.20 0.20 0.15\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/equal/5\"\n",
"[1] \"-> Done.\"\n",
"[1] \"##########\"\n",
"[1] \"-> Distribution: heterogeneous, Nb clusters: 10\"\n",
"[1] \"-> Simulating data...\"\n",
" [1] 0.20 0.10 0.07 0.10 0.15 0.13 0.10 0.08 0.05 0.02\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/heterogeneous/10\"\n",
"[1] \"-> Done.\"\n",
"[1] \"##########\"\n",
"[1] \"-> Distribution: equal, Nb clusters: 10\"\n",
"[1] \"-> Simulating data...\"\n",
" [1] 0.15 0.10 0.10 0.10 0.10 0.10 0.05 0.10 0.10 0.10\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/equal/10\"\n",
"[1] \"-> Done.\"\n",
"[1] \"##########\"\n",
"[1] \"-> Distribution: heterogeneous, Nb clusters: 15\"\n",
"[1] \"-> Simulating data...\"\n",
" [1] 0.10 0.08 0.04 0.03 0.12 0.03 0.10 0.03 0.05 0.02 0.10 0.20 0.03 0.02 0.05\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/heterogeneous/15\"\n",
"[1] \"-> Done.\"\n",
"[1] \"##########\"\n",
"[1] \"-> Distribution: equal, Nb clusters: 15\"\n",
"[1] \"-> Simulating data...\"\n",
" [1] 0.07 0.07 0.07 0.06 0.07 0.07 0.07 0.06 0.07 0.06 0.07 0.06 0.07 0.06 0.07\n",
"[1] 1\n",
"[1] TRUE\n",
"[1] \"../data/simulations_20210329212141/equal/15\"\n",
"[1] \"-> Done.\"\n"
]
}
],
"source": [
"## Simulate data, factorize and compare the results\n",
"\n",
"list_clusters <- seq(5,15,5)\n",
"list_distrib <- c(\"heterogeneous\",\"equal\")\n",
"\n",
"# For a given number of clusters\n",
"for(num.clusters in list_clusters) {\n",
" # Data distribution among clusters will either be heterogeneous or equal \n",
" for (size in list_distrib) {\n",
" \n",
" print(\"##########\")\n",
" print(paste0(\"-> Distribution: \", size, \", Nb clusters: \", num.clusters))\n",
" \n",
" # Make simulated data\n",
" print(\"-> Simulating data...\")\n",
" simulated_data_generation(simul_folder, num.clusters, size, predefined=TRUE)\n",
" \n",
" print(\"-> Done.\")\n",
" }\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Warning message in createMOFAobject(omics):\n",
"“View names are not specified in the data, renaming them to: view_1, view_2, view_3\n",
"”\n",
"Creating MOFA object from list of matrices,\n",
" please make sure that samples are columns and features are rows...\n",
"\n",
"\n",
"Checking data options...\n",
"\n",
"Checking training options...\n",
"\n",
"Checking model options...\n",
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1] \"No output file provided, using a temporary file...\"\n",
"Generating warm start... \n",
"K=6:12\n"
]
}
],
"source": [
"out <- runfactorization(\"../data/simulations_20210329212141/equal/5\", paste0(\"omics\",1:3,\".txt\"), 5, sep=\"\\t\", filtering=\"none\")"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" [,1]\n",
"subject1 9\n",
"subject2 1\n",
"subject3 12\n",
"subject4 13\n",
"subject5 11\n",
"subject6 14\n",
"subject7 12\n",
"subject8 12\n",
"subject9 16\n",
"subject10 15\n",
"subject11 3\n",
"subject12 3\n",
"subject13 12\n",
"subject14 15\n",
"subject15 16\n",
"subject16 14\n",
"subject17 5\n",
"subject18 15\n",
"subject19 15\n",
"subject20 15\n",
"subject21 3\n",
"subject22 9\n",
"subject23 10\n",
"subject24 12\n",
"subject25 1\n",
"subject26 14\n",
"subject27 7\n",
"subject28 12\n",
"subject29 7\n",
"subject30 12\n",
"subject31 8\n",
"subject32 12\n",
"subject33 16\n",
"subject34 16\n",
"subject35 1\n",
"subject36 14\n",
"subject37 9\n",
"subject38 12\n",
"subject39 6\n",
"subject40 9\n",
"subject41 10\n",
"subject42 14\n",
"subject43 4\n",
"subject44 13\n",
"subject45 12\n",
"subject46 11\n",
"subject47 15\n",
"subject48 13\n",
"subject49 3\n",
"subject50 4\n",
"subject51 2\n",
"subject52 16\n",
"subject53 10\n",
"subject54 4\n",
"subject55 7\n",
"subject56 3\n",
"subject57 15\n",
"subject58 8\n",
"subject59 13\n",
"subject60 16\n",
"subject61 8\n",
"subject62 9\n",
"subject63 12\n",
"subject64 2\n",
"subject65 4\n",
"subject66 13\n",
"subject67 12\n",
"subject68 14\n",
"subject69 10\n",
"subject70 2\n",
"subject71 6\n",
"subject72 5\n",
"subject73 15\n",
"subject74 16\n",
"subject75 9\n",
"subject76 16\n",
"subject77 12\n",
"subject78 16\n",
"subject79 6\n",
"subject80 13\n",
"subject81 16\n",
"subject82 3\n",
"subject83 14\n",
"subject84 1\n",
"subject85 8\n",
"subject86 10\n",
"subject87 14\n",
"subject88 1\n",
"subject89 3\n",
"subject90 14\n",
"subject91 9\n",
"subject92 3\n",
"subject93 5\n",
"subject94 12\n",
"subject95 8\n",
"subject96 2\n",
"subject97 2\n",
"subject98 10\n",
"subject99 11\n",
"subject100 10\n"
]
}
],
"source": [
"print(out$icluster.clusters)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Loading required package: MASS\n",
"\n",
"Loading required package: NMF\n",
"\n",
"Loading required package: pkgmaker\n",
"\n",
"Loading required package: registry\n",
"\n",
"Loading required package: rngtools\n",
"\n",
"Loading required package: cluster\n",
"\n",
"NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 27/28\n",
"\n",
" To enable shared memory capabilities, try: install.extras('\n",
"NMF\n",
"')\n",
"\n",
"Loading required package: mclust\n",
"\n",
"Package 'mclust' version 5.4.6\n",
"Type 'citation(\"mclust\")' for citing this R package in publications.\n",
"\n",
"Loading required package: InterSIM\n",
"\n",
"Loading required package: tools\n",
"\n",
"Loading required package: ade4\n",
"\n",
"\n",
"Attaching package: ‘ade4’\n",
"\n",
"\n",
"The following object is masked from ‘package:BiocGenerics’:\n",
"\n",
" score\n",
"\n",
"\n",
"\n",
"Attaching package: ‘GPArotation’\n",
"\n",
"\n",
"The following object is masked from ‘package:NMF’:\n",
"\n",
" entropy\n",
"\n",
"\n",
"\n",
"Attaching package: ‘MOFAtools’\n",
"\n",
"\n",
"The following objects are masked from ‘package:NMF’:\n",
"\n",
" featureNames, featureNames<-, predict, sampleNames, sampleNames<-\n",
"\n",
"\n",
"The following objects are masked from ‘package:Biobase’:\n",
"\n",
" featureNames, featureNames<-, sampleNames, sampleNames<-\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" predict\n",
"\n",
"\n",
"Loading required package: JADE\n",
"\n",
"Loading required package: lattice\n",
"\n",
"Loading required package: caTools\n",
"\n",
"Loading required package: gdata\n",
"\n",
"gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.\n",
"\n",
"\n",
"\n",
"gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.\n",
"\n",
"\n",
"Attaching package: ‘gdata’\n",
"\n",
"\n",
"The following object is masked from ‘package:Biobase’:\n",
"\n",
" combine\n",
"\n",
"\n",
"The following object is masked from ‘package:BiocGenerics’:\n",
"\n",
" combine\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" nobs\n",
"\n",
"\n",
"The following object is masked from ‘package:utils’:\n",
"\n",
" object.size\n",
"\n",
"\n",
"The following object is masked from ‘package:base’:\n",
"\n",
" startsWith\n",
"\n",
"\n",
"Loading required package: gtools\n",
"\n",
"\n",
"Attaching package: ‘gtools’\n",
"\n",
"\n",
"The following object is masked from ‘package:InterSIM’:\n",
"\n",
" logit\n",
"\n",
"\n",
"Loading required package: gplots\n",
"\n",
"\n",
"Attaching package: ‘gplots’\n",
"\n",
"\n",
"The following object is masked from ‘package:stats’:\n",
"\n",
" lowess\n",
"\n",
"\n"
]
}
],
"source": [
"##### runfactoization runs all the considered multi-omics factorization\n",
"### the required inputs are:\n",
"### \"folder\" corresponding to the path to the folder where the input files are contained, in the idea that all omics matrices are organized inside a unique folder\n",
"### \"file.names\" corresponding to a vector containing the names of all the omics files\n",
"### \"num.factors\" containing the number of factors in which we desire to decompose the matrices\n",
"### \"sep=\" \"\" corresponding to the separator used in the omics files required to properly read them\n",
"### \"single.cell\" indicating if the data are single cell data. In this case the filtering of the data will be more intense in respect to other data types\n",
"### \"filtering\"\n",
"\n",
"### the input files need to be log2 transformed before running the analysis\n",
"\n",
"\n",
"library(\"RGCCA\")\n",
"library(\"r.jive\")\n",
"library(\"IntNMF\")\n",
"library(\"omicade4\")\n",
"library(\"MSFA\")\n",
"library(\"GPArotation\")\n",
"library(\"MOFAtools\")\n",
"library(\"tensorBSS\")\n",
"source(\"tICA.R\")\n",
"library(\"iCluster\")\n",
"\n",
"testrunfactorization <- function(folder,file.names,num.factors,sep=\" \",filtering=\"none\"){\n",
" factorizations<-list()\n",
" t<-1\n",
" method<-numeric(0)\n",
" \n",
" num.factors<-as.numeric(num.factors)\n",
"\n",
" \n",
" ##creating list of omics\n",
" omics <- list()\n",
" for(i in 1:length(file.names)){\n",
" omics[[i]]<-as.matrix(read.table(paste(folder,file.names[i],sep=\"/\"),sep=sep,row.names=1,header=T))\n",
" }\n",
" #print(omics)\n",
" \n",
" ####\n",
" #omics<-lapply(omics, function(x) t(x))\n",
" ######\n",
" \n",
" ##restricting to common samples and filtering\n",
" samples<-colnames(omics[[1]])\n",
" for(j in 1:length(omics)){\n",
" samples<-intersect(samples,colnames(omics[[j]]))\n",
" }\n",
" for(j in 1:length(omics)){\n",
" omics[[j]]<-omics[[j]][,samples]\n",
" if(filtering!=\"none\"){\n",
" x<-apply( omics[[j]],1,sd)\n",
" x<-as.matrix(sort(x, decreasing = T))\n",
" w<-which(x>0)\n",
" if(filtering==\"stringent\"){\n",
" selected<-rownames(x)[1:min(w[length(w)],5000)]\n",
" }else{\n",
" selected<-rownames(x)[1:min(w[length(w)],6000)]\n",
" }\n",
" m<-match(rownames(omics[[j]]),selected)\n",
" w<-which(!is.na(m))\n",
" omics[[j]]<-omics[[j]][w,]\n",
" }else{\n",
" omics[[j]]<-omics[[j]][which(apply(omics[[j]],2,sd)>0),]\n",
" }\n",
" }\n",
" print(length(omics)) \n",
" \n",
" \n",
" ##RGCCA \n",
" factorizations_RGCCA<-rgcca(lapply(omics, function(x) t(x)), ncomp = rep(num.factors, length(omics)), scheme = \"centroid\", scale = TRUE, init = \"svd\",bias = TRUE, tol = 1e-08, verbose = F)\n",
" factors_rgcca<-as.matrix(factorizations_RGCCA$Y[[1]])\n",
" metagenes_rgcca <- list()\n",
" for(j in 1:length(omics)){\n",
" metagenes_rgcca[[j]]<-as.matrix(factorizations_RGCCA$a[[j]])\n",
" rownames(metagenes_rgcca[[j]])<-rownames(omics[[j]])\n",
" colnames(metagenes_rgcca[[j]])<-1:num.factors\n",
" }\n",
" print(factors_rgcca) \n",
" factorizations[[t]]<-list(factors_rgcca,metagenes_rgcca)\n",
" t<-t+1\n",
" method<-c(method,\"RGCCA\")\n",
" \n",
" \n",
" \n",
" \n",
" \n",
" \n",
" out<-list(factorizations=factorizations,method=method)\n",
" \n",
" return(out)\n",
"}\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1] 3\n",
" comp1 comp2 comp3 comp4 comp5\n",
"subject1 -0.66795710 -0.1975975691 -0.300867807 -0.27752304 0.046597119\n",
"subject2 0.34576508 -0.2629359330 0.241120840 -0.28930964 -0.084342734\n",
"subject3 -0.18025509 -0.0176580168 0.248585176 0.28288886 -0.563893934\n",
"subject4 0.36050703 -0.1890522412 -0.408620222 0.17398881 -0.043598118\n",
"subject5 0.35911618 -0.3781877286 0.258566999 -0.36205334 0.226873122\n",
"subject6 0.28325320 -0.1622556746 0.181241457 -0.21227011 -0.559915019\n",
"subject7 -0.11612513 0.0788346274 0.220124930 0.33526312 -0.408510876\n",
"subject8 -0.07780757 -0.0141900772 0.335851483 0.28675003 -0.508347353\n",
"subject9 0.23910572 -0.1559110417 -0.458080182 0.26396763 -0.191666676\n",
"subject10 0.29560944 -0.1561401151 0.260168096 -0.14995656 -0.479010526\n",
"subject11 -0.48458731 -0.0735627161 -0.102832592 -0.12385138 -0.621762842\n",
"subject12 -0.40942839 -0.1172649178 -0.123315575 -0.13509267 -0.508532015\n",
"subject13 -0.19549696 -0.0472492050 0.451490816 0.50806521 -0.123621935\n",
"subject14 0.39955927 -0.2851241355 0.271590149 -0.31162352 0.072921505\n",
"subject15 0.32758984 -0.2064551003 -0.653680908 0.34347063 0.560935168\n",
"subject16 0.30672961 -0.1742978200 0.213687656 -0.20118681 -0.315973999\n",
"subject17 -0.34042109 0.0094594151 0.498483605 0.42013004 0.375227744\n",
"subject18 0.40118542 -0.2734121639 0.251444907 -0.24741560 -0.035026155\n",
"subject19 0.37087343 -0.2281502347 0.227306543 -0.13034463 -0.294658628\n",
"subject20 0.33360340 -0.2361817170 0.369069661 -0.26769134 0.022237249\n",
"subject21 -0.52471917 -0.1427221966 -0.160799669 -0.21163478 -0.034265692\n",
"subject22 -0.69679088 -0.1816307996 -0.190834122 -0.28495996 0.012379644\n",
"subject23 0.12198428 0.9913928035 -0.044774322 -0.13749865 0.118102528\n",
"subject24 -0.15083689 -0.0048478563 0.355681978 0.39781971 -0.290817913\n",
"subject25 0.37459760 -0.2149748122 0.333619860 -0.32522255 0.050167823\n",
"subject26 0.40536926 -0.3524025172 0.341182290 -0.31587600 0.569370103\n",
"subject27 0.11113972 1.2053399506 -0.164090254 -0.19666250 0.737646931\n",
"subject28 -0.26649175 -0.0039560291 0.373027247 0.46078534 -0.088915510\n",
"subject29 0.13245557 0.9972172785 -0.180399738 -0.18447479 0.036228901\n",
"subject30 0.04381088 -0.0209174788 0.230704944 0.27547222 -0.819244333\n",
"subject31 -0.42005698 -0.1287161305 -0.155971367 -0.15704278 -0.372743880\n",
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"subject34 0.36639250 -0.2101325265 -0.489283192 0.30912583 0.088598721\n",
"subject35 0.40052578 -0.2974581772 0.255015971 -0.45895052 0.290803574\n",
"subject36 0.32790701 -0.1703322633 0.240954041 -0.07700836 -0.524146348\n",
"subject37 -0.61693839 -0.0942186029 -0.177411533 -0.18328804 -0.247984667\n",
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"subject39 -0.41820019 0.0546330698 0.603785400 0.64903814 1.044504163\n",
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"subject45 -0.32035124 0.0046356596 0.477170403 0.47590852 0.234729477\n",
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"subject47 0.33933161 -0.1961931092 0.165805850 -0.22897229 -0.350842819\n",
"subject48 0.32737821 -0.0920039617 -0.230312555 0.17569330 -0.632712306\n",
"subject49 -0.62112071 -0.0938839090 -0.075833583 -0.18950765 -0.262536893\n",
"subject50 0.39773655 -0.2355097842 -0.639536514 0.36126441 0.572461179\n",
"subject51 0.12040917 0.7432439531 -0.018828592 -0.12949232 -0.079918547\n",
"subject52 0.29100778 -0.2047539625 -0.592615932 0.33531966 0.255890133\n",
"subject53 0.14404575 0.8066309601 -0.028532983 -0.13038362 -0.167896287\n",
"subject54 0.43806126 -0.2719940971 -0.666439000 0.27156816 0.468453204\n",
"subject55 0.16338689 0.7534885853 -0.046822843 -0.14356642 -0.258904701\n",
"subject56 -0.54330671 -0.1888214867 -0.182831910 -0.17865797 -0.066583743\n",
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"subject63 -0.16479915 -0.0090984830 0.356200241 0.39062847 -0.183072327\n",
"subject64 0.04786201 1.1937650392 -0.043303979 -0.19370464 0.250076084\n",
"subject65 0.30532165 -0.1704268507 -0.358892836 0.27005600 -0.249180710\n",
"subject66 0.37707053 -0.1771229460 -0.454937274 0.24098709 0.062682104\n",
"subject67 -0.22037895 0.0177286001 0.417926483 0.36863521 0.071323646\n",
"subject68 0.39512069 -0.2366673774 0.216649037 -0.29284511 0.008576342\n",
"subject69 0.12827505 0.8567863582 -0.013746448 -0.11409165 0.081832362\n",
"subject70 0.15024314 0.7453052610 0.005392764 -0.06270430 -0.173802527\n",
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"subject77 -0.27789916 -0.0048473473 0.345856825 0.39243126 -0.234121870\n",
"subject78 0.38427805 -0.2223340178 -0.656837020 0.25087347 0.354163259\n",
"subject79 -0.39981804 -0.0196969046 0.584051104 0.53694953 1.134921916\n",
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"subject81 0.31335961 -0.2561279021 -0.682036273 0.35385352 0.453455172\n",
"subject82 -0.43985970 -0.1495504622 -0.095994877 -0.20146180 -0.264895053\n",
"subject83 0.44732835 -0.2583292762 0.202537607 -0.26059137 -0.098211699\n",
"subject84 0.39698952 -0.3499256864 0.325258636 -0.40885985 0.289307634\n",
"subject85 -0.75136801 -0.1232615110 -0.231802292 -0.26259688 -0.074211961\n",
"subject86 0.12936870 0.8954234066 -0.093754585 -0.13571839 0.105100811\n",
"subject87 0.35678871 -0.2465073482 0.249338939 -0.29102546 -0.027625860\n",
"subject88 0.45373993 -0.2961290693 0.331510086 -0.41422877 0.355016508\n",
"subject89 -0.55235599 -0.0882347574 -0.133777889 -0.24414535 -0.415535261\n",
"subject90 0.39405941 -0.3377337316 0.432651264 -0.28667185 0.678702952\n",
"subject91 -0.91228550 -0.1851716392 -0.320023754 -0.44279513 0.559760637\n",
"subject92 -0.59550423 -0.1053352454 -0.159220342 -0.25166634 -0.258521010\n",
"subject93 -0.40457224 0.0165940814 0.477644984 0.57539863 0.640072913\n",
"subject94 -0.18494150 0.0596899207 0.354371616 0.41316953 -0.272703209\n",
"subject95 -0.71579607 -0.1496541724 -0.296889784 -0.28595335 0.138126582\n",
"subject96 0.21892346 0.5690727182 -0.064691902 -0.10351738 -0.497977461\n",
"subject97 0.09944305 0.8931895607 -0.037956288 -0.10140124 0.008295167\n",
"subject98 0.14312408 0.8875227295 -0.014458296 -0.12274998 0.103570903\n",
"subject99 0.47719454 -0.3540176751 0.237126518 -0.39867246 0.707972555\n",
"subject100 0.16961816 1.0156947761 -0.069745172 -0.14946591 0.462672836\n",
" comp6 comp7 comp8 comp9 comp10\n",
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"subject2 0.004226896 0.213313895 0.056469727 -0.0621672992 -0.082684709\n",
"subject3 -0.009572400 -0.050562396 -0.177692353 0.0132125699 -0.030125332\n",
"subject4 -0.233439107 -0.004897228 -0.042481797 -0.0431395365 0.042920360\n",
"subject5 -0.101725554 0.152754911 -0.064126811 -0.1048910435 -0.026664461\n",
"subject6 -0.121315872 0.065821450 -0.133365238 -0.0471982522 0.047490306\n",
"subject7 -0.074883798 0.073023859 -0.251574325 0.0015331721 -0.034307365\n",
"subject8 0.031263663 0.232016560 0.064997932 0.1407648072 0.020675983\n",
"subject9 -0.002449634 -0.048508331 -0.137655422 0.0621313298 -0.199873772\n",
"subject10 -0.007289828 0.050208836 0.092218099 -0.0833417404 -0.003616362\n",
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"subject12 0.063767411 0.115550550 0.036992505 -0.0671939782 -0.047665225\n",
"subject13 0.186032236 -0.107735814 0.184641855 0.0231450173 -0.120664078\n",
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"subject100 -0.054739884 0.175063171 0.017107780 -0.0267241288 0.061461970\n"
]
}
],
"source": [
"out2 <- testrunfactorization(\"../data/simulations_20210329212141/equal/5\", paste0(\"omics\",1:3,\".txt\"), 10, sep=\"\\t\", filtering=\"none\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[[1]]\n",
"[[1]][[1]]\n",
" comp1 comp2 comp3 comp4 comp5\n",
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"subject87 -0.097703326 -0.015676309 0.156453234 -0.0203886958 -0.177227533\n",
"subject88 0.181105495 0.110829521 0.244295694 0.0699982015 0.195790279\n",
"subject89 0.088550607 0.074659343 0.072658776 -0.0131414793 0.142865901\n",
"subject90 0.111185160 -0.374737809 0.372786719 0.2175164061 0.156073099\n",
"subject91 -0.063241156 -0.035320425 0.147811183 -0.0950638683 -0.074931190\n",
"subject92 0.032442412 -0.101095705 0.056549284 0.0915908694 0.251762188\n",
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"subject95 -0.205438321 -0.075315520 -0.258885805 0.0732863894 -0.147775141\n",
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"subject99 -0.072723416 -0.007263865 -0.302585519 0.0525258812 -0.070646477\n",
"subject100 -0.054739884 0.175063171 0.017107780 -0.0267241288 0.061461970\n",
"\n",
"[[1]][[2]]\n",
"[[1]][[2]][[1]]\n",
" 1 2 3 4\n",
"cg20139214 -1.998182e-01 -0.0214569130 -0.1050743144 -0.1340864385\n",
"cg10999429 2.436173e-02 0.0117950961 -0.0116255213 -0.0008131201\n",
"cg23640701 1.305839e-02 -0.0278297573 0.0030397937 -0.0147799394\n",
"cg02956093 -3.315323e-02 0.0281695761 -0.0019699719 -0.0037421399\n",
"cg08711674 -2.217898e-01 -0.0411499187 0.0860261728 0.0705078954\n",
"cg09842540 -1.805685e-01 -0.0204251895 -0.0840965191 -0.1112591752\n",
"cg11739626 1.618832e-01 -0.1127695984 -0.0569626305 -0.0329293044\n",
"cg19073614 -3.848398e-02 -0.0827814612 0.0192287044 -0.2494513225\n",
"cg01894895 1.367579e-01 -0.0631459179 0.0547535150 -0.1318915388\n",
"cg01086868 1.629820e-02 0.2096644512 -0.0367409556 -0.0490403101\n",
"cg04755662 1.265591e-01 -0.0849238280 0.0814143068 -0.1332677954\n",
"cg05019001 8.596026e-04 -0.0276692660 -0.0133722345 0.0112721664\n",
"cg05786601 -1.786337e-01 -0.0333525566 -0.1026860373 -0.1273420694\n",
"cg07780118 3.064776e-02 0.1897745726 -0.0208630198 -0.0336585121\n",
"cg12589433 5.009120e-02 0.2113016371 -0.0403342162 -0.0775475921\n",
"cg14807303 -5.689657e-02 0.0711259928 -0.2495637414 -0.0294008212\n",
"cg16679837 -8.976965e-02 0.0523592622 0.1593712385 -0.1265128601\n",
"cg20878850 6.184810e-02 -0.0646328090 -0.1662740502 0.1149602411\n",
"cg21966410 -8.458515e-02 -0.0893072781 -0.2358558718 0.0132879277\n",
"cg27271368 1.312689e-01 -0.1612754559 0.0658534658 0.1454312102\n",
"cg04283377 1.572627e-02 -0.0027684147 -0.0165752909 0.0522837506\n",
"cg10455133 -1.890420e-01 -0.0359625127 0.0386907512 0.0865264737\n",
"cg01245656 -1.840544e-01 0.1037613386 0.0629446809 0.0486359927\n",
"cg14785449 -1.960222e-01 -0.0210067044 -0.0993539149 -0.1230358187\n",
"cg01800843 1.842359e-01 0.0269339931 -0.0530040309 -0.0746342593\n",
"cg03165700 -1.784032e-01 -0.0168573914 -0.0909093841 -0.1118593550\n",
"cg18457775 6.739214e-02 -0.0655234113 -0.1676469258 0.1307786785\n",
"cg22477592 -4.740641e-02 -0.0737514931 0.0113900755 -0.2245804122\n",
"cg24027342 8.882959e-02 -0.0900769343 -0.1651967300 0.0995918948\n",
"cg00925229 3.610238e-02 0.2464215712 -0.0211853152 -0.0526340880\n",
"cg07588779 -9.022292e-05 -0.0280726756 0.0087570604 0.0001292806\n",
"cg13620770 -9.065881e-03 -0.0035174072 0.0342894233 -0.0054209452\n",
"cg07679836 -6.766326e-02 -0.0396612814 0.1703493475 0.2160478691\n",
"cg14666892 -1.471954e-02 -0.0033786208 0.0496468774 -0.0162737329\n",
"cg22753768 -1.041897e-01 -0.1099092249 0.1672774178 -0.0932874003\n",
"cg24747396 1.866957e-01 -0.1224264471 -0.0580966960 -0.0424592983\n",
"cg14833160 -5.201762e-02 -0.0348700686 0.0030904223 -0.0001325541\n",
"cg15951107 2.984169e-02 0.2315055988 -0.0171939602 -0.0424804457\n",
"cg01803238 1.582203e-01 -0.1116372246 -0.0362645185 -0.0303896218\n",
"cg03813215 -3.252602e-02 0.0076383403 0.0183964210 -0.0163683599\n",
"cg08223235 -1.355856e-01 -0.1213929267 -0.0800035497 0.1784682354\n",
"cg08554462 -2.079760e-02 0.0075560047 0.0201175658 0.0068589937\n",
"cg09752703 9.048428e-02 0.1193918498 -0.1753183809 0.0810995300\n",
"cg11255230 -1.374272e-01 -0.0892909459 -0.0439696552 0.1671354990\n",
"cg11330108 1.531043e-02 -0.1307471024 -0.1452693557 -0.1258570602\n",
"cg12459502 1.150659e-01 -0.0723245040 0.0287363935 -0.1285489334\n",
"cg14455307 3.992597e-02 -0.0781812582 0.2049237630 0.0372688142\n",
"cg17602451 -3.471746e-02 -0.0722287966 0.0110837104 -0.2110211348\n",
"cg21602520 8.369835e-03 -0.0581420774 -0.0161931713 -0.0038580935\n",
"cg23756272 2.553128e-02 -0.0548722143 -0.0800428908 -0.0257682179\n",
"cg25059899 6.145889e-02 -0.0440103563 -0.1473016768 0.0366329284\n",
"cg00782854 -1.609597e-02 0.0051941460 0.0007177902 0.0168716345\n",
"cg16137862 -1.017091e-01 -0.0702187361 -0.2151085281 0.0125138733\n",
"cg27608154 4.485358e-02 0.1301531066 -0.0166941485 -0.0428101556\n",
"cg16225441 1.591144e-02 -0.0262436927 -0.0059459751 0.0313368250\n",
"cg26709863 -3.623720e-02 -0.0489914094 0.1628769103 0.1942529352\n",
"cg05566965 -2.100117e-02 -0.0186868401 0.0634978308 0.0027788870\n",
"cg03148461 -2.045014e-01 -0.0190397393 -0.0912175189 -0.1249560221\n",
"cg10141022 -6.865888e-02 -0.0717018423 -0.2151127357 0.0287095947\n",
"cg11414046 -2.198245e-02 -0.0028140721 0.0042863282 0.0356729568\n",
"cg14094063 1.237665e-01 -0.0709845609 0.1107100278 -0.1542230717\n",
"cg17095753 -2.596851e-02 -0.0298739810 0.0199483322 0.0665652234\n",
"cg21043558 -4.937191e-02 -0.0901378852 0.0201336245 -0.2447650058\n",
"cg23066879 -7.023439e-02 -0.0347972166 0.1838574760 0.2077950846\n",
"cg12836863 2.299353e-02 -0.0109319147 -0.0262541705 0.0097736080\n",
"cg27253386 -3.717562e-02 0.1150073223 0.1411597732 0.1479508511\n",
"cg22906389 7.021167e-02 -0.0652406967 -0.1718132131 0.1271219168\n",
"cg04677163 9.166773e-04 -0.0202540212 0.0387159096 0.0027456764\n",
"cg07964538 7.213909e-02 -0.0642885687 -0.1714185641 0.1310378257\n",
"cg17469978 -2.533875e-02 -0.0249445671 -0.0028036921 0.0452127574\n",
"cg18329349 1.363163e-01 -0.0860267268 0.1277136248 -0.1794072613\n",
"cg22126032 -3.737478e-02 0.1401891187 0.1415643068 0.1425821720\n",
"cg27242945 -3.692249e-03 0.0005167594 0.0062475594 0.0098697454\n",
"cg13849825 7.635998e-02 0.1617125530 -0.0903083547 -0.0303523290\n",
"cg23935746 3.658103e-02 0.2113897330 -0.0167199391 -0.0523549962\n",
"cg00858899 1.359960e-01 -0.0813369222 0.1177217202 -0.1641196252\n",
"cg00953256 5.426032e-02 0.1159419230 0.0176062741 0.0169889218\n",
"cg02723533 -4.761620e-04 -0.1083395596 -0.0358727059 -0.0186385110\n",
"cg04717045 -7.906173e-02 -0.1417306408 0.1509377367 -0.0466492452\n",
"cg05164185 1.473396e-02 -0.1157737652 -0.1217653545 -0.1048328146\n",
"cg05200606 1.020154e-01 0.1379524317 -0.1982444864 0.0848712982\n",
"cg06539449 3.649220e-02 0.0015292001 0.0042385830 0.0137989482\n",
"cg08170622 1.627275e-01 -0.1064622597 -0.0398413760 -0.0388536139\n",
"cg09637363 5.532293e-03 0.0095832033 0.0419885944 0.0031970005\n",
"cg10539418 -2.163660e-01 -0.0542200827 0.0818440658 0.0804101886\n",
"cg11802013 1.506523e-01 -0.1159202925 0.0003023888 0.0315859408\n",
"cg12266049 3.348925e-02 -0.0094300381 0.0301865236 -0.0030378946\n",
"cg13608094 -7.156075e-02 0.0921365265 -0.0577862535 -0.0888700686\n",
"cg16794682 1.415216e-01 -0.0350973892 0.1075894878 -0.1343804251\n",
"cg19047670 3.842232e-02 -0.0117361139 0.0645675212 0.0428203709\n",
"cg25060573 8.181338e-02 -0.0692594126 -0.2010767752 0.1514946483\n",
"cg26605086 -1.661809e-01 0.0873054613 0.0564355645 0.0421194588\n",
"cg12187567 -1.837935e-01 -0.0172248186 -0.0959742410 -0.1201402068\n",
"cg16328273 3.293909e-02 0.2292614196 -0.0214804271 -0.0461673800\n",
"cg11255163 6.269549e-04 0.0459358658 0.0260376404 0.0190380024\n",
"cg11667754 3.595623e-02 0.2250716540 -0.0090028243 -0.0501089110\n",
"cg17655614 -2.033407e-01 -0.0217101645 -0.0940529132 -0.1367491679\n",
"cg20716119 -7.206442e-04 0.0185698571 0.0310857854 -0.0042302835\n",
"cg22832044 2.208774e-02 0.2381400411 -0.0079094293 -0.0389560226\n",
"cg23989635 3.642093e-02 0.2453521061 -0.0158799620 -0.0497458958\n",
" 5 6 7 8 9\n",
"cg20139214 1.191702e-02 -0.033407743 -0.003471416 0.0446939060 1.891871e-02\n",
"cg10999429 1.335283e-01 -0.240681344 -0.101276210 0.2021944023 -2.131737e-03\n",
"cg23640701 -1.194878e-02 -0.217273447 -0.226365260 0.0751636367 -7.110590e-02\n",
"cg02956093 1.164428e-01 0.022486468 0.035403918 0.3189389677 2.869513e-01\n",
"cg08711674 -2.645669e-02 0.034832812 -0.016647198 0.0238948367 3.553509e-02\n",
"cg09842540 4.951281e-02 -0.031115396 -0.000727749 0.0623103909 -3.264866e-02\n",
"cg11739626 1.875304e-02 -0.075092294 0.020346789 0.0040866819 -1.245343e-01\n",
"cg19073614 6.182635e-02 0.020040327 -0.032070394 -0.0169291668 1.605448e-02\n",
"cg01894895 -8.616114e-02 -0.189528662 -0.113759898 -0.0254973048 4.950709e-02\n",
"cg01086868 -3.354395e-02 -0.063951860 0.097514088 -0.1243207940 -6.075905e-02\n",
"cg04755662 1.981694e-02 -0.123232250 0.042776517 -0.1605932084 -6.304571e-02\n",
"cg05019001 2.681751e-03 -0.056481365 0.048232845 -0.4779714517 2.548833e-01\n",
"cg05786601 -4.690777e-02 0.013944403 0.129799810 -0.1123544069 -7.634561e-02\n",
"cg07780118 1.453806e-02 -0.065142820 -0.080440692 -0.1923455430 2.419407e-01\n",
"cg12589433 1.832834e-02 -0.090876259 -0.105970756 -0.1279930418 1.206163e-01\n",
"cg14807303 7.783294e-03 -0.072911108 -0.044233078 -0.1321493318 -1.265950e-01\n",
"cg16679837 -9.362176e-03 -0.059888433 0.141617524 -0.1913580874 1.455272e-02\n",
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"cg13849825 -1.018683e-01 -0.045797493 0.043910461 0.0470949884 8.140363e-03\n",
"cg23935746 8.726273e-02 0.020185726 0.116721667 -0.0041578738 -5.342620e-02\n",
"cg00858899 7.917459e-02 0.123523252 -0.015758887 0.0312246077 -5.538007e-02\n",
"cg00953256 -3.174401e-02 -0.089083841 0.166040427 0.0056242601 4.049423e-02\n",
"cg02723533 -3.900157e-02 -0.194696803 0.009285833 0.1252619083 2.526024e-01\n",
"cg04717045 -5.831463e-02 -0.125768245 0.093426931 -0.0460140153 1.094484e-01\n",
"cg05164185 9.970093e-02 -0.043228178 0.063133001 0.0005539495 1.145531e-01\n",
"cg05200606 3.607500e-02 -0.046433440 -0.068964280 0.0420371065 6.363339e-03\n",
"cg06539449 -1.203098e-02 -0.150797965 0.233326383 0.1957503807 3.136770e-02\n",
"cg08170622 1.254542e-01 0.068488151 -0.027452638 0.0147941586 1.087937e-01\n",
"cg09637363 4.102344e-02 -0.092241403 0.183867708 0.0475945689 -5.114048e-02\n",
"cg10539418 3.166040e-02 -0.010957071 0.038981608 -0.0169973274 5.157786e-02\n",
"cg11802013 3.766704e-02 -0.113612709 0.025850766 0.1794698158 -1.338142e-01\n",
"cg12266049 -4.328629e-02 -0.214993113 0.122240545 0.0204164730 2.194064e-01\n",
"cg13608094 -7.609505e-02 -0.076627653 0.203093998 0.0825533198 1.942374e-02\n",
"cg16794682 -3.578745e-03 -0.125061307 0.106922532 0.0204016497 2.753403e-02\n",
"cg19047670 -3.897142e-05 -0.146023428 0.093908714 0.0476894817 3.633930e-02\n",
"cg25060573 6.358982e-02 0.057702707 -0.020977440 0.0086796431 7.540517e-05\n",
"cg26605086 9.550536e-02 -0.050433543 0.106733080 -0.0173557147 -7.085433e-02\n",
"cg12187567 3.158224e-02 -0.040912703 -0.008532636 0.0619718337 2.588840e-02\n",
"cg16328273 9.340860e-02 0.015822188 -0.035917440 0.0155915178 -6.649149e-03\n",
"cg11255163 1.833700e-01 -0.011812378 -0.013894003 0.0304328164 -1.110034e-01\n",
"cg11667754 8.723824e-02 0.041686094 -0.077975796 -0.0946710815 -3.604659e-02\n",
"cg17655614 2.580228e-02 0.037931679 -0.030052667 -0.0035120434 -5.851575e-02\n",
"cg20716119 1.963394e-01 0.036165107 -0.152992714 0.0307312469 -5.589369e-02\n",
"cg22832044 1.025453e-01 -0.017578024 0.082553566 0.0015110562 2.967508e-03\n",
"cg23989635 7.077825e-02 -0.016170697 -0.012306511 -0.0267608514 -8.931635e-03\n",
" 10\n",
"cg20139214 1.002827e-02\n",
"cg10999429 1.207567e-01\n",
"cg23640701 4.811143e-02\n",
"cg02956093 -1.457258e-02\n",
"cg08711674 7.699848e-02\n",
"cg09842540 -9.750224e-03\n",
"cg11739626 1.198649e-01\n",
"cg19073614 -9.956525e-03\n",
"cg01894895 -5.104505e-02\n",
"cg01086868 -2.342288e-02\n",
"cg04755662 2.595450e-02\n",
"cg05019001 1.093703e-01\n",
"cg05786601 8.672699e-02\n",
"cg07780118 -4.531470e-02\n",
"cg12589433 -7.313747e-02\n",
"cg14807303 1.381747e-01\n",
"cg16679837 3.905897e-02\n",
"cg20878850 -5.482074e-02\n",
"cg21966410 2.768413e-02\n",
"cg27271368 2.927637e-02\n",
"cg04283377 1.113183e-01\n",
"cg10455133 4.371044e-02\n",
"cg01245656 -4.635368e-02\n",
"cg14785449 8.597418e-04\n",
"cg01800843 4.243511e-02\n",
"cg03165700 8.178434e-05\n",
"cg18457775 -2.869589e-02\n",
"cg22477592 -9.244359e-03\n",
"cg24027342 -1.259806e-02\n",
"cg00925229 -5.525808e-02\n",
"cg07588779 2.060592e-02\n",
"cg13620770 -1.347061e-01\n",
"cg07679836 -1.835603e-02\n",
"cg14666892 -2.840567e-01\n",
"cg22753768 2.840300e-02\n",
"cg24747396 -9.927170e-03\n",
"cg14833160 -2.541554e-01\n",
"cg15951107 -5.673391e-02\n",
"cg01803238 3.996537e-02\n",
"cg03813215 -1.303554e-01\n",
"cg08223235 3.647351e-02\n",
"cg08554462 -1.375980e-02\n",
"cg09752703 -3.113491e-02\n",
"cg11255230 -9.855680e-02\n",
"cg11330108 5.368550e-02\n",
"cg12459502 -7.276521e-02\n",
"cg14455307 -1.284859e-02\n",
"cg17602451 -1.132514e-01\n",
"cg21602520 -2.076095e-01\n",
"cg23756272 8.120470e-02\n",
"cg25059899 -1.735700e-02\n",
"cg00782854 -1.107485e-01\n",
"cg16137862 -2.936238e-02\n",
"cg27608154 -9.386994e-02\n",
"cg16225441 -3.754163e-02\n",
"cg26709863 4.522898e-02\n",
"cg05566965 -3.555575e-02\n",
"cg03148461 -4.347388e-02\n",
"cg10141022 -6.485247e-02\n",
"cg11414046 -2.199963e-02\n",
"cg14094063 4.866011e-02\n",
"cg17095753 4.363418e-02\n",
"cg21043558 -1.034292e-02\n",
"cg23066879 -4.168903e-03\n",
"cg12836863 -2.954105e-01\n",
"cg27253386 -1.659819e-02\n",
"cg22906389 2.879171e-02\n",
"cg04677163 -3.142131e-02\n",
"cg07964538 3.533510e-03\n",
"cg17469978 -2.100395e-01\n",
"cg18329349 -3.303018e-02\n",
"cg22126032 9.173847e-03\n",
"cg27242945 1.966446e-01\n",
"cg13849825 -8.569561e-03\n",
"cg23935746 6.327782e-02\n",
"cg00858899 -2.712912e-02\n",
"cg00953256 -1.584662e-01\n",
"cg02723533 -1.505044e-01\n",
"cg04717045 -1.056002e-01\n",
"cg05164185 2.868877e-02\n",
"cg05200606 -3.557128e-02\n",
"cg06539449 8.024698e-02\n",
"cg08170622 4.273189e-02\n",
"cg09637363 3.085258e-01\n",
"cg10539418 4.648956e-02\n",
"cg11802013 -1.445410e-01\n",
"cg12266049 2.288073e-02\n",
"cg13608094 4.867725e-02\n",
"cg16794682 7.356945e-02\n",
"cg19047670 2.350505e-01\n",
"cg25060573 3.123252e-03\n",
"cg26605086 -6.529743e-02\n",
"cg12187567 2.038545e-02\n",
"cg16328273 -5.917483e-02\n",
"cg11255163 2.115901e-01\n",
"cg11667754 8.885887e-02\n",
"cg17655614 7.256193e-02\n",
"cg20716119 2.657788e-01\n",
"cg22832044 -5.546603e-02\n",
"cg23989635 8.374022e-02\n",
"\n",
"[[1]][[2]][[2]]\n",
" 1 2 3 4 5\n",
"ACACA -1.922805e-01 0.0142860854 -0.0681175148 -1.356159e-01 0.0079582934\n",
"ACVRL1 8.993108e-04 0.0390918095 0.0011819377 -7.204728e-04 0.2684468882\n",
"AKT1 -3.876608e-02 0.0172230435 0.0347359172 1.380618e-02 -0.0786571823\n",
"AKT1S1 -3.419939e-02 0.2215019363 0.0239869858 1.800339e-03 -0.0467832356\n",
"ANXA1 9.770849e-02 0.0591090071 0.0454229166 -1.363267e-01 0.0089829165\n",
"AR -1.806369e-02 -0.0200951835 0.0135228620 4.279454e-02 -0.0564137487\n",
"ARAF -1.913711e-01 0.0400354340 0.0794077339 4.189909e-02 0.0958157841\n",
"ASNS -1.691223e-01 -0.1224522167 0.0745847761 4.208192e-02 -0.0763015853\n",
"ATM 5.943876e-02 -0.0275742410 -0.1562454782 -1.553762e-01 -0.0954280664\n",
"BAD 4.263850e-02 -0.2236227302 -0.0042706736 -6.555145e-03 -0.0545151070\n",
"BAK1 -6.624015e-02 0.0232505460 0.1602588101 1.550227e-01 -0.0564431602\n",
"BAP1 -4.336555e-02 0.2148854501 0.0249733551 -6.004445e-03 -0.0332800617\n",
"BAX 3.553488e-02 -0.2275709958 -0.0010978081 1.160798e-02 0.0454711543\n",
"BCL2 9.446225e-05 0.0062387018 -0.0164626860 3.035738e-02 0.0032833886\n",
"BCL2L1 -7.633627e-02 0.0934935093 -0.2143311356 -4.946933e-03 -0.0314505973\n",
"BCL2L11 1.383360e-02 -0.2272458053 -0.0027417299 4.325218e-02 -0.1518272899\n",
"BECN1 -7.329712e-02 0.0232428081 0.1596873776 1.855094e-01 0.0066192709\n",
"BID -2.090075e-02 0.0099671683 0.0305736661 -3.668786e-02 -0.0344355285\n",
"BRAF -3.817766e-02 0.1954544848 0.0224735658 -1.734189e-02 -0.0063251555\n",
"BRCA2 -1.678795e-02 -0.1449090055 0.1356671010 1.272382e-01 -0.1498827500\n",
"CASP7 7.121977e-02 0.0609404253 -0.1844966583 1.056027e-01 0.0301115857\n",
"CAV1 1.532671e-01 -0.0201017067 0.0649903355 1.143789e-01 0.0739845508\n",
"CCNB1 4.162289e-02 -0.2036975961 0.0138212683 4.258207e-03 -0.0018271031\n",
"CCND1 -2.683148e-02 0.0402352996 -0.0063840713 -2.034746e-02 -0.0739442193\n",
"CCNE1 -1.319072e-01 -0.1147913564 0.0650475543 5.579030e-02 -0.0725196417\n",
"CCNE2 -8.784915e-02 -0.1502069979 -0.0649630933 -9.769081e-02 -0.0309854967\n",
"CDH1 -1.680456e-01 -0.1304620321 0.0801704783 4.763322e-02 0.0110291057\n",
"CDH2 -8.957333e-02 0.0129241473 -0.0341230531 -4.536218e-02 -0.0018174089\n",
"CDH3 -2.495631e-02 -0.1126081350 0.1022487767 1.115934e-01 -0.0487312253\n",
"CDKN1A -4.904522e-02 0.0428565646 -0.0015293561 3.528269e-03 -0.0579418236\n",
"CDKN1B 1.778657e-01 0.1104485957 -0.0543390508 2.059417e-06 0.0831193820\n",
"CHEK1 1.880590e-01 -0.0511632510 -0.0356408084 -3.898712e-02 -0.0621812564\n",
"CHEK2 1.439941e-02 -0.0536506277 0.0005284004 4.615686e-02 -0.2993494507\n",
"CLDN7 -1.909107e-01 0.0131801513 -0.0415829490 -6.942468e-02 0.0368603050\n",
"COL6A1 -5.266419e-02 -0.0664471684 -0.1957180132 -1.449808e-02 0.0960334977\n",
"CTNNB1 -1.706452e-01 0.0225153702 -0.0589304919 -1.434670e-01 0.0048677240\n",
"DIRAS3 -8.390967e-03 0.0004314582 -0.0055933533 8.314133e-03 0.0320976233\n",
"DVL3 4.767421e-03 0.0350494797 0.0031562541 -2.680572e-02 -0.2051677772\n",
"EEF2 1.363936e-01 -0.0841207275 0.0738460803 -1.495446e-01 -0.0162651326\n",
"EEF2K 1.297108e-01 -0.1095042026 0.0893211460 -1.369450e-01 0.0001610050\n",
"EGFR -1.923415e-01 0.0265404516 0.0814095357 1.925468e-02 0.0082448249\n",
"EIF4E 2.200403e-02 0.0217374605 0.0385182418 5.170885e-02 0.2041760323\n",
"EIF4EBP1 -1.215446e-01 -0.1323776889 -0.0625531603 -1.080387e-01 -0.0424860293\n",
"EIF4G1 -6.980910e-02 0.0162035683 0.1569502683 1.597224e-01 -0.1037699183\n",
"ERBB2 8.314938e-02 -0.0367379603 -0.1463150435 -1.545506e-01 0.0673444804\n",
"ERBB3 -1.144515e-01 0.0906829502 0.1643169625 -9.157749e-02 0.0349554761\n",
"ERRFI1 -7.379959e-02 0.0433981725 0.1327659884 1.480376e-01 0.0430790690\n",
"ESR1 -2.953070e-02 -0.0435233528 0.0005699838 5.133280e-02 -0.0241064605\n",
"ETS1 -6.192161e-02 -0.0959641959 -0.1947313925 -1.143377e-02 0.0750346022\n",
"FASN -1.425217e-01 0.0805002466 -0.0615203045 1.297970e-01 -0.0350857204\n",
"FN1 -1.116781e-01 -0.0846945616 -0.0568107780 -8.516664e-02 0.2120297431\n",
"FOXM1 -1.388456e-02 0.1854059320 0.0301141537 -2.319670e-02 -0.1789810726\n",
"FOXO3 5.387568e-02 0.0802142229 0.2083231288 -7.051124e-03 -0.0146483463\n",
"G6PD -1.419602e-01 -0.1415341771 -0.0624264970 -1.057744e-01 0.0408146209\n",
"GAB2 9.677943e-02 0.0638959883 0.0729326549 -1.615252e-01 -0.0808415428\n",
"GAPDH 1.209388e-01 -0.0859006724 0.0924702716 -1.495118e-01 -0.0221876420\n",
"GATA3 1.099621e-01 0.0906266151 0.0916962534 -1.785345e-01 0.0531891688\n",
"GSK3A 9.278926e-02 0.0690228933 -0.1729869145 1.537905e-01 -0.0306937404\n",
"HSPA1A 9.262086e-03 0.0083334740 0.0452416726 4.404835e-02 0.0687951100\n",
"IGFBP2 -4.281623e-02 0.0391010718 -0.1563420736 2.440855e-02 -0.1384126056\n",
"IRS1 6.668070e-02 0.0493708320 -0.1722733939 1.118580e-01 0.0456669811\n",
"ITGA2 -1.588541e-01 0.0057131971 -0.0538611564 -1.411402e-01 0.0047985680\n",
"JUN -2.560712e-02 0.0953449588 -0.0026398968 -1.907789e-01 -0.0656198514\n",
"KDR 8.916064e-02 -0.0823326677 0.1980962353 1.389394e-02 0.1223054927\n",
"KIT -1.010126e-01 0.0083156756 -0.0461163036 -1.094299e-01 0.2012419339\n",
"LCK -6.987622e-02 0.0316056265 0.1390726487 1.295769e-01 0.0645479175\n",
"MAP2K1 -2.731534e-02 0.2316529990 -0.0013345732 -6.925288e-03 -0.0840269253\n",
"MAPK1 9.096303e-02 -0.1171078175 -0.1427561471 1.409121e-01 -0.0008842903\n",
"MAPK14 -1.886998e-01 0.0255104012 -0.0787444857 -1.247127e-01 -0.0241145766\n",
"MAPK9 -7.369324e-03 0.0031566208 0.0248262612 2.705669e-02 0.4227877187\n",
"MET -1.822598e-01 0.0240323433 0.0676525254 2.182503e-02 -0.0126449001\n",
"MRE11A 1.458894e-01 -0.0908127258 0.0823642706 -1.461441e-01 -0.0324264841\n",
"MYC -1.846915e-01 0.0126227733 0.0574525948 6.043469e-02 -0.0097722021\n",
"MYH11 2.586325e-02 0.0566704434 0.0142000339 -1.765898e-02 0.0909864085\n",
"NDRG1 -1.463543e-01 0.0701344806 -0.0512731542 9.024288e-02 -0.0845659603\n",
"NF2 -1.807622e-01 0.0060011897 -0.0556196909 -1.364257e-01 0.0046573408\n",
"NFKB1 -2.306134e-02 0.0277289094 0.0304446389 6.609401e-03 0.1070514804\n",
"NOTCH1 -3.182347e-02 0.0094550727 -0.0154892683 -7.058497e-02 0.0982244154\n",
"NRAS -5.758506e-02 -0.0597215417 0.1732397462 -8.262892e-02 -0.0046841381\n",
"NRG1 1.496318e-01 -0.0215844226 0.0733758520 8.643988e-02 -0.0161604568\n",
"PARK7 2.983364e-02 -0.0205305344 -0.0039231477 7.531367e-02 -0.0378533331\n",
"PCNA -6.483663e-02 -0.0580387903 0.1808925937 -1.093270e-01 -0.0449620662\n",
"PDCD4 5.291690e-02 0.0961894374 0.2118163865 -2.674133e-03 0.0170407783\n",
"PDK1 -1.031884e-01 0.0723797515 0.1644491709 -9.710483e-02 -0.0970815523\n",
"PEA15 6.234964e-02 0.0980220410 0.1969660379 1.240774e-02 -0.0546596749\n",
"PGR 1.095082e-02 -0.1382249731 0.0100151371 2.041291e-02 -0.1997597672\n",
"PIK3R1 3.539498e-02 -0.1935240943 0.0326723496 -9.210021e-04 0.0750922554\n",
"PRDX1 1.353994e-01 -0.0911206627 0.0995174562 -1.239505e-01 -0.0503531268\n",
"PREX1 -2.246995e-02 -0.1397932196 0.1125773421 1.529635e-01 0.1170022605\n",
"PRKAA1 1.119774e-01 0.0758407949 0.0976224451 -1.687660e-01 -0.0396929883\n",
"PRKCD -3.746693e-02 -0.0827459108 0.0100210789 -2.403332e-01 -0.0751569220\n",
"PTEN -7.196702e-02 -0.0399927872 0.1575713437 -1.261308e-01 0.2121704074\n",
"PXN 8.684981e-02 0.0642126881 -0.1923442325 1.289572e-01 -0.0372918458\n",
"RAB25 -3.146321e-02 0.0941574957 0.0332263818 1.675747e-02 0.1165241977\n",
"RAD50 1.759505e-01 0.1285646042 -0.0759876678 -3.203240e-02 -0.0189439620\n",
"RAD51 -1.055621e-01 -0.1602330852 -0.0425701952 -1.089201e-01 -0.1385659711\n",
"RAF1 -1.370305e-01 -0.0928246024 -0.0898864345 1.660775e-01 -0.0519176456\n",
"RB1 2.179497e-03 0.0351169196 0.0540174596 5.209941e-02 -0.0519214324\n",
"RBM15 -2.968653e-02 0.2199943820 -0.0005566858 3.543472e-03 -0.0899800715\n",
"RPS6 4.041759e-02 -0.0982178249 -0.0216528934 2.337913e-01 0.0706640613\n",
" 6 7 8 9 10\n",
"ACACA -0.0054879690 -0.008538992 -0.0829485828 0.0868392025 0.0692186251\n",
"ACVRL1 -0.0386061861 0.123642071 -0.0545415797 -0.0200401287 0.2074588280\n",
"AKT1 -0.2816575572 0.055785526 0.2797503101 -0.2239372573 -0.0884694578\n",
"AKT1S1 -0.1016391925 0.027465324 0.0460240907 -0.0603020327 0.0659469434\n",
"ANXA1 -0.0433245351 0.076914197 -0.0208120412 -0.1673134556 0.0166884816\n",
"AR 0.1884040662 -0.072834224 0.1648958270 -0.0356965586 0.0898768831\n",
"ARAF -0.0633474852 -0.034024648 0.0426319252 -0.1159526368 -0.0170729623\n",
"ASNS -0.0047474444 0.015620051 -0.1534890217 0.0131642609 -0.0646944610\n",
"ATM 0.1082017208 -0.010102847 -0.0383862144 0.0196795603 -0.1444462459\n",
"BAD 0.0720269307 0.109507219 0.0039037512 -0.0064865703 0.0352614745\n",
"BAK1 -0.1532439547 0.086343951 0.0162062564 0.0357545378 0.0326392820\n",
"BAP1 -0.1211242148 -0.035989717 0.0320913599 -0.0732699752 -0.0425631119\n",
"BAX -0.0261342368 -0.009802316 0.0573912170 -0.0017800072 0.0782885118\n",
"BCL2 0.1903280632 -0.032262581 -0.0924099558 0.0495860941 -0.0523356318\n",
"BCL2L1 -0.0119749807 0.019923347 0.0195720700 0.0212388802 0.0063260487\n",
"BCL2L11 -0.0488508305 0.083668722 0.0180966965 -0.0556360896 -0.0303831044\n",
"BECN1 0.0178247410 -0.028773113 0.0360598249 0.0642015737 0.0013701023\n",
"BID -0.1868507403 0.170284714 -0.1407427435 0.1245808434 -0.0838610278\n",
"BRAF -0.0815603461 0.009053676 -0.1091464326 -0.2704193310 0.1074515040\n",
"BRCA2 -0.0102825140 0.032693879 0.0666148797 0.0225517912 0.1236109342\n",
"CASP7 -0.0723293036 0.113951007 0.0353809286 -0.1544875859 -0.0127362527\n",
"CAV1 0.0689865365 0.004026757 0.0226809103 0.0881955453 0.0449187879\n",
"CCNB1 -0.1135991921 -0.044714201 -0.0318841160 0.0930498691 -0.0133204415\n",
"CCND1 0.2176563354 -0.053568103 0.3008025689 -0.0696165907 -0.1528141863\n",
"CCNE1 -0.1461029297 0.130859784 0.0390921014 0.1503522182 -0.0008939865\n",
"CCNE2 -0.0562502468 0.038213534 -0.2190835792 -0.1129101495 0.0545041316\n",
"CDH1 0.0568635883 -0.027287971 0.0530404071 -0.1320654961 -0.0093925418\n",
"CDH2 0.0579034420 -0.193508927 -0.0389098494 0.0584966426 -0.3404984286\n",
"CDH3 -0.0463506161 -0.184595437 0.0858898060 -0.0075023799 0.0706684056\n",
"CDKN1A -0.0950183952 0.131648525 -0.0724590502 0.0030368449 0.0527878564\n",
"CDKN1B -0.1132520460 -0.019038098 -0.0379291266 0.0104993850 -0.0201925716\n",
"CHEK1 -0.1439846499 0.036701352 -0.1299384966 0.0414525042 -0.0346914676\n",
"CHEK2 -0.2050322851 0.029481948 -0.0703456163 0.1989091209 -0.0837541728\n",
"CLDN7 -0.0162130657 -0.017570489 0.0707706140 -0.0014928393 0.0141860331\n",
"COL6A1 -0.0908492634 0.075047076 0.1392580780 0.0933842608 0.0252934393\n",
"CTNNB1 -0.0820559798 -0.036791572 0.0171657823 -0.0757722126 0.0005885137\n",
"DIRAS3 -0.1627705247 -0.300211530 0.2970395908 0.1257447716 0.0262857397\n",
"DVL3 -0.0344889800 0.167917437 0.2846062870 -0.0027059060 -0.0133633002\n",
"EEF2 0.0090078651 0.063907140 0.1603175532 0.0019444459 -0.1018194259\n",
"EEF2K -0.0257720429 0.055538613 0.0785352882 -0.0646285382 -0.0214454224\n",
"EGFR 0.1208001201 0.075540478 0.0046412058 0.0027589320 -0.0084248463\n",
"EIF4E -0.1975920748 -0.231992475 -0.0515412019 -0.0122882846 -0.2218915934\n",
"EIF4EBP1 -0.0457520269 0.015582610 -0.0453595753 0.0308731309 0.1236310452\n",
"EIF4G1 -0.0078869390 0.123221496 0.0858604483 0.0246805789 -0.0055137906\n",
"ERBB2 0.0796949273 0.028696757 0.0957540200 -0.0081587276 0.0101083670\n",
"ERBB3 -0.0041415903 0.110805306 0.0072068986 0.0082387679 0.0621099964\n",
"ERRFI1 0.0367515110 0.008789995 -0.0609411134 0.0978803358 0.0234183577\n",
"ESR1 0.0673602808 -0.062616169 0.0312084323 -0.4305359824 0.0873697019\n",
"ETS1 -0.0601776548 0.107477295 0.0015095010 -0.0009426077 0.0428396414\n",
"FASN -0.0623766288 0.022086019 0.0803178724 -0.0445698744 -0.0261054418\n",
"FN1 -0.0576971282 0.087175099 0.0930739407 0.1011001426 -0.0024638102\n",
"FOXM1 -0.1067347422 0.021783431 0.0015977806 -0.0071580036 0.0318370322\n",
"FOXO3 0.0672226180 -0.062265582 0.1048331482 0.0184330790 0.0620849197\n",
"G6PD -0.0412773612 -0.052791044 0.0594839228 -0.0144604930 -0.0772299146\n",
"GAB2 0.0308035836 0.113155543 0.0316930107 -0.0915965831 0.0710456949\n",
"GAPDH -0.0486693716 0.032504630 0.0658235911 -0.0549631554 -0.0700148847\n",
"GATA3 -0.0486528181 -0.010852403 0.0086047127 0.0923686258 -0.0983070879\n",
"GSK3A -0.0509799375 0.058897089 0.0283102970 0.0008862686 0.0527898573\n",
"HSPA1A -0.1439698981 0.214066517 0.1514818498 -0.0419677512 -0.3601984500\n",
"IGFBP2 -0.2271504785 -0.196385680 0.1240356153 0.0025277186 0.0329673441\n",
"IRS1 0.0178381345 -0.089896898 0.0596697305 0.0300632692 0.0769469702\n",
"ITGA2 0.1171792498 -0.023458787 -0.0193333493 0.0368762124 -0.0654758695\n",
"JUN 0.0946757645 -0.066883795 -0.0301183932 0.1419815067 0.0625892158\n",
"KDR -0.0313244096 0.052760999 0.0304078440 -0.0085166863 0.0777014449\n",
"KIT -0.0722785501 -0.078068957 0.0691734144 0.2665073834 -0.0146628386\n",
"LCK -0.0699757898 0.125790635 -0.0790612369 0.1587968457 -0.0567623959\n",
"MAP2K1 -0.0605089471 -0.039548098 0.0594285128 0.0089403171 -0.0891493128\n",
"MAPK1 -0.1781366959 0.112028144 -0.0173204461 -0.0263586656 -0.0811466866\n",
"MAPK14 -0.0428846170 -0.080963026 0.0277345656 -0.0663576879 0.0571648129\n",
"MAPK9 -0.2493265222 -0.098469547 -0.0070611047 -0.2128009202 0.0363995819\n",
"MET 0.1122638237 0.049479862 -0.0374679974 -0.1068620454 -0.0620993660\n",
"MRE11A -0.0100217393 0.016766148 0.0010011451 -0.0355053598 0.0064988572\n",
"MYC 0.1576968616 -0.112107212 0.0173427672 -0.1095388279 -0.0890847565\n",
"MYH11 0.0108531992 0.060751759 0.0335129158 0.2669629031 0.1879886254\n",
"NDRG1 0.0153876872 0.228796707 -0.0402766268 -0.0218539048 0.0666892801\n",
"NF2 -0.0879697958 0.039488654 0.0432297252 0.0764433250 -0.0724061895\n",
"NFKB1 0.1397588035 0.268997554 -0.0187504554 0.0151567294 -0.2194182913\n",
"NOTCH1 0.1131135312 0.228016962 0.2107767582 0.0599665139 0.2355869746\n",
"NRAS -0.1092195455 -0.076935820 -0.0258563830 0.0922164527 0.0589834444\n",
"NRG1 0.1409002577 -0.072277328 -0.0276009175 0.0429231169 -0.2059023317\n",
"PARK7 -0.0418723049 -0.222611457 -0.0874407156 0.0880219435 0.2014845264\n",
"PCNA -0.0831181259 -0.044954976 -0.1078422602 -0.0917522150 -0.0212480760\n",
"PDCD4 0.0005813872 -0.073252124 0.0028244564 0.0251628501 0.0319641840\n",
"PDK1 -0.1173185400 -0.123205753 -0.0757563623 0.0190040212 -0.0044889871\n",
"PEA15 -0.0243585810 0.078810475 0.0111123852 -0.0495830454 0.0555739892\n",
"PGR -0.0280881614 -0.104287461 -0.0314635508 -0.0467115998 0.2081541423\n",
"PIK3R1 0.0068862986 -0.006088678 0.1123135460 -0.1671074318 -0.0590148516\n",
"PRDX1 -0.0923360002 -0.041610632 0.0421099041 -0.0075900264 -0.0574057013\n",
"PREX1 -0.0762560808 0.086166621 0.0260401682 0.0651106387 -0.1110746915\n",
"PRKAA1 -0.0539248149 -0.013536037 -0.0351639496 -0.0159619527 0.0785231848\n",
"PRKCD -0.0420830485 0.102177278 0.0657539268 -0.0448629702 0.0133295772\n",
"PTEN 0.1111038073 0.038703230 0.0124092234 -0.0050063860 -0.0714470083\n",
"PXN 0.0463995725 0.075583711 0.0628786553 0.0241667989 -0.0454527296\n",
"RAB25 -0.0409968111 0.119965117 0.1775014285 0.0733075977 0.2122433167\n",
"RAD50 -0.0449579379 0.006852360 -0.0009571342 -0.0109169727 0.0111816718\n",
"RAD51 -0.0094255508 -0.010572308 0.0163863583 -0.0007045560 0.0470430785\n",
"RAF1 -0.0111800914 -0.005503908 0.0003697090 0.0160304941 -0.0684696719\n",
"RB1 0.0964458141 -0.106218778 0.3416520683 0.1516762375 -0.0081803658\n",
"RBM15 0.0429700275 0.074035878 -0.1267399253 0.0195343464 -0.1329087760\n",
"RPS6 0.0792556717 -0.039591293 -0.0744506713 -0.0934816936 0.0378285711\n",
"\n",
"[[1]][[2]][[3]]\n",
" 1 2 3 4\n",
"ACC1 -0.148689116 0.0464705410 -0.078182626 0.1142004389\n",
"ACC_pS79 -0.149167425 0.0386757803 -0.080265475 0.1196517312\n",
"ACVRL1 -0.021036552 0.0471769535 0.011427153 0.0301869094\n",
"Akt_pS473 -0.023096244 0.0246262884 0.026419173 0.0189205576\n",
"PRAS40_pT246 -0.033814499 0.2357681044 0.003455191 0.0118030506\n",
"Annexin.1 0.086981532 0.0931502030 0.095782132 0.1582274647\n",
"AR -0.006168150 0.0007461875 -0.008226675 -0.0173869910\n",
"A.Raf_pS299 -0.183378645 0.0435391640 0.070233110 -0.0453757470\n",
"ASNS -0.148104028 -0.1177011976 0.051471108 -0.0551072373\n",
"ATM 0.064379622 -0.0187647970 -0.142537569 0.1322364064\n",
"Bad_pS112 0.027939079 -0.2076974197 0.018002807 0.0064603288\n",
"Bak -0.063514870 0.0149612299 0.162450649 -0.1746956321\n",
"Bap1.c.4 -0.023632160 0.2308733647 -0.008636205 -0.0088888680\n",
"Bax 0.021935753 -0.2369733654 0.008196731 -0.0151743619\n",
"Bcl.2 -0.018310593 -0.0149616187 0.029184903 0.0387188944\n",
"Bcl.xL -0.074451004 0.0753318965 -0.219691473 -0.0151086009\n",
"Bim 0.035912881 -0.2252218708 -0.012283692 -0.0034265606\n",
"Beclin -0.062286197 0.0198041284 0.157368004 -0.1708907861\n",
"Bid -0.027968102 -0.0617984552 0.001310626 0.0009496965\n",
"B.Raf -0.027300038 0.2162626098 -0.013259786 0.0109835701\n",
"BRCA2 -0.030949037 -0.1674038903 0.130719288 -0.1535551747\n",
"Caspase.7_cleavedD198 0.057445947 0.0448817640 -0.145574461 -0.1399267823\n",
"Caveolin.1 0.089807242 -0.0218040095 0.040004833 -0.0761454730\n",
"Cyclin_B1 0.038121442 -0.1654459140 -0.006084344 -0.0231990874\n",
"Cyclin_D1 -0.018329067 -0.0138987086 0.010064294 0.0343449119\n",
"Cyclin_E1 -0.146487771 -0.1182033270 0.032509498 -0.0353308873\n",
"Cyclin_E2 -0.113728036 -0.1557942450 -0.055492676 0.1030690723\n",
"E.Cadherin -0.127775637 -0.1187367235 0.041387398 -0.0227036946\n",
"N.Cadherin -0.158867078 0.0222552629 -0.080677945 0.1203997895\n",
"P.Cadherin -0.033029860 -0.1609079502 0.128466602 -0.1487428780\n",
"p21 -0.016230748 -0.0441671638 0.008090589 0.0050649389\n",
"p27 0.151603579 0.1286379481 -0.053762895 0.0526513381\n",
"p27_pT157 0.164892673 0.1254087898 -0.067411948 0.0529058029\n",
"p27_pT198 0.163382809 0.1264388156 -0.062416807 0.0422740937\n",
"Chk1 0.188712813 -0.0482959503 -0.058984720 0.0488951930\n",
"Chk1_pS345 0.188705342 -0.0512535067 -0.063370152 0.0486964594\n",
"Chk2 0.047192976 -0.0030387623 -0.046254437 -0.0242168595\n",
"Chk2_pT68 0.031961749 -0.0298119246 -0.039804185 0.0254295610\n",
"Claudin.7 -0.113362302 0.0162284490 -0.078708511 0.0874823456\n",
"Collagen_VI -0.060716170 -0.1059311481 -0.181736647 -0.0326438616\n",
"beta.Catenin -0.127354249 0.0247847085 -0.096834310 0.1052042832\n",
"ARHI -0.027800488 0.0256744569 0.018271011 0.0402709687\n",
"Dvl3 -0.002331544 -0.0080543794 -0.036735396 0.0023847164\n",
"eEF2 0.134379359 -0.0985366236 0.084624658 0.1600226682\n",
"eEF2K 0.134737748 -0.0886166607 0.067760343 0.1483959549\n",
"EGFR -0.188660211 0.0433645624 0.067391230 -0.0403642835\n",
"EGFR_pY1068 -0.174375962 0.0397580813 0.067139466 -0.0336435716\n",
"EGFR_pY1173 -0.193118047 0.0353877181 0.065075957 -0.0343565081\n",
"eIF4E 0.023470764 0.0356174837 -0.019612538 -0.0292507896\n",
"4E.BP1 -0.112510972 -0.1573910547 -0.065788329 0.0780261637\n",
"4E.BP1_pS65 -0.110821545 -0.1516857969 -0.068717127 0.1032039330\n",
"4E.BP1_pT70 -0.112413345 -0.1585988525 -0.068314782 0.0918423996\n",
"eIF4G -0.044350264 0.0197971278 0.109233150 -0.1590951368\n",
"HER2 0.067479442 -0.0193927266 -0.140486759 0.1479326304\n",
"HER2_pY1248 0.061239096 -0.0207602839 -0.141919994 0.1649160823\n",
"HER3 -0.089764407 0.1102597317 0.150255093 0.1381511890\n",
"HER3_pY1289 -0.084647207 0.1218879404 0.155411378 0.1179195209\n",
"MIG.6 -0.064580229 0.0091562692 0.158797045 -0.1779914466\n",
"ER.alpha 0.001214476 0.0169567804 -0.003560290 -0.0187349585\n",
"ER.alpha_pS118 0.030927817 0.0162763780 -0.010134779 0.0308334102\n",
"ETS.1 -0.051785336 -0.0957828275 -0.210048583 -0.0213687218\n",
"FASN -0.116562726 0.0845297627 -0.069264012 -0.1638411762\n",
"Fibronectin -0.097436291 -0.1143418761 -0.034546479 0.0445751094\n",
"FoxM1 -0.017998814 0.1919005123 -0.002643953 0.0025981992\n",
"FOXO3a 0.050281691 0.0850883242 0.214696457 0.0391155021\n",
"FOXO3a_pS318_S321 0.049424222 0.0871965031 0.214533656 0.0261372819\n",
"G6PD -0.119111256 -0.1494754940 -0.064196039 0.0994732404\n",
"GAB2 0.102789810 0.0688194782 0.072005267 0.1631442680\n",
"GAPDH 0.112781069 -0.0663133972 0.063070627 0.1173573927\n",
"GATA3 0.116092432 0.0918639550 0.099394328 0.1966954491\n",
"GSK3.alpha.beta 0.063427556 0.0636810096 -0.173066702 -0.1511303149\n",
"GSK3.alpha.beta_pS21_S9 0.056054275 0.0609298103 -0.162150220 -0.1459257792\n",
"GSK3_pS9 0.050260561 0.0660833913 -0.160176431 -0.1404731137\n",
"HSP70 -0.014241717 -0.0369177599 0.011754217 0.0142490266\n",
"IGFBP2 -0.067391037 0.0643025232 -0.180861021 -0.0221979552\n",
"IRS1 0.069858489 0.0557690222 -0.185065458 -0.1519147707\n",
"CD49b -0.166612159 0.0351921354 -0.070875620 0.1253580064\n",
"c.Jun_pS73 -0.032327670 0.1055897249 0.031234900 0.2618848838\n",
"VEGFR2 0.070757030 -0.0705938107 0.194279599 0.0267963365\n",
"c.Kit -0.144089037 0.0328509916 -0.065425860 0.1253446211\n",
"Lck -0.067125420 0.0130916421 0.152976085 -0.1599750804\n",
"MEK1 -0.012630777 0.2183507074 0.001308527 -0.0093474438\n",
"MEK1_pS217_S221 -0.030941528 0.2318928285 0.004010297 0.0083449824\n",
"ERK2 0.087565692 -0.1079920787 -0.139325221 -0.1254722842\n",
"p38_MAPK -0.161538014 0.0338754166 -0.076456544 0.1288425695\n",
"p38_pT180_Y182 -0.138012404 0.0436444044 -0.043680183 0.1167648673\n",
"JNK2 -0.012411337 0.0334635336 -0.004481356 -0.0354013123\n",
"c.Met_pY1235 -0.191591526 0.0382267582 0.061028161 -0.0420255564\n",
"Mre11 0.128420186 -0.1048844159 0.082303311 0.1685214665\n",
"c.Myc -0.190408782 0.0345809924 0.057704053 -0.0414294087\n",
"MYH11 -0.021060375 -0.0392854684 0.029025648 -0.0242927570\n",
"NDRG1_pT346 -0.124694096 0.0945253399 -0.066096362 -0.1231505329\n",
"NF2 -0.154265482 0.0237446020 -0.094382821 0.1229357778\n",
"NF.kB.p65_pS536 -0.002041525 -0.0061295643 0.008685604 -0.0307085765\n",
"Notch1 0.010048334 -0.0315432552 0.004176455 0.0125401124\n",
"N.Ras -0.076543536 -0.0577973189 0.185070246 0.1522937155\n",
"Heregulin 0.166827050 -0.0240122544 0.086482035 -0.1128214538\n",
"DJ.1 0.010437762 0.0009256618 0.005567332 -0.0166874375\n",
"PCNA -0.060578704 -0.0661905360 0.178153081 0.1634771358\n",
"PDCD4 0.043876756 0.1001616576 0.170416491 0.0181978212\n",
" 5 6 7 8\n",
"ACC1 -1.590916e-02 0.056637657 -0.0291572261 0.027014913\n",
"ACC_pS79 -3.672456e-05 0.067375789 -0.0215268690 0.047032868\n",
"ACVRL1 4.434559e-02 -0.019930508 -0.3379945786 -0.002002896\n",
"Akt_pS473 3.647476e-01 -0.231426290 0.2764927898 0.081113490\n",
"PRAS40_pT246 2.495298e-02 -0.005037642 0.0378536741 0.001180361\n",
"Annexin.1 -7.169524e-02 -0.021427751 0.1379080602 -0.099117637\n",
"AR -1.012086e-01 0.168390767 -0.0029531798 0.022855752\n",
"A.Raf_pS299 6.129378e-02 -0.013264752 0.0107638984 -0.026841046\n",
"ASNS -5.205255e-02 0.043039331 0.0126585860 -0.009228605\n",
"ATM -8.443678e-03 0.028295835 -0.0082518084 0.033904678\n",
"Bad_pS112 1.775954e-01 -0.015398281 0.1432272984 -0.202980362\n",
"Bak -1.113021e-02 -0.021492782 -0.0191994975 0.074005413\n",
"Bap1.c.4 -2.766827e-02 -0.032993727 -0.0602527315 0.068603073\n",
"Bax -2.527365e-03 -0.089684646 -0.0324889383 0.020198051\n",
"Bcl.2 1.947428e-01 -0.236299873 -0.2075945756 -0.122770401\n",
"Bcl.xL -1.159638e-02 -0.017889347 -0.0123764841 0.027058239\n",
"Bim 5.354875e-02 0.015700904 -0.1059000834 0.159624174\n",
"Beclin -2.370605e-02 0.047774411 0.0176662273 -0.077263626\n",
"Bid -2.192471e-01 0.163874024 -0.0380478557 0.014818161\n",
"B.Raf 7.216991e-02 0.118980205 0.0132925866 0.055094621\n",
"BRCA2 -5.277151e-03 0.012115117 -0.0045415401 0.001353572\n",
"Caspase.7_cleavedD198 -4.476196e-02 0.085136739 0.0493808789 -0.124240940\n",
"Caveolin.1 -1.685529e-01 -0.140679058 0.0415099938 0.142024070\n",
"Cyclin_B1 6.094770e-02 0.059594691 -0.0517403469 0.246032239\n",
"Cyclin_D1 -2.617888e-01 0.010794255 0.0899183499 -0.111948803\n",
"Cyclin_E1 4.338835e-02 0.072081960 0.0157535765 0.037394170\n",
"Cyclin_E2 -7.510310e-03 -0.043727599 -0.0492400256 0.037904038\n",
"E.Cadherin 6.083599e-02 0.090208653 0.0408111561 -0.221822410\n",
"N.Cadherin -1.679289e-02 -0.024245271 -0.0606337979 0.046249788\n",
"P.Cadherin 3.155054e-02 0.111604160 0.0667626986 0.009271805\n",
"p21 -2.921662e-01 -0.046596456 0.1933973552 0.233406309\n",
"p27 -2.227482e-02 -0.057994676 -0.0148583321 0.041492502\n",
"p27_pT157 -2.734349e-03 -0.007793828 -0.0018647547 -0.009119116\n",
"p27_pT198 -6.573849e-02 -0.024021745 0.0022642643 0.076815028\n",
"Chk1 -3.065943e-02 -0.092659723 -0.0214575696 -0.061071157\n",
"Chk1_pS345 -2.181779e-03 -0.043151349 0.0122576965 -0.047931655\n",
"Chk2 1.519296e-01 0.170745089 -0.1951028069 0.048401597\n",
"Chk2_pT68 1.478490e-01 0.069482105 -0.0776790368 -0.078945641\n",
"Claudin.7 -9.116777e-02 0.170758265 -0.0877943258 -0.139610300\n",
"Collagen_VI -9.821704e-02 -0.064771399 -0.0547173641 -0.025915551\n",
"beta.Catenin 5.572662e-02 0.032778495 0.0738730216 -0.115072998\n",
"ARHI -3.852530e-02 -0.195149079 -0.3613434423 0.077513579\n",
"Dvl3 9.357551e-02 -0.187034600 -0.0329803210 0.041823357\n",
"eEF2 -6.949445e-03 0.068602100 0.0096395134 -0.010223256\n",
"eEF2K -2.855109e-03 0.068850218 -0.0367871688 -0.088135612\n",
"EGFR -3.346978e-03 0.007159569 -0.0018417113 -0.021917589\n",
"EGFR_pY1068 1.831675e-02 0.112286057 -0.0043077245 0.046551938\n",
"EGFR_pY1173 -7.272145e-03 0.028026964 -0.0055559491 -0.003116126\n",
"eIF4E 9.693457e-02 -0.201545515 -0.0404870428 0.118147883\n",
"4E.BP1 -1.336148e-02 -0.044283442 -0.0221473820 0.056449365\n",
"4E.BP1_pS65 3.608542e-02 -0.002823710 0.0146358025 -0.046536973\n",
"4E.BP1_pT70 2.088600e-02 -0.019241786 0.0103147696 -0.018972511\n",
"eIF4G 3.297306e-02 0.126185241 -0.0232710441 0.148061417\n",
"HER2 -5.387541e-02 0.188236916 0.0631591644 0.101619075\n",
"HER2_pY1248 -6.650418e-02 0.095353350 -0.0049441661 0.076503004\n",
"HER3 -8.087102e-02 0.053212705 0.0491936889 -0.030630060\n",
"HER3_pY1289 -2.673808e-02 -0.073479502 -0.0067628283 0.056382878\n",
"MIG.6 -5.745966e-02 0.030867523 -0.0003629101 0.037605596\n",
"ER.alpha 3.057090e-02 0.254903715 -0.1709248514 -0.022525331\n",
"ER.alpha_pS118 -2.950234e-03 0.226883161 -0.0452795211 -0.201670453\n",
"ETS.1 -3.109059e-02 -0.017083967 -0.0251064705 -0.043981848\n",
"FASN 1.918802e-03 0.111012624 -0.1278032895 0.060660363\n",
"Fibronectin -9.564361e-02 -0.084854579 0.1117021167 0.211576291\n",
"FoxM1 9.844516e-02 0.058565636 -0.1097909505 0.177603141\n",
"FOXO3a 8.046785e-04 -0.005642557 -0.0163627252 0.055767564\n",
"FOXO3a_pS318_S321 -5.138558e-02 0.006838428 0.0605184814 0.045686863\n",
"G6PD 4.801222e-02 -0.011593056 -0.0068687968 -0.010232130\n",
"GAB2 3.090316e-02 0.173965451 -0.1096912705 0.045770380\n",
"GAPDH 1.472107e-01 0.235912189 0.0521034554 0.093595042\n",
"GATA3 1.299640e-02 -0.005892770 -0.0083276622 -0.002887516\n",
"GSK3.alpha.beta -1.562603e-02 0.031177638 0.0868463383 0.015022635\n",
"GSK3.alpha.beta_pS21_S9 9.549126e-02 -0.042409720 0.0795487928 -0.122360096\n",
"GSK3_pS9 1.152648e-01 -0.046144329 0.0700173533 -0.098335665\n",
"HSP70 -2.779555e-01 -0.079680351 -0.0689728047 -0.258213162\n",
"IGFBP2 -6.021270e-02 0.023170170 -0.0259773415 0.082125959\n",
"IRS1 -5.333218e-02 -0.016160521 -0.0306911051 -0.032450202\n",
"CD49b -3.273944e-02 -0.010940969 0.0250894241 0.008393707\n",
"c.Jun_pS73 3.864512e-02 0.002798426 0.0358482698 0.047795588\n",
"VEGFR2 -5.194025e-02 -0.117063449 0.1571438734 -0.025740083\n",
"c.Kit 1.532138e-02 -0.054946258 0.0836905486 0.072677989\n",
"Lck -2.248814e-02 -0.015239892 -0.0346068462 -0.063421200\n",
"MEK1 -9.315295e-02 0.020555002 -0.0469722791 0.005571314\n",
"MEK1_pS217_S221 -7.943575e-03 -0.037296737 0.1036411428 -0.081038923\n",
"ERK2 3.618475e-02 0.115845232 0.0962519088 -0.018074625\n",
"p38_MAPK 5.842730e-03 -0.078780167 0.0671295784 -0.066105179\n",
"p38_pT180_Y182 1.193773e-01 -0.142461140 0.0869447202 -0.204896479\n",
"JNK2 1.643955e-01 0.318699239 0.1813775234 0.030481037\n",
"c.Met_pY1235 2.211256e-03 0.012885186 0.0044558942 -0.018451216\n",
"Mre11 -4.638794e-02 -0.004655554 0.0315293053 -0.042148287\n",
"c.Myc -4.312237e-02 0.050670897 -0.0166974123 -0.012504146\n",
"MYH11 -2.347654e-01 -0.131087603 -0.0699010925 0.105206268\n",
"NDRG1_pT346 2.810678e-02 -0.123388223 0.0964591517 0.051989701\n",
"NF2 9.354895e-04 -0.013249259 0.0260392080 0.035480666\n",
"NF.kB.p65_pS536 2.627501e-03 -0.027749889 -0.3050347795 -0.281544336\n",
"Notch1 4.554585e-02 -0.077173525 -0.3083447049 0.042058640\n",
"N.Ras 1.294464e-02 0.012584551 -0.0563697378 0.007501046\n",
"Heregulin -1.076455e-02 -0.047356253 -0.0794210971 0.034309763\n",
"DJ.1 3.514215e-01 0.010367383 -0.0439090375 0.170588349\n",
"PCNA 7.834237e-02 0.027250663 -0.0395295758 0.058374930\n",
"PDCD4 5.579626e-02 -0.027653604 0.0270696469 -0.289718117\n",
" 9 10\n",
"ACC1 0.0114817550 -0.012752389\n",
"ACC_pS79 0.0446109106 -0.026128661\n",
"ACVRL1 0.0451577903 -0.347354807\n",
"Akt_pS473 0.0926598082 -0.097244266\n",
"PRAS40_pT246 0.0682105150 -0.041147230\n",
"Annexin.1 0.0526605879 0.019164135\n",
"AR -0.0425510415 0.081453198\n",
"A.Raf_pS299 0.0030370480 -0.024854489\n",
"ASNS 0.0705018700 -0.000600001\n",
"ATM -0.0664362513 0.077362522\n",
"Bad_pS112 0.0119289106 -0.100710658\n",
"Bak -0.0236948958 -0.036631421\n",
"Bap1.c.4 0.0260582048 0.061137537\n",
"Bax -0.0438368846 0.002664077\n",
"Bcl.2 -0.4090067674 0.133395459\n",
"Bcl.xL 0.0008857576 -0.024103568\n",
"Bim -0.0233034418 0.046015459\n",
"Beclin 0.0509081720 0.009786699\n",
"Bid -0.0854986397 -0.060598186\n",
"B.Raf -0.0344198321 0.151985225\n",
"BRCA2 0.0240657976 0.013884553\n",
"Caspase.7_cleavedD198 -0.0045306094 -0.058949736\n",
"Caveolin.1 -0.1671768965 0.051333255\n",
"Cyclin_B1 0.1528798894 0.185673663\n",
"Cyclin_D1 -0.1006977642 -0.170148614\n",
"Cyclin_E1 0.1440821308 0.007736146\n",
"Cyclin_E2 -0.0007672942 -0.019289437\n",
"E.Cadherin -0.0339441354 0.069161749\n",
"N.Cadherin 0.0632266327 0.017876046\n",
"P.Cadherin -0.0157946629 -0.066851655\n",
"p21 0.1272696400 -0.070974101\n",
"p27 -0.0418486426 0.028254105\n",
"p27_pT157 0.0026602109 -0.032013875\n",
"p27_pT198 -0.0076277832 -0.019257229\n",
"Chk1 0.0244436735 -0.005668330\n",
"Chk1_pS345 0.0216846891 0.012746231\n",
"Chk2 0.0774645629 -0.179509646\n",
"Chk2_pT68 0.2663443725 -0.077993954\n",
"Claudin.7 -0.1017987479 0.099981431\n",
"Collagen_VI -0.0912967043 0.008524742\n",
"beta.Catenin -0.0000509920 0.184855993\n",
"ARHI 0.0256562665 -0.231036781\n",
"Dvl3 0.2919486530 0.278113789\n",
"eEF2 0.0087893978 0.014485302\n",
"eEF2K 0.0355001523 0.105488709\n",
"EGFR -0.0339473632 -0.030156694\n",
"EGFR_pY1068 -0.0698220800 -0.053395517\n",
"EGFR_pY1173 -0.0205144876 -0.010791584\n",
"eIF4E -0.0739320945 -0.126362580\n",
"4E.BP1 -0.0172546276 -0.008676656\n",
"4E.BP1_pS65 0.0451709723 0.077385544\n",
"4E.BP1_pT70 0.0450598591 0.038727817\n",
"eIF4G 0.1461122410 0.189946728\n",
"HER2 -0.0136513465 -0.080286270\n",
"HER2_pY1248 0.0036445093 -0.082847651\n",
"HER3 -0.0368694827 -0.032804463\n",
"HER3_pY1289 0.0748268424 -0.039070364\n",
"MIG.6 0.0250656524 -0.070596313\n",
"ER.alpha 0.0335580674 0.012876857\n",
"ER.alpha_pS118 0.0520642215 -0.018212079\n",
"ETS.1 -0.0157225661 -0.103580696\n",
"FASN 0.0063518857 -0.038141014\n",
"Fibronectin -0.0011194370 -0.037079665\n",
"FoxM1 0.0970963894 0.128974406\n",
"FOXO3a -0.0765152415 0.014497060\n",
"FOXO3a_pS318_S321 -0.0132366244 -0.011959437\n",
"G6PD -0.0360939218 -0.037468093\n",
"GAB2 0.1168798415 0.019126130\n",
"GAPDH -0.1320396355 -0.071109679\n",
"GATA3 -0.0525255638 -0.022867855\n",
"GSK3.alpha.beta -0.0040756739 0.083468456\n",
"GSK3.alpha.beta_pS21_S9 -0.0077938375 -0.006356566\n",
"GSK3_pS9 0.0102960691 -0.023594230\n",
"HSP70 -0.0030839057 -0.132714557\n",
"IGFBP2 -0.0298943695 0.120678979\n",
"IRS1 -0.0318865937 -0.010640542\n",
"CD49b 0.0525262181 0.002449562\n",
"c.Jun_pS73 0.0403203821 -0.001307756\n",
"VEGFR2 -0.0535339976 0.106013548\n",
"c.Kit -0.1579858723 0.047462532\n",
"Lck -0.0738757809 -0.057426485\n",
"MEK1 -0.1110452532 0.038131300\n",
"MEK1_pS217_S221 -0.0024521375 -0.001351452\n",
"ERK2 -0.0270946368 -0.054761515\n",
"p38_MAPK -0.0309559062 0.003253390\n",
"p38_pT180_Y182 -0.0345738306 -0.088339644\n",
"JNK2 -0.4182992402 -0.007975316\n",
"c.Met_pY1235 0.0284006038 0.017920557\n",
"Mre11 0.0187340906 0.026156432\n",
"c.Myc -0.0163078605 -0.001689716\n",
"MYH11 -0.2553814960 0.288479720\n",
"NDRG1_pT346 0.0474405498 -0.055798171\n",
"NF2 -0.0034813792 -0.032068760\n",
"NF.kB.p65_pS536 0.0741507798 0.423519937\n",
"Notch1 -0.1622839848 -0.114651255\n",
"N.Ras 0.0242513748 -0.011715821\n",
"Heregulin -0.0059969500 -0.058164105\n",
"DJ.1 -0.2408137053 0.020894517\n",
"PCNA -0.0635315667 0.024288568\n",
"PDCD4 0.0520780157 -0.046847938\n",
"\n",
"\n",
"\n"
]
}
],
"source": [
"print(out2$factorizations)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[1] \"RGCCA\"\n"
]
}
],
"source": [
"print(out2$method)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"## Compare factorizations obtained through different methods\n",
"## INPUTS: \n",
"# factorizations = list of factorization results\n",
"# methods = list of ran factorization methods\n",
"# in.folder = path to input folder\n",
"# out.folder = path to output folder\n",
"# icluster.clusters = clustering result of iCluster\n",
"# intNMF.clusters = clustering result of intNMF\n",
"# number_cl = number of clusters\n",
"## OUPUTS: matrix of Jaccard Indexes is saved to table in out.folder\n",
"clusters_comparison <- function(factorizations, methods, in.folder, out.folder,number_cl) {\n",
"\n",
" ind <- 0\n",
" JI_final <- matrix(data=NA, nrow=number_cl, ncol=length(factorizations))\n",
" #cat(JI_final,\"\\n\")\n",
" # Read clusters imposed on simulated data \n",
" cl <- as.matrix(read.table(paste0(in.folder, \"clusters.txt\"), \n",
" sep=\"\\t\", row.names=1, header=TRUE))\n",
" print(cl)\n",
" #cat(\"cl:\",cl,\"\\t\")\n",
" cl2 <- as.matrix(as.numeric(cl[,2]))\n",
" cat(\"cl2:\",cl2[,1],\"\\n\")\n",
" rownames(cl2) <- cl[,1]\n",
" #print(length(factorizations))\n",
" # Assigning samples to cluster based on factors\n",
" for (i in 1:length(factorizations)) {\n",
" \n",
" if (methods[i]==\"iCluster\" || methods[i]==\"intNMF\") {\n",
" \n",
" } else {\n",
" \n",
" factors <- factorizations[[i]][[1]]\n",
" print(\"factors:\")\n",
" print(factors)\n",
" # Clustering by Kmeans\n",
" JI_good <- numeric(0)\n",
" for (run in 1:1) {\n",
" kmeans.out <- kmeans(factors, centers=number_cl) \n",
" clust_iCluster <- as.matrix(kmeans.out$cluster)\n",
" cat(\"clust_iCluster:\",clust_iCluster,\"\\n\")\n",
" ######creation sets of samples\n",
" JI_mat <- numeric(0)\n",
" for (p in 1:number_cl) {\n",
" x1 <- rownames(clust_iCluster)[which(clust_iCluster[,1]==p)]\n",
" print(x1)\n",
" \n",
" row <- numeric(0)\n",
" for(j in 1:number_cl) {\n",
" x2 <- rownames(cl2)[which(cl2[,1]==j)]\n",
" cat(\"x2:\",x2,\"\\n\")\n",
" I <- length(intersect(x1,x2))#交集\n",
" cat(\"I:\",I,\"\\n\")\n",
" S <- I/(length(x1)+length(x2)-I)\n",
" cat(\"S:\",S,\"\\n\")\n",
" row <- cbind(row,S)\n",
" cat(\"row:\",row,\"\\n\")\n",
" }\n",
" JI_mat <- rbind(JI_mat,row)\n",
" cat(\"JI_mat:\",JI_mat,\"\\n\")\n",
" print(JI_mat)\n",
" \n",
" \n",
" }\n",
" JI_good <- rbind(JI_good,apply(JI_mat,1,max))\n",
" cat(\"JI_good:\",JI_good,\"\\n\")\n",
" }\n",
" JI_final[1:number_cl,i] <- apply(JI_good,2,mean)\n",
" }\n",
" }\n",
" \n",
" # Export JI values to a file \n",
" write.table(JI_final, paste0(out.folder,\"/JI.txt\"), sep=\"\\t\", row.names=FALSE, col.names=methods)\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {},
"outputs": [],
"source": [
"factorization=read.table(\"../data/simulations_20210329212141/equal/5/AE_FAETC_EM.txt\", sep=\" \", header=FALSE)"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<caption>A data.frame: 100 × 15</caption>\n",
"<thead>\n",
"\t<tr><th scope=col>V1</th><th scope=col>V2</th><th scope=col>V3</th><th scope=col>V4</th><th scope=col>V5</th><th scope=col>V6</th><th scope=col>V7</th><th scope=col>V8</th><th scope=col>V9</th><th scope=col>V10</th><th scope=col>V11</th><th scope=col>V12</th><th scope=col>V13</th><th scope=col>V14</th><th scope=col>V15</th></tr>\n",
"\t<tr><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th></tr>\n",
"</thead>\n",
"<tbody>\n",
"\t<tr><td>1.364614</td><td>-6.106272</td><td>-9.1133595</td><td>-5.9061093</td><td>-1.12540197</td><td>-5.149353504</td><td> 8.110886574</td><td>-12.86491</td><td>-3.4131663</td><td> -5.428276</td><td> 1.327641</td><td> 0.8208714</td><td> 4.85717201</td><td> 1.830986</td><td>-6.8246655</td></tr>\n",
"\t<tr><td>2.595337</td><td>-5.938760</td><td>-3.6227093</td><td>-0.7225778</td><td> 3.49704957</td><td>-2.792010307</td><td>-0.336862415</td><td>-18.69882</td><td>-0.8183411</td><td>-11.961297</td><td>-4.329017</td><td> 1.4387116</td><td> 2.34280133</td><td>-5.000385</td><td>-1.2720186</td></tr>\n",
"\t<tr><td>3.708545</td><td>-2.392595</td><td>-5.1247411</td><td>-0.6224614</td><td> 0.54852670</td><td> 0.879745245</td><td> 5.656763077</td><td>-15.47860</td><td>-1.7644137</td><td>-14.102664</td><td> 4.162706</td><td>-2.7230189</td><td> 3.05050159</td><td>-3.451958</td><td>-5.3215613</td></tr>\n",
"\t<tr><td>5.767153</td><td>-5.985087</td><td>-1.3936334</td><td>-1.9246240</td><td>-0.09592111</td><td>-5.213550568</td><td> 4.338903904</td><td>-19.56525</td><td> 2.5292537</td><td>-10.912452</td><td> 2.073539</td><td> 1.2014283</td><td> 5.25957203</td><td>-7.206652</td><td>-3.0671186</td></tr>\n",
"\t<tr><td>3.541591</td><td>-7.022198</td><td>-3.9639640</td><td>-1.1304803</td><td> 4.94482708</td><td>-2.593570471</td><td> 0.063670896</td><td>-18.75797</td><td>-0.7224302</td><td>-12.040921</td><td>-2.402636</td><td> 1.0178714</td><td>-0.03812202</td><td>-7.610836</td><td> 1.0129657</td></tr>\n",
"\t<tr><td>2.421503</td><td>-5.166163</td><td>-3.4402585</td><td>-0.3120118</td><td> 1.93865383</td><td>-2.545686722</td><td>-0.200865120</td><td>-17.53624</td><td>-0.6945462</td><td>-12.145635</td><td>-3.268605</td><td> 1.0533069</td><td> 0.36909178</td><td>-6.418007</td><td>-0.4841153</td></tr>\n",
"\t<tr><td>4.150049</td><td>-2.254474</td><td>-5.3667531</td><td>-0.9332458</td><td> 0.43465179</td><td> 0.406963378</td><td> 5.575583935</td><td>-14.51855</td><td>-1.6430770</td><td>-13.642753</td><td> 3.455180</td><td>-2.6348953</td><td> 2.54848194</td><td>-3.242677</td><td>-6.6115537</td></tr>\n",
"\t<tr><td>3.827635</td><td>-2.537562</td><td>-4.7054524</td><td>-0.4838656</td><td> 0.57435292</td><td>-0.080945529</td><td> 6.261950016</td><td>-15.05157</td><td>-1.5113701</td><td>-13.822030</td><td> 3.711386</td><td>-2.7433469</td><td> 3.76614356</td><td>-3.393880</td><td>-5.3013635</td></tr>\n",
"\t<tr><td>5.795492</td><td>-5.154980</td><td>-0.9332798</td><td>-1.4626205</td><td>-0.40671271</td><td>-4.489341736</td><td> 2.773021221</td><td>-16.90816</td><td> 3.2329519</td><td> -8.983538</td><td> 2.222119</td><td> 0.7351513</td><td> 4.32916212</td><td>-7.979029</td><td>-3.2727027</td></tr>\n",
"\t<tr><td>1.849412</td><td>-4.391167</td><td>-3.0255575</td><td>-0.2331904</td><td> 2.35564685</td><td>-2.259174824</td><td> 0.274122059</td><td>-16.74387</td><td>-1.4031473</td><td>-10.049000</td><td>-3.127479</td><td> 2.0756233</td><td> 1.02622116</td><td>-7.171580</td><td>-0.6122004</td></tr>\n",
"\t<tr><td>1.552489</td><td>-4.110096</td><td>-5.0476685</td><td>-2.6812036</td><td>-0.98579681</td><td>-5.176226616</td><td> 7.615598679</td><td>-13.31031</td><td>-2.9576387</td><td> -6.647234</td><td> 1.821403</td><td> 1.0560647</td><td> 5.72816753</td><td> 1.565586</td><td>-7.4634547</td></tr>\n",
"\t<tr><td>1.236442</td><td>-4.504412</td><td>-5.8166695</td><td>-3.2444904</td><td>-0.99929255</td><td>-4.876768589</td><td> 8.112017632</td><td>-13.83120</td><td>-3.7243154</td><td> -6.103724</td><td> 2.105867</td><td>-0.1509407</td><td> 4.77471638</td><td> 3.423587</td><td>-7.0119233</td></tr>\n",
"\t<tr><td>4.216510</td><td>-2.317232</td><td>-5.4863706</td><td>-0.6890665</td><td> 1.32607293</td><td>-0.473360509</td><td> 5.301970005</td><td>-15.46400</td><td>-1.5542859</td><td>-14.349189</td><td> 5.744266</td><td>-2.0513182</td><td> 2.37798476</td><td>-2.994759</td><td>-5.0165834</td></tr>\n",
"\t<tr><td>2.592076</td><td>-5.894144</td><td>-2.9799986</td><td>-0.7899423</td><td> 3.67174220</td><td>-3.070579052</td><td> 0.131115586</td><td>-18.77938</td><td>-0.7902449</td><td>-12.933554</td><td>-2.872724</td><td> 2.4071269</td><td> 1.14506173</td><td>-7.564617</td><td>-1.2979107</td></tr>\n",
"\t<tr><td>9.414653</td><td>-7.718376</td><td> 0.2931430</td><td>-2.7612970</td><td> 0.07285737</td><td>-4.688628197</td><td> 2.346898317</td><td>-15.45988</td><td> 3.3585019</td><td> -7.827687</td><td> 1.389345</td><td> 2.1458004</td><td> 4.89003038</td><td>-8.474400</td><td>-3.9662571</td></tr>\n",
"\t<tr><td>2.135017</td><td>-4.512797</td><td>-3.1149621</td><td>-0.6912211</td><td> 2.36023521</td><td>-3.102366447</td><td>-0.125342697</td><td>-18.72714</td><td>-0.6737446</td><td>-12.904139</td><td>-4.015753</td><td> 1.3522795</td><td> 1.21443474</td><td>-6.400146</td><td>-0.3348852</td></tr>\n",
"\t<tr><td>6.150630</td><td>-2.117392</td><td>-7.6357203</td><td>-1.1690760</td><td> 2.25795364</td><td>-0.003877617</td><td> 4.861887932</td><td>-14.79570</td><td>-1.4861823</td><td>-14.267993</td><td> 4.918198</td><td>-3.7151437</td><td> 2.21812177</td><td>-1.412993</td><td>-5.3857493</td></tr>\n",
"\t<tr><td>2.312166</td><td>-5.685179</td><td>-2.8385687</td><td>-0.8936508</td><td> 3.65207744</td><td>-2.871114254</td><td> 0.681894660</td><td>-20.18568</td><td>-0.8540531</td><td>-13.591594</td><td>-2.791981</td><td> 1.6250285</td><td> 0.64879322</td><td>-7.775698</td><td>-0.2633811</td></tr>\n",
"\t<tr><td>2.429922</td><td>-4.932943</td><td>-2.6174059</td><td>-0.8195862</td><td> 2.17509794</td><td>-2.780509472</td><td> 0.045440339</td><td>-17.16429</td><td>-1.3006248</td><td>-11.506498</td><td>-4.298565</td><td> 2.3186226</td><td> 1.95389259</td><td>-7.208811</td><td>-0.7329761</td></tr>\n",
"\t<tr><td>2.254678</td><td>-4.960459</td><td>-2.8935974</td><td>-0.6894010</td><td> 4.19933748</td><td>-2.056086540</td><td> 0.432444483</td><td>-18.75689</td><td>-0.8170811</td><td>-12.882384</td><td>-3.683805</td><td> 1.2375404</td><td> 0.45104983</td><td>-7.683989</td><td>-0.6559558</td></tr>\n",
"\t<tr><td>2.205649</td><td>-5.913129</td><td>-6.9990859</td><td>-4.5424247</td><td>-0.84446913</td><td>-4.734327316</td><td> 7.841816425</td><td>-11.71596</td><td>-3.4425547</td><td> -5.544622</td><td> 3.152965</td><td> 0.6267796</td><td> 5.87554359</td><td> 2.998562</td><td>-5.5737910</td></tr>\n",
"\t<tr><td>1.810154</td><td>-5.327662</td><td>-7.9744616</td><td>-5.6502333</td><td>-1.02558923</td><td>-6.010929585</td><td> 7.475661755</td><td>-12.04173</td><td>-3.7144790</td><td> -5.123187</td><td> 2.177110</td><td> 1.4698161</td><td> 4.98864174</td><td> 2.221669</td><td>-6.5479803</td></tr>\n",
"\t<tr><td>4.685986</td><td>-5.116011</td><td>-3.1311259</td><td> 0.8566008</td><td>-3.44091296</td><td>-8.548442841</td><td> 1.476135373</td><td>-12.91754</td><td>-3.0472486</td><td> -9.819015</td><td> 4.450594</td><td> 4.3443832</td><td>-1.29453611</td><td>-3.905795</td><td>-1.7515311</td></tr>\n",
"\t<tr><td>4.453277</td><td>-2.539899</td><td>-5.8208671</td><td>-0.8443363</td><td> 0.69092727</td><td> 1.077887058</td><td> 4.765635014</td><td>-13.51657</td><td>-0.8940221</td><td>-13.050684</td><td> 5.226885</td><td>-1.9341412</td><td> 2.98280501</td><td>-2.753903</td><td>-5.2867203</td></tr>\n",
"\t<tr><td>2.527725</td><td>-5.494924</td><td>-3.1933997</td><td>-0.8952646</td><td> 4.07469130</td><td>-3.641104221</td><td> 0.292647034</td><td>-19.27273</td><td>-0.9903327</td><td>-13.815386</td><td>-3.444628</td><td> 2.1892321</td><td> 1.76097059</td><td>-7.238525</td><td>-0.6136954</td></tr>\n",
"\t<tr><td>3.103855</td><td>-6.742973</td><td>-3.5297267</td><td>-2.0476065</td><td> 6.32211161</td><td>-2.486951590</td><td> 0.005822206</td><td>-18.06101</td><td>-0.7176652</td><td>-12.309981</td><td>-3.116259</td><td> 1.8818451</td><td>-0.58147472</td><td>-6.959402</td><td> 2.5841742</td></tr>\n",
"\t<tr><td>5.988764</td><td>-6.884144</td><td>-3.9173372</td><td> 2.5298469</td><td>-4.67566061</td><td>-9.430804253</td><td> 2.601134062</td><td>-11.58389</td><td>-3.3441653</td><td> -9.453644</td><td> 4.865941</td><td> 4.1122088</td><td>-1.13433194</td><td>-4.462288</td><td>-3.2808540</td></tr>\n",
"\t<tr><td>4.379490</td><td>-2.066716</td><td>-5.8044329</td><td>-0.9604352</td><td> 1.19236827</td><td> 0.312468559</td><td> 5.911241055</td><td>-15.86650</td><td>-2.0005322</td><td>-13.652694</td><td> 4.565659</td><td>-3.5513661</td><td> 2.80084538</td><td>-1.744902</td><td>-5.3310199</td></tr>\n",
"\t<tr><td>4.342060</td><td>-4.860115</td><td>-2.9849405</td><td> 1.1048417</td><td>-2.97053623</td><td>-8.818906784</td><td> 2.848891973</td><td>-15.38535</td><td>-2.5427375</td><td>-10.871824</td><td> 4.184150</td><td> 2.9246807</td><td>-2.52695537</td><td>-2.322521</td><td>-3.4124339</td></tr>\n",
"\t<tr><td>3.050938</td><td>-3.352108</td><td>-4.2128959</td><td>-0.2189043</td><td> 0.17008510</td><td> 0.643936157</td><td> 5.411861897</td><td>-12.82839</td><td>-1.6516005</td><td>-12.974924</td><td> 4.789909</td><td>-2.1248729</td><td> 3.62720108</td><td>-3.038718</td><td>-5.1394057</td></tr>\n",
"\t<tr><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td><td>⋮</td></tr>\n",
"\t<tr><td>4.568026</td><td>-1.580006</td><td> -5.7653575</td><td> -1.2712021</td><td> 1.4136478901</td><td>-0.15090951</td><td> 5.92859268</td><td>-17.53403</td><td>-1.8591350</td><td>-16.006456</td><td> 4.7152524</td><td>-3.3079474</td><td> 2.3683727</td><td>-1.749003</td><td>-4.7701387</td></tr>\n",
"\t<tr><td>4.638977</td><td>-2.231600</td><td> -6.1335502</td><td> -0.6928905</td><td> 1.4882037640</td><td> 0.57408309</td><td> 5.57630920</td><td>-15.55637</td><td>-1.7714077</td><td>-14.134931</td><td> 3.8968377</td><td>-2.5810466</td><td> 2.6179118</td><td>-3.479542</td><td>-6.4095054</td></tr>\n",
"\t<tr><td>2.554769</td><td>-5.719078</td><td> -3.5181692</td><td> -0.5363890</td><td> 3.1886093616</td><td>-4.29229975</td><td> 1.61574495</td><td>-21.29429</td><td>-1.2954823</td><td>-13.825887</td><td>-2.5001032</td><td> 2.3772862</td><td> 1.2030927</td><td>-8.640922</td><td>-0.2206428</td></tr>\n",
"\t<tr><td>6.997326</td><td>-5.011719</td><td> 0.8019572</td><td> -2.3327296</td><td>-0.0902997032</td><td>-4.05709743</td><td> 2.32674885</td><td>-13.16608</td><td> 2.8190386</td><td> -6.616040</td><td> 2.3638618</td><td> 1.8632438</td><td> 4.5743742</td><td>-8.239238</td><td>-3.0091286</td></tr>\n",
"\t<tr><td>2.108623</td><td>-7.906268</td><td>-12.8760176</td><td>-10.1564293</td><td>-0.3261828423</td><td>-5.45073509</td><td> 8.47327328</td><td>-14.24173</td><td>-3.3009071</td><td> -6.392434</td><td> 2.1642957</td><td> 1.1111578</td><td> 5.8463268</td><td> 1.772806</td><td>-6.6452203</td></tr>\n",
"\t<tr><td>5.739309</td><td>-5.118634</td><td> -0.7052121</td><td> -1.9376416</td><td>-0.1254920661</td><td>-4.34498072</td><td> 2.72932315</td><td>-15.68990</td><td> 3.2943606</td><td> -8.407866</td><td> 1.0114187</td><td> 1.7510997</td><td> 5.0616970</td><td>-6.371283</td><td>-2.7987578</td></tr>\n",
"\t<tr><td>4.352842</td><td>-2.290206</td><td> -6.0016479</td><td> -0.6265063</td><td> 1.2788192034</td><td>-0.59810448</td><td> 5.52771187</td><td>-15.34131</td><td>-1.5754925</td><td>-14.513073</td><td> 4.1602216</td><td>-2.3213527</td><td> 2.8614898</td><td>-3.471461</td><td>-5.9957261</td></tr>\n",
"\t<tr><td>8.203038</td><td>-6.737101</td><td> 0.6308022</td><td> -2.6791546</td><td> 0.0331112072</td><td>-4.44884872</td><td> 3.04271936</td><td>-16.22462</td><td> 3.3452938</td><td> -9.058146</td><td> 0.8915003</td><td> 1.7142127</td><td> 5.5755992</td><td>-7.383893</td><td>-4.1187649</td></tr>\n",
"\t<tr><td>9.683000</td><td>-2.138233</td><td>-10.8349619</td><td> -2.0128343</td><td> 3.7677421570</td><td>-0.62864161</td><td> 6.15969086</td><td>-15.54685</td><td>-1.8161896</td><td>-15.213776</td><td> 5.6375279</td><td>-2.4573510</td><td> 2.4149096</td><td>-2.970704</td><td>-4.3525071</td></tr>\n",
"\t<tr><td>5.065584</td><td>-4.819563</td><td> -1.1874355</td><td> -1.6336071</td><td>-0.3672036529</td><td>-5.05415821</td><td> 3.50948167</td><td>-16.78403</td><td> 2.8720467</td><td> -8.697453</td><td> 1.2968588</td><td> 1.0252613</td><td> 5.0780172</td><td>-6.404398</td><td>-3.5434029</td></tr>\n",
"\t<tr><td>8.155322</td><td>-6.406314</td><td> 0.7154618</td><td> -2.7522581</td><td> 0.0002044067</td><td>-3.99534893</td><td> 0.79592109</td><td>-14.30064</td><td> 3.7953365</td><td> -7.784212</td><td> 1.5141768</td><td> 1.3084570</td><td> 5.5818005</td><td>-6.562686</td><td>-2.9888823</td></tr>\n",
"\t<tr><td>2.037210</td><td>-5.748902</td><td> -7.2167077</td><td> -3.8441615</td><td>-0.8778251410</td><td>-5.02795029</td><td> 7.20830011</td><td>-10.12536</td><td>-3.5305285</td><td> -3.485076</td><td> 2.4987838</td><td> 1.0515349</td><td> 4.9519787</td><td> 2.422310</td><td>-5.8234034</td></tr>\n",
"\t<tr><td>2.549152</td><td>-5.778267</td><td> -2.5680861</td><td> -0.8840805</td><td> 3.4824593067</td><td>-2.21734452</td><td> 0.30072370</td><td>-17.59094</td><td>-1.5749041</td><td>-10.843613</td><td>-2.8605871</td><td> 1.0696204</td><td> 0.6033388</td><td>-7.399768</td><td>-0.1852023</td></tr>\n",
"\t<tr><td>3.290432</td><td>-7.053134</td><td> -3.6329198</td><td> -1.1331015</td><td> 4.9401106834</td><td>-2.90880346</td><td>-0.44940862</td><td>-17.51407</td><td>-1.0047024</td><td>-11.673330</td><td>-4.0656734</td><td>-0.2132214</td><td> 0.4301564</td><td>-5.902227</td><td>-0.5074827</td></tr>\n",
"\t<tr><td>2.088002</td><td>-5.836352</td><td> -8.4787912</td><td> -5.4655275</td><td>-1.2730693817</td><td>-5.26897335</td><td> 7.97211409</td><td>-13.41879</td><td>-3.0513813</td><td> -6.089839</td><td> 1.7254858</td><td> 1.8032290</td><td> 4.8907895</td><td> 1.325236</td><td>-8.4227810</td></tr>\n",
"\t<tr><td>4.730251</td><td>-5.462926</td><td> -3.5259504</td><td> 1.5797091</td><td>-3.4017002583</td><td>-8.72756290</td><td> 2.15470767</td><td>-12.69422</td><td>-2.9002886</td><td>-10.065287</td><td> 3.1706443</td><td> 2.9299498</td><td>-2.1684637</td><td>-3.836938</td><td>-3.5421708</td></tr>\n",
"\t<tr><td>2.519696</td><td>-6.206445</td><td> -3.4693151</td><td> -0.5791476</td><td> 3.6860020161</td><td>-3.09619904</td><td>-0.09280834</td><td>-17.92822</td><td>-1.1767925</td><td>-12.469215</td><td>-2.6421485</td><td> 2.1279385</td><td> 1.2929267</td><td>-8.515422</td><td>-0.6013060</td></tr>\n",
"\t<tr><td>3.051261</td><td>-6.164137</td><td> -3.0902605</td><td> -1.2714670</td><td> 4.5201320648</td><td>-2.99722004</td><td> 0.18775597</td><td>-16.98655</td><td>-0.7562402</td><td>-11.177454</td><td>-3.5248618</td><td> 0.9328425</td><td> 0.8078923</td><td>-6.104471</td><td> 0.8842458</td></tr>\n",
"\t<tr><td>1.073783</td><td>-4.613420</td><td> -6.3512692</td><td> -3.8319449</td><td>-1.1131196022</td><td>-5.25494576</td><td> 7.46743917</td><td>-12.47251</td><td>-3.2143519</td><td> -5.923545</td><td> 1.8268092</td><td> 0.2752512</td><td> 4.5594120</td><td> 2.688883</td><td>-7.2799592</td></tr>\n",
"\t<tr><td>3.049418</td><td>-6.526370</td><td> -3.3531973</td><td> -1.5409517</td><td> 5.9906334877</td><td>-3.15830564</td><td>-0.49258718</td><td>-16.15066</td><td>-1.0405034</td><td>-10.777252</td><td>-2.7216291</td><td> 2.3298395</td><td> 1.3262671</td><td>-7.742356</td><td> 0.7600487</td></tr>\n",
"\t<tr><td>2.299257</td><td>-6.576549</td><td>-11.1815224</td><td> -8.6209688</td><td>-0.3008396626</td><td>-5.88015747</td><td> 6.96856928</td><td>-12.34746</td><td>-3.4155140</td><td> -6.228897</td><td> 2.2964327</td><td> 1.7340368</td><td> 5.5737391</td><td> 1.621253</td><td>-6.8108306</td></tr>\n",
"\t<tr><td>1.978040</td><td>-5.101249</td><td> -6.9519877</td><td> -4.3321543</td><td>-0.9555765390</td><td>-4.55864906</td><td> 7.44492292</td><td>-13.12647</td><td>-3.4570978</td><td> -5.639615</td><td> 1.2233088</td><td> 0.1023000</td><td> 4.9460096</td><td> 2.714372</td><td>-6.9929123</td></tr>\n",
"\t<tr><td>7.351749</td><td>-1.355803</td><td> -8.2382669</td><td> -1.1935792</td><td> 1.7584133148</td><td> 0.17264697</td><td> 6.06365252</td><td>-17.30200</td><td>-2.4722471</td><td>-15.670676</td><td> 5.4404073</td><td>-1.9588546</td><td> 2.0936201</td><td>-3.130454</td><td>-5.1776347</td></tr>\n",
"\t<tr><td>3.614705</td><td>-1.751079</td><td> -4.6328015</td><td> -0.8231169</td><td> 0.8779423833</td><td> 0.08133652</td><td> 5.52687597</td><td>-14.87722</td><td>-1.1260140</td><td>-14.548677</td><td> 3.7598212</td><td>-2.1644452</td><td> 3.2774484</td><td>-3.430882</td><td>-6.0524898</td></tr>\n",
"\t<tr><td>2.115447</td><td>-6.168517</td><td> -8.7798109</td><td> -6.1212263</td><td>-0.8637107611</td><td>-5.51797819</td><td> 7.84722757</td><td>-12.17093</td><td>-3.2496598</td><td> -5.268707</td><td> 1.7024575</td><td> 0.5100074</td><td> 4.9548903</td><td> 2.214145</td><td>-7.7204466</td></tr>\n",
"\t<tr><td>3.559060</td><td>-4.317487</td><td> -3.0177283</td><td> 0.3407646</td><td>-1.9263570309</td><td>-8.09674168</td><td> 1.70674980</td><td>-11.62743</td><td>-2.7164323</td><td> -9.439749</td><td> 3.9634116</td><td> 3.7463126</td><td>-1.9930896</td><td>-5.052331</td><td>-3.1405520</td></tr>\n",
"\t<tr><td>4.570605</td><td>-5.248532</td><td> -3.4832544</td><td> 0.7583200</td><td>-3.1959526539</td><td>-8.19375896</td><td> 2.27919364</td><td>-10.96759</td><td>-2.8234141</td><td> -8.845697</td><td> 3.2261248</td><td> 4.1440792</td><td>-0.9228735</td><td>-4.618789</td><td>-3.9137733</td></tr>\n",
"\t<tr><td>4.472492</td><td>-4.890934</td><td> -2.8845019</td><td> 1.1547174</td><td>-2.7677462101</td><td>-8.72113419</td><td> 1.92387354</td><td>-10.56394</td><td>-3.1129119</td><td> -7.769747</td><td> 4.6511006</td><td> 3.7833085</td><td>-1.6304593</td><td>-5.594076</td><td>-2.5928376</td></tr>\n",
"\t<tr><td>3.624304</td><td>-7.847561</td><td> -4.0640669</td><td> -2.0619318</td><td> 6.9316506386</td><td>-2.27580905</td><td> 0.33176556</td><td>-19.14009</td><td>-1.1348858</td><td>-11.961175</td><td>-1.9076225</td><td> 1.2473679</td><td> 0.5517591</td><td>-8.137267</td><td> 0.6829665</td></tr>\n",
"\t<tr><td>5.600024</td><td>-6.079413</td><td> -3.2682271</td><td> 2.0289369</td><td>-4.1170182228</td><td>-8.73837376</td><td> 3.27058840</td><td>-13.87365</td><td>-2.9598057</td><td> -9.943305</td><td> 4.3723140</td><td> 4.5461845</td><td>-1.0018466</td><td>-4.417732</td><td>-3.1890416</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"A data.frame: 100 × 15\n",
"\\begin{tabular}{lllllllllllllll}\n",
" V1 & V2 & V3 & V4 & V5 & V6 & V7 & V8 & V9 & V10 & V11 & V12 & V13 & V14 & V15\\\\\n",
" <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl> & <dbl>\\\\\n",
"\\hline\n",
"\t 1.364614 & -6.106272 & -9.1133595 & -5.9061093 & -1.12540197 & -5.149353504 & 8.110886574 & -12.86491 & -3.4131663 & -5.428276 & 1.327641 & 0.8208714 & 4.85717201 & 1.830986 & -6.8246655\\\\\n",
"\t 2.595337 & -5.938760 & -3.6227093 & -0.7225778 & 3.49704957 & -2.792010307 & -0.336862415 & -18.69882 & -0.8183411 & -11.961297 & -4.329017 & 1.4387116 & 2.34280133 & -5.000385 & -1.2720186\\\\\n",
"\t 3.708545 & -2.392595 & -5.1247411 & -0.6224614 & 0.54852670 & 0.879745245 & 5.656763077 & -15.47860 & -1.7644137 & -14.102664 & 4.162706 & -2.7230189 & 3.05050159 & -3.451958 & -5.3215613\\\\\n",
"\t 5.767153 & -5.985087 & -1.3936334 & -1.9246240 & -0.09592111 & -5.213550568 & 4.338903904 & -19.56525 & 2.5292537 & -10.912452 & 2.073539 & 1.2014283 & 5.25957203 & -7.206652 & -3.0671186\\\\\n",
"\t 3.541591 & -7.022198 & -3.9639640 & -1.1304803 & 4.94482708 & -2.593570471 & 0.063670896 & -18.75797 & -0.7224302 & -12.040921 & -2.402636 & 1.0178714 & -0.03812202 & -7.610836 & 1.0129657\\\\\n",
"\t 2.421503 & -5.166163 & -3.4402585 & -0.3120118 & 1.93865383 & -2.545686722 & -0.200865120 & -17.53624 & -0.6945462 & -12.145635 & -3.268605 & 1.0533069 & 0.36909178 & -6.418007 & -0.4841153\\\\\n",
"\t 4.150049 & -2.254474 & -5.3667531 & -0.9332458 & 0.43465179 & 0.406963378 & 5.575583935 & -14.51855 & -1.6430770 & -13.642753 & 3.455180 & -2.6348953 & 2.54848194 & -3.242677 & -6.6115537\\\\\n",
"\t 3.827635 & -2.537562 & -4.7054524 & -0.4838656 & 0.57435292 & -0.080945529 & 6.261950016 & -15.05157 & -1.5113701 & -13.822030 & 3.711386 & -2.7433469 & 3.76614356 & -3.393880 & -5.3013635\\\\\n",
"\t 5.795492 & -5.154980 & -0.9332798 & -1.4626205 & -0.40671271 & -4.489341736 & 2.773021221 & -16.90816 & 3.2329519 & -8.983538 & 2.222119 & 0.7351513 & 4.32916212 & -7.979029 & -3.2727027\\\\\n",
"\t 1.849412 & -4.391167 & -3.0255575 & -0.2331904 & 2.35564685 & -2.259174824 & 0.274122059 & -16.74387 & -1.4031473 & -10.049000 & -3.127479 & 2.0756233 & 1.02622116 & -7.171580 & -0.6122004\\\\\n",
"\t 1.552489 & -4.110096 & -5.0476685 & -2.6812036 & -0.98579681 & -5.176226616 & 7.615598679 & -13.31031 & -2.9576387 & -6.647234 & 1.821403 & 1.0560647 & 5.72816753 & 1.565586 & -7.4634547\\\\\n",
"\t 1.236442 & -4.504412 & -5.8166695 & -3.2444904 & -0.99929255 & -4.876768589 & 8.112017632 & -13.83120 & -3.7243154 & -6.103724 & 2.105867 & -0.1509407 & 4.77471638 & 3.423587 & -7.0119233\\\\\n",
"\t 4.216510 & -2.317232 & -5.4863706 & -0.6890665 & 1.32607293 & -0.473360509 & 5.301970005 & -15.46400 & -1.5542859 & -14.349189 & 5.744266 & -2.0513182 & 2.37798476 & -2.994759 & -5.0165834\\\\\n",
"\t 2.592076 & -5.894144 & -2.9799986 & -0.7899423 & 3.67174220 & -3.070579052 & 0.131115586 & -18.77938 & -0.7902449 & -12.933554 & -2.872724 & 2.4071269 & 1.14506173 & -7.564617 & -1.2979107\\\\\n",
"\t 9.414653 & -7.718376 & 0.2931430 & -2.7612970 & 0.07285737 & -4.688628197 & 2.346898317 & -15.45988 & 3.3585019 & -7.827687 & 1.389345 & 2.1458004 & 4.89003038 & -8.474400 & -3.9662571\\\\\n",
"\t 2.135017 & -4.512797 & -3.1149621 & -0.6912211 & 2.36023521 & -3.102366447 & -0.125342697 & -18.72714 & -0.6737446 & -12.904139 & -4.015753 & 1.3522795 & 1.21443474 & -6.400146 & -0.3348852\\\\\n",
"\t 6.150630 & -2.117392 & -7.6357203 & -1.1690760 & 2.25795364 & -0.003877617 & 4.861887932 & -14.79570 & -1.4861823 & -14.267993 & 4.918198 & -3.7151437 & 2.21812177 & -1.412993 & -5.3857493\\\\\n",
"\t 2.312166 & -5.685179 & -2.8385687 & -0.8936508 & 3.65207744 & -2.871114254 & 0.681894660 & -20.18568 & -0.8540531 & -13.591594 & -2.791981 & 1.6250285 & 0.64879322 & -7.775698 & -0.2633811\\\\\n",
"\t 2.429922 & -4.932943 & -2.6174059 & -0.8195862 & 2.17509794 & -2.780509472 & 0.045440339 & -17.16429 & -1.3006248 & -11.506498 & -4.298565 & 2.3186226 & 1.95389259 & -7.208811 & -0.7329761\\\\\n",
"\t 2.254678 & -4.960459 & -2.8935974 & -0.6894010 & 4.19933748 & -2.056086540 & 0.432444483 & -18.75689 & -0.8170811 & -12.882384 & -3.683805 & 1.2375404 & 0.45104983 & -7.683989 & -0.6559558\\\\\n",
"\t 2.205649 & -5.913129 & -6.9990859 & -4.5424247 & -0.84446913 & -4.734327316 & 7.841816425 & -11.71596 & -3.4425547 & -5.544622 & 3.152965 & 0.6267796 & 5.87554359 & 2.998562 & -5.5737910\\\\\n",
"\t 1.810154 & -5.327662 & -7.9744616 & -5.6502333 & -1.02558923 & -6.010929585 & 7.475661755 & -12.04173 & -3.7144790 & -5.123187 & 2.177110 & 1.4698161 & 4.98864174 & 2.221669 & -6.5479803\\\\\n",
"\t 4.685986 & -5.116011 & -3.1311259 & 0.8566008 & -3.44091296 & -8.548442841 & 1.476135373 & -12.91754 & -3.0472486 & -9.819015 & 4.450594 & 4.3443832 & -1.29453611 & -3.905795 & -1.7515311\\\\\n",
"\t 4.453277 & -2.539899 & -5.8208671 & -0.8443363 & 0.69092727 & 1.077887058 & 4.765635014 & -13.51657 & -0.8940221 & -13.050684 & 5.226885 & -1.9341412 & 2.98280501 & -2.753903 & -5.2867203\\\\\n",
"\t 2.527725 & -5.494924 & -3.1933997 & -0.8952646 & 4.07469130 & -3.641104221 & 0.292647034 & -19.27273 & -0.9903327 & -13.815386 & -3.444628 & 2.1892321 & 1.76097059 & -7.238525 & -0.6136954\\\\\n",
"\t 3.103855 & -6.742973 & -3.5297267 & -2.0476065 & 6.32211161 & -2.486951590 & 0.005822206 & -18.06101 & -0.7176652 & -12.309981 & -3.116259 & 1.8818451 & -0.58147472 & -6.959402 & 2.5841742\\\\\n",
"\t 5.988764 & -6.884144 & -3.9173372 & 2.5298469 & -4.67566061 & -9.430804253 & 2.601134062 & -11.58389 & -3.3441653 & -9.453644 & 4.865941 & 4.1122088 & -1.13433194 & -4.462288 & -3.2808540\\\\\n",
"\t 4.379490 & -2.066716 & -5.8044329 & -0.9604352 & 1.19236827 & 0.312468559 & 5.911241055 & -15.86650 & -2.0005322 & -13.652694 & 4.565659 & -3.5513661 & 2.80084538 & -1.744902 & -5.3310199\\\\\n",
"\t 4.342060 & -4.860115 & -2.9849405 & 1.1048417 & -2.97053623 & -8.818906784 & 2.848891973 & -15.38535 & -2.5427375 & -10.871824 & 4.184150 & 2.9246807 & -2.52695537 & -2.322521 & -3.4124339\\\\\n",
"\t 3.050938 & -3.352108 & -4.2128959 & -0.2189043 & 0.17008510 & 0.643936157 & 5.411861897 & -12.82839 & -1.6516005 & -12.974924 & 4.789909 & -2.1248729 & 3.62720108 & -3.038718 & -5.1394057\\\\\n",
"\t ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮ & ⋮\\\\\n",
"\t 4.568026 & -1.580006 & -5.7653575 & -1.2712021 & 1.4136478901 & -0.15090951 & 5.92859268 & -17.53403 & -1.8591350 & -16.006456 & 4.7152524 & -3.3079474 & 2.3683727 & -1.749003 & -4.7701387\\\\\n",
"\t 4.638977 & -2.231600 & -6.1335502 & -0.6928905 & 1.4882037640 & 0.57408309 & 5.57630920 & -15.55637 & -1.7714077 & -14.134931 & 3.8968377 & -2.5810466 & 2.6179118 & -3.479542 & -6.4095054\\\\\n",
"\t 2.554769 & -5.719078 & -3.5181692 & -0.5363890 & 3.1886093616 & -4.29229975 & 1.61574495 & -21.29429 & -1.2954823 & -13.825887 & -2.5001032 & 2.3772862 & 1.2030927 & -8.640922 & -0.2206428\\\\\n",
"\t 6.997326 & -5.011719 & 0.8019572 & -2.3327296 & -0.0902997032 & -4.05709743 & 2.32674885 & -13.16608 & 2.8190386 & -6.616040 & 2.3638618 & 1.8632438 & 4.5743742 & -8.239238 & -3.0091286\\\\\n",
"\t 2.108623 & -7.906268 & -12.8760176 & -10.1564293 & -0.3261828423 & -5.45073509 & 8.47327328 & -14.24173 & -3.3009071 & -6.392434 & 2.1642957 & 1.1111578 & 5.8463268 & 1.772806 & -6.6452203\\\\\n",
"\t 5.739309 & -5.118634 & -0.7052121 & -1.9376416 & -0.1254920661 & -4.34498072 & 2.72932315 & -15.68990 & 3.2943606 & -8.407866 & 1.0114187 & 1.7510997 & 5.0616970 & -6.371283 & -2.7987578\\\\\n",
"\t 4.352842 & -2.290206 & -6.0016479 & -0.6265063 & 1.2788192034 & -0.59810448 & 5.52771187 & -15.34131 & -1.5754925 & -14.513073 & 4.1602216 & -2.3213527 & 2.8614898 & -3.471461 & -5.9957261\\\\\n",
"\t 8.203038 & -6.737101 & 0.6308022 & -2.6791546 & 0.0331112072 & -4.44884872 & 3.04271936 & -16.22462 & 3.3452938 & -9.058146 & 0.8915003 & 1.7142127 & 5.5755992 & -7.383893 & -4.1187649\\\\\n",
"\t 9.683000 & -2.138233 & -10.8349619 & -2.0128343 & 3.7677421570 & -0.62864161 & 6.15969086 & -15.54685 & -1.8161896 & -15.213776 & 5.6375279 & -2.4573510 & 2.4149096 & -2.970704 & -4.3525071\\\\\n",
"\t 5.065584 & -4.819563 & -1.1874355 & -1.6336071 & -0.3672036529 & -5.05415821 & 3.50948167 & -16.78403 & 2.8720467 & -8.697453 & 1.2968588 & 1.0252613 & 5.0780172 & -6.404398 & -3.5434029\\\\\n",
"\t 8.155322 & -6.406314 & 0.7154618 & -2.7522581 & 0.0002044067 & -3.99534893 & 0.79592109 & -14.30064 & 3.7953365 & -7.784212 & 1.5141768 & 1.3084570 & 5.5818005 & -6.562686 & -2.9888823\\\\\n",
"\t 2.037210 & -5.748902 & -7.2167077 & -3.8441615 & -0.8778251410 & -5.02795029 & 7.20830011 & -10.12536 & -3.5305285 & -3.485076 & 2.4987838 & 1.0515349 & 4.9519787 & 2.422310 & -5.8234034\\\\\n",
"\t 2.549152 & -5.778267 & -2.5680861 & -0.8840805 & 3.4824593067 & -2.21734452 & 0.30072370 & -17.59094 & -1.5749041 & -10.843613 & -2.8605871 & 1.0696204 & 0.6033388 & -7.399768 & -0.1852023\\\\\n",
"\t 3.290432 & -7.053134 & -3.6329198 & -1.1331015 & 4.9401106834 & -2.90880346 & -0.44940862 & -17.51407 & -1.0047024 & -11.673330 & -4.0656734 & -0.2132214 & 0.4301564 & -5.902227 & -0.5074827\\\\\n",
"\t 2.088002 & -5.836352 & -8.4787912 & -5.4655275 & -1.2730693817 & -5.26897335 & 7.97211409 & -13.41879 & -3.0513813 & -6.089839 & 1.7254858 & 1.8032290 & 4.8907895 & 1.325236 & -8.4227810\\\\\n",
"\t 4.730251 & -5.462926 & -3.5259504 & 1.5797091 & -3.4017002583 & -8.72756290 & 2.15470767 & -12.69422 & -2.9002886 & -10.065287 & 3.1706443 & 2.9299498 & -2.1684637 & -3.836938 & -3.5421708\\\\\n",
"\t 2.519696 & -6.206445 & -3.4693151 & -0.5791476 & 3.6860020161 & -3.09619904 & -0.09280834 & -17.92822 & -1.1767925 & -12.469215 & -2.6421485 & 2.1279385 & 1.2929267 & -8.515422 & -0.6013060\\\\\n",
"\t 3.051261 & -6.164137 & -3.0902605 & -1.2714670 & 4.5201320648 & -2.99722004 & 0.18775597 & -16.98655 & -0.7562402 & -11.177454 & -3.5248618 & 0.9328425 & 0.8078923 & -6.104471 & 0.8842458\\\\\n",
"\t 1.073783 & -4.613420 & -6.3512692 & -3.8319449 & -1.1131196022 & -5.25494576 & 7.46743917 & -12.47251 & -3.2143519 & -5.923545 & 1.8268092 & 0.2752512 & 4.5594120 & 2.688883 & -7.2799592\\\\\n",
"\t 3.049418 & -6.526370 & -3.3531973 & -1.5409517 & 5.9906334877 & -3.15830564 & -0.49258718 & -16.15066 & -1.0405034 & -10.777252 & -2.7216291 & 2.3298395 & 1.3262671 & -7.742356 & 0.7600487\\\\\n",
"\t 2.299257 & -6.576549 & -11.1815224 & -8.6209688 & -0.3008396626 & -5.88015747 & 6.96856928 & -12.34746 & -3.4155140 & -6.228897 & 2.2964327 & 1.7340368 & 5.5737391 & 1.621253 & -6.8108306\\\\\n",
"\t 1.978040 & -5.101249 & -6.9519877 & -4.3321543 & -0.9555765390 & -4.55864906 & 7.44492292 & -13.12647 & -3.4570978 & -5.639615 & 1.2233088 & 0.1023000 & 4.9460096 & 2.714372 & -6.9929123\\\\\n",
"\t 7.351749 & -1.355803 & -8.2382669 & -1.1935792 & 1.7584133148 & 0.17264697 & 6.06365252 & -17.30200 & -2.4722471 & -15.670676 & 5.4404073 & -1.9588546 & 2.0936201 & -3.130454 & -5.1776347\\\\\n",
"\t 3.614705 & -1.751079 & -4.6328015 & -0.8231169 & 0.8779423833 & 0.08133652 & 5.52687597 & -14.87722 & -1.1260140 & -14.548677 & 3.7598212 & -2.1644452 & 3.2774484 & -3.430882 & -6.0524898\\\\\n",
"\t 2.115447 & -6.168517 & -8.7798109 & -6.1212263 & -0.8637107611 & -5.51797819 & 7.84722757 & -12.17093 & -3.2496598 & -5.268707 & 1.7024575 & 0.5100074 & 4.9548903 & 2.214145 & -7.7204466\\\\\n",
"\t 3.559060 & -4.317487 & -3.0177283 & 0.3407646 & -1.9263570309 & -8.09674168 & 1.70674980 & -11.62743 & -2.7164323 & -9.439749 & 3.9634116 & 3.7463126 & -1.9930896 & -5.052331 & -3.1405520\\\\\n",
"\t 4.570605 & -5.248532 & -3.4832544 & 0.7583200 & -3.1959526539 & -8.19375896 & 2.27919364 & -10.96759 & -2.8234141 & -8.845697 & 3.2261248 & 4.1440792 & -0.9228735 & -4.618789 & -3.9137733\\\\\n",
"\t 4.472492 & -4.890934 & -2.8845019 & 1.1547174 & -2.7677462101 & -8.72113419 & 1.92387354 & -10.56394 & -3.1129119 & -7.769747 & 4.6511006 & 3.7833085 & -1.6304593 & -5.594076 & -2.5928376\\\\\n",
"\t 3.624304 & -7.847561 & -4.0640669 & -2.0619318 & 6.9316506386 & -2.27580905 & 0.33176556 & -19.14009 & -1.1348858 & -11.961175 & -1.9076225 & 1.2473679 & 0.5517591 & -8.137267 & 0.6829665\\\\\n",
"\t 5.600024 & -6.079413 & -3.2682271 & 2.0289369 & -4.1170182228 & -8.73837376 & 3.27058840 & -13.87365 & -2.9598057 & -9.943305 & 4.3723140 & 4.5461845 & -1.0018466 & -4.417732 & -3.1890416\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"A data.frame: 100 × 15\n",
"\n",
"| V1 <dbl> | V2 <dbl> | V3 <dbl> | V4 <dbl> | V5 <dbl> | V6 <dbl> | V7 <dbl> | V8 <dbl> | V9 <dbl> | V10 <dbl> | V11 <dbl> | V12 <dbl> | V13 <dbl> | V14 <dbl> | V15 <dbl> |\n",
"|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
"| 1.364614 | -6.106272 | -9.1133595 | -5.9061093 | -1.12540197 | -5.149353504 | 8.110886574 | -12.86491 | -3.4131663 | -5.428276 | 1.327641 | 0.8208714 | 4.85717201 | 1.830986 | -6.8246655 |\n",
"| 2.595337 | -5.938760 | -3.6227093 | -0.7225778 | 3.49704957 | -2.792010307 | -0.336862415 | -18.69882 | -0.8183411 | -11.961297 | -4.329017 | 1.4387116 | 2.34280133 | -5.000385 | -1.2720186 |\n",
"| 3.708545 | -2.392595 | -5.1247411 | -0.6224614 | 0.54852670 | 0.879745245 | 5.656763077 | -15.47860 | -1.7644137 | -14.102664 | 4.162706 | -2.7230189 | 3.05050159 | -3.451958 | -5.3215613 |\n",
"| 5.767153 | -5.985087 | -1.3936334 | -1.9246240 | -0.09592111 | -5.213550568 | 4.338903904 | -19.56525 | 2.5292537 | -10.912452 | 2.073539 | 1.2014283 | 5.25957203 | -7.206652 | -3.0671186 |\n",
"| 3.541591 | -7.022198 | -3.9639640 | -1.1304803 | 4.94482708 | -2.593570471 | 0.063670896 | -18.75797 | -0.7224302 | -12.040921 | -2.402636 | 1.0178714 | -0.03812202 | -7.610836 | 1.0129657 |\n",
"| 2.421503 | -5.166163 | -3.4402585 | -0.3120118 | 1.93865383 | -2.545686722 | -0.200865120 | -17.53624 | -0.6945462 | -12.145635 | -3.268605 | 1.0533069 | 0.36909178 | -6.418007 | -0.4841153 |\n",
"| 4.150049 | -2.254474 | -5.3667531 | -0.9332458 | 0.43465179 | 0.406963378 | 5.575583935 | -14.51855 | -1.6430770 | -13.642753 | 3.455180 | -2.6348953 | 2.54848194 | -3.242677 | -6.6115537 |\n",
"| 3.827635 | -2.537562 | -4.7054524 | -0.4838656 | 0.57435292 | -0.080945529 | 6.261950016 | -15.05157 | -1.5113701 | -13.822030 | 3.711386 | -2.7433469 | 3.76614356 | -3.393880 | -5.3013635 |\n",
"| 5.795492 | -5.154980 | -0.9332798 | -1.4626205 | -0.40671271 | -4.489341736 | 2.773021221 | -16.90816 | 3.2329519 | -8.983538 | 2.222119 | 0.7351513 | 4.32916212 | -7.979029 | -3.2727027 |\n",
"| 1.849412 | -4.391167 | -3.0255575 | -0.2331904 | 2.35564685 | -2.259174824 | 0.274122059 | -16.74387 | -1.4031473 | -10.049000 | -3.127479 | 2.0756233 | 1.02622116 | -7.171580 | -0.6122004 |\n",
"| 1.552489 | -4.110096 | -5.0476685 | -2.6812036 | -0.98579681 | -5.176226616 | 7.615598679 | -13.31031 | -2.9576387 | -6.647234 | 1.821403 | 1.0560647 | 5.72816753 | 1.565586 | -7.4634547 |\n",
"| 1.236442 | -4.504412 | -5.8166695 | -3.2444904 | -0.99929255 | -4.876768589 | 8.112017632 | -13.83120 | -3.7243154 | -6.103724 | 2.105867 | -0.1509407 | 4.77471638 | 3.423587 | -7.0119233 |\n",
"| 4.216510 | -2.317232 | -5.4863706 | -0.6890665 | 1.32607293 | -0.473360509 | 5.301970005 | -15.46400 | -1.5542859 | -14.349189 | 5.744266 | -2.0513182 | 2.37798476 | -2.994759 | -5.0165834 |\n",
"| 2.592076 | -5.894144 | -2.9799986 | -0.7899423 | 3.67174220 | -3.070579052 | 0.131115586 | -18.77938 | -0.7902449 | -12.933554 | -2.872724 | 2.4071269 | 1.14506173 | -7.564617 | -1.2979107 |\n",
"| 9.414653 | -7.718376 | 0.2931430 | -2.7612970 | 0.07285737 | -4.688628197 | 2.346898317 | -15.45988 | 3.3585019 | -7.827687 | 1.389345 | 2.1458004 | 4.89003038 | -8.474400 | -3.9662571 |\n",
"| 2.135017 | -4.512797 | -3.1149621 | -0.6912211 | 2.36023521 | -3.102366447 | -0.125342697 | -18.72714 | -0.6737446 | -12.904139 | -4.015753 | 1.3522795 | 1.21443474 | -6.400146 | -0.3348852 |\n",
"| 6.150630 | -2.117392 | -7.6357203 | -1.1690760 | 2.25795364 | -0.003877617 | 4.861887932 | -14.79570 | -1.4861823 | -14.267993 | 4.918198 | -3.7151437 | 2.21812177 | -1.412993 | -5.3857493 |\n",
"| 2.312166 | -5.685179 | -2.8385687 | -0.8936508 | 3.65207744 | -2.871114254 | 0.681894660 | -20.18568 | -0.8540531 | -13.591594 | -2.791981 | 1.6250285 | 0.64879322 | -7.775698 | -0.2633811 |\n",
"| 2.429922 | -4.932943 | -2.6174059 | -0.8195862 | 2.17509794 | -2.780509472 | 0.045440339 | -17.16429 | -1.3006248 | -11.506498 | -4.298565 | 2.3186226 | 1.95389259 | -7.208811 | -0.7329761 |\n",
"| 2.254678 | -4.960459 | -2.8935974 | -0.6894010 | 4.19933748 | -2.056086540 | 0.432444483 | -18.75689 | -0.8170811 | -12.882384 | -3.683805 | 1.2375404 | 0.45104983 | -7.683989 | -0.6559558 |\n",
"| 2.205649 | -5.913129 | -6.9990859 | -4.5424247 | -0.84446913 | -4.734327316 | 7.841816425 | -11.71596 | -3.4425547 | -5.544622 | 3.152965 | 0.6267796 | 5.87554359 | 2.998562 | -5.5737910 |\n",
"| 1.810154 | -5.327662 | -7.9744616 | -5.6502333 | -1.02558923 | -6.010929585 | 7.475661755 | -12.04173 | -3.7144790 | -5.123187 | 2.177110 | 1.4698161 | 4.98864174 | 2.221669 | -6.5479803 |\n",
"| 4.685986 | -5.116011 | -3.1311259 | 0.8566008 | -3.44091296 | -8.548442841 | 1.476135373 | -12.91754 | -3.0472486 | -9.819015 | 4.450594 | 4.3443832 | -1.29453611 | -3.905795 | -1.7515311 |\n",
"| 4.453277 | -2.539899 | -5.8208671 | -0.8443363 | 0.69092727 | 1.077887058 | 4.765635014 | -13.51657 | -0.8940221 | -13.050684 | 5.226885 | -1.9341412 | 2.98280501 | -2.753903 | -5.2867203 |\n",
"| 2.527725 | -5.494924 | -3.1933997 | -0.8952646 | 4.07469130 | -3.641104221 | 0.292647034 | -19.27273 | -0.9903327 | -13.815386 | -3.444628 | 2.1892321 | 1.76097059 | -7.238525 | -0.6136954 |\n",
"| 3.103855 | -6.742973 | -3.5297267 | -2.0476065 | 6.32211161 | -2.486951590 | 0.005822206 | -18.06101 | -0.7176652 | -12.309981 | -3.116259 | 1.8818451 | -0.58147472 | -6.959402 | 2.5841742 |\n",
"| 5.988764 | -6.884144 | -3.9173372 | 2.5298469 | -4.67566061 | -9.430804253 | 2.601134062 | -11.58389 | -3.3441653 | -9.453644 | 4.865941 | 4.1122088 | -1.13433194 | -4.462288 | -3.2808540 |\n",
"| 4.379490 | -2.066716 | -5.8044329 | -0.9604352 | 1.19236827 | 0.312468559 | 5.911241055 | -15.86650 | -2.0005322 | -13.652694 | 4.565659 | -3.5513661 | 2.80084538 | -1.744902 | -5.3310199 |\n",
"| 4.342060 | -4.860115 | -2.9849405 | 1.1048417 | -2.97053623 | -8.818906784 | 2.848891973 | -15.38535 | -2.5427375 | -10.871824 | 4.184150 | 2.9246807 | -2.52695537 | -2.322521 | -3.4124339 |\n",
"| 3.050938 | -3.352108 | -4.2128959 | -0.2189043 | 0.17008510 | 0.643936157 | 5.411861897 | -12.82839 | -1.6516005 | -12.974924 | 4.789909 | -2.1248729 | 3.62720108 | -3.038718 | -5.1394057 |\n",
"| ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |\n",
"| 4.568026 | -1.580006 | -5.7653575 | -1.2712021 | 1.4136478901 | -0.15090951 | 5.92859268 | -17.53403 | -1.8591350 | -16.006456 | 4.7152524 | -3.3079474 | 2.3683727 | -1.749003 | -4.7701387 |\n",
"| 4.638977 | -2.231600 | -6.1335502 | -0.6928905 | 1.4882037640 | 0.57408309 | 5.57630920 | -15.55637 | -1.7714077 | -14.134931 | 3.8968377 | -2.5810466 | 2.6179118 | -3.479542 | -6.4095054 |\n",
"| 2.554769 | -5.719078 | -3.5181692 | -0.5363890 | 3.1886093616 | -4.29229975 | 1.61574495 | -21.29429 | -1.2954823 | -13.825887 | -2.5001032 | 2.3772862 | 1.2030927 | -8.640922 | -0.2206428 |\n",
"| 6.997326 | -5.011719 | 0.8019572 | -2.3327296 | -0.0902997032 | -4.05709743 | 2.32674885 | -13.16608 | 2.8190386 | -6.616040 | 2.3638618 | 1.8632438 | 4.5743742 | -8.239238 | -3.0091286 |\n",
"| 2.108623 | -7.906268 | -12.8760176 | -10.1564293 | -0.3261828423 | -5.45073509 | 8.47327328 | -14.24173 | -3.3009071 | -6.392434 | 2.1642957 | 1.1111578 | 5.8463268 | 1.772806 | -6.6452203 |\n",
"| 5.739309 | -5.118634 | -0.7052121 | -1.9376416 | -0.1254920661 | -4.34498072 | 2.72932315 | -15.68990 | 3.2943606 | -8.407866 | 1.0114187 | 1.7510997 | 5.0616970 | -6.371283 | -2.7987578 |\n",
"| 4.352842 | -2.290206 | -6.0016479 | -0.6265063 | 1.2788192034 | -0.59810448 | 5.52771187 | -15.34131 | -1.5754925 | -14.513073 | 4.1602216 | -2.3213527 | 2.8614898 | -3.471461 | -5.9957261 |\n",
"| 8.203038 | -6.737101 | 0.6308022 | -2.6791546 | 0.0331112072 | -4.44884872 | 3.04271936 | -16.22462 | 3.3452938 | -9.058146 | 0.8915003 | 1.7142127 | 5.5755992 | -7.383893 | -4.1187649 |\n",
"| 9.683000 | -2.138233 | -10.8349619 | -2.0128343 | 3.7677421570 | -0.62864161 | 6.15969086 | -15.54685 | -1.8161896 | -15.213776 | 5.6375279 | -2.4573510 | 2.4149096 | -2.970704 | -4.3525071 |\n",
"| 5.065584 | -4.819563 | -1.1874355 | -1.6336071 | -0.3672036529 | -5.05415821 | 3.50948167 | -16.78403 | 2.8720467 | -8.697453 | 1.2968588 | 1.0252613 | 5.0780172 | -6.404398 | -3.5434029 |\n",
"| 8.155322 | -6.406314 | 0.7154618 | -2.7522581 | 0.0002044067 | -3.99534893 | 0.79592109 | -14.30064 | 3.7953365 | -7.784212 | 1.5141768 | 1.3084570 | 5.5818005 | -6.562686 | -2.9888823 |\n",
"| 2.037210 | -5.748902 | -7.2167077 | -3.8441615 | -0.8778251410 | -5.02795029 | 7.20830011 | -10.12536 | -3.5305285 | -3.485076 | 2.4987838 | 1.0515349 | 4.9519787 | 2.422310 | -5.8234034 |\n",
"| 2.549152 | -5.778267 | -2.5680861 | -0.8840805 | 3.4824593067 | -2.21734452 | 0.30072370 | -17.59094 | -1.5749041 | -10.843613 | -2.8605871 | 1.0696204 | 0.6033388 | -7.399768 | -0.1852023 |\n",
"| 3.290432 | -7.053134 | -3.6329198 | -1.1331015 | 4.9401106834 | -2.90880346 | -0.44940862 | -17.51407 | -1.0047024 | -11.673330 | -4.0656734 | -0.2132214 | 0.4301564 | -5.902227 | -0.5074827 |\n",
"| 2.088002 | -5.836352 | -8.4787912 | -5.4655275 | -1.2730693817 | -5.26897335 | 7.97211409 | -13.41879 | -3.0513813 | -6.089839 | 1.7254858 | 1.8032290 | 4.8907895 | 1.325236 | -8.4227810 |\n",
"| 4.730251 | -5.462926 | -3.5259504 | 1.5797091 | -3.4017002583 | -8.72756290 | 2.15470767 | -12.69422 | -2.9002886 | -10.065287 | 3.1706443 | 2.9299498 | -2.1684637 | -3.836938 | -3.5421708 |\n",
"| 2.519696 | -6.206445 | -3.4693151 | -0.5791476 | 3.6860020161 | -3.09619904 | -0.09280834 | -17.92822 | -1.1767925 | -12.469215 | -2.6421485 | 2.1279385 | 1.2929267 | -8.515422 | -0.6013060 |\n",
"| 3.051261 | -6.164137 | -3.0902605 | -1.2714670 | 4.5201320648 | -2.99722004 | 0.18775597 | -16.98655 | -0.7562402 | -11.177454 | -3.5248618 | 0.9328425 | 0.8078923 | -6.104471 | 0.8842458 |\n",
"| 1.073783 | -4.613420 | -6.3512692 | -3.8319449 | -1.1131196022 | -5.25494576 | 7.46743917 | -12.47251 | -3.2143519 | -5.923545 | 1.8268092 | 0.2752512 | 4.5594120 | 2.688883 | -7.2799592 |\n",
"| 3.049418 | -6.526370 | -3.3531973 | -1.5409517 | 5.9906334877 | -3.15830564 | -0.49258718 | -16.15066 | -1.0405034 | -10.777252 | -2.7216291 | 2.3298395 | 1.3262671 | -7.742356 | 0.7600487 |\n",
"| 2.299257 | -6.576549 | -11.1815224 | -8.6209688 | -0.3008396626 | -5.88015747 | 6.96856928 | -12.34746 | -3.4155140 | -6.228897 | 2.2964327 | 1.7340368 | 5.5737391 | 1.621253 | -6.8108306 |\n",
"| 1.978040 | -5.101249 | -6.9519877 | -4.3321543 | -0.9555765390 | -4.55864906 | 7.44492292 | -13.12647 | -3.4570978 | -5.639615 | 1.2233088 | 0.1023000 | 4.9460096 | 2.714372 | -6.9929123 |\n",
"| 7.351749 | -1.355803 | -8.2382669 | -1.1935792 | 1.7584133148 | 0.17264697 | 6.06365252 | -17.30200 | -2.4722471 | -15.670676 | 5.4404073 | -1.9588546 | 2.0936201 | -3.130454 | -5.1776347 |\n",
"| 3.614705 | -1.751079 | -4.6328015 | -0.8231169 | 0.8779423833 | 0.08133652 | 5.52687597 | -14.87722 | -1.1260140 | -14.548677 | 3.7598212 | -2.1644452 | 3.2774484 | -3.430882 | -6.0524898 |\n",
"| 2.115447 | -6.168517 | -8.7798109 | -6.1212263 | -0.8637107611 | -5.51797819 | 7.84722757 | -12.17093 | -3.2496598 | -5.268707 | 1.7024575 | 0.5100074 | 4.9548903 | 2.214145 | -7.7204466 |\n",
"| 3.559060 | -4.317487 | -3.0177283 | 0.3407646 | -1.9263570309 | -8.09674168 | 1.70674980 | -11.62743 | -2.7164323 | -9.439749 | 3.9634116 | 3.7463126 | -1.9930896 | -5.052331 | -3.1405520 |\n",
"| 4.570605 | -5.248532 | -3.4832544 | 0.7583200 | -3.1959526539 | -8.19375896 | 2.27919364 | -10.96759 | -2.8234141 | -8.845697 | 3.2261248 | 4.1440792 | -0.9228735 | -4.618789 | -3.9137733 |\n",
"| 4.472492 | -4.890934 | -2.8845019 | 1.1547174 | -2.7677462101 | -8.72113419 | 1.92387354 | -10.56394 | -3.1129119 | -7.769747 | 4.6511006 | 3.7833085 | -1.6304593 | -5.594076 | -2.5928376 |\n",
"| 3.624304 | -7.847561 | -4.0640669 | -2.0619318 | 6.9316506386 | -2.27580905 | 0.33176556 | -19.14009 | -1.1348858 | -11.961175 | -1.9076225 | 1.2473679 | 0.5517591 | -8.137267 | 0.6829665 |\n",
"| 5.600024 | -6.079413 | -3.2682271 | 2.0289369 | -4.1170182228 | -8.73837376 | 3.27058840 | -13.87365 | -2.9598057 | -9.943305 | 4.3723140 | 4.5461845 | -1.0018466 | -4.417732 | -3.1890416 |\n",
"\n"
],
"text/plain": [
" V1 V2 V3 V4 V5 V6 \n",
"1 1.364614 -6.106272 -9.1133595 -5.9061093 -1.12540197 -5.149353504\n",
"2 2.595337 -5.938760 -3.6227093 -0.7225778 3.49704957 -2.792010307\n",
"3 3.708545 -2.392595 -5.1247411 -0.6224614 0.54852670 0.879745245\n",
"4 5.767153 -5.985087 -1.3936334 -1.9246240 -0.09592111 -5.213550568\n",
"5 3.541591 -7.022198 -3.9639640 -1.1304803 4.94482708 -2.593570471\n",
"6 2.421503 -5.166163 -3.4402585 -0.3120118 1.93865383 -2.545686722\n",
"7 4.150049 -2.254474 -5.3667531 -0.9332458 0.43465179 0.406963378\n",
"8 3.827635 -2.537562 -4.7054524 -0.4838656 0.57435292 -0.080945529\n",
"9 5.795492 -5.154980 -0.9332798 -1.4626205 -0.40671271 -4.489341736\n",
"10 1.849412 -4.391167 -3.0255575 -0.2331904 2.35564685 -2.259174824\n",
"11 1.552489 -4.110096 -5.0476685 -2.6812036 -0.98579681 -5.176226616\n",
"12 1.236442 -4.504412 -5.8166695 -3.2444904 -0.99929255 -4.876768589\n",
"13 4.216510 -2.317232 -5.4863706 -0.6890665 1.32607293 -0.473360509\n",
"14 2.592076 -5.894144 -2.9799986 -0.7899423 3.67174220 -3.070579052\n",
"15 9.414653 -7.718376 0.2931430 -2.7612970 0.07285737 -4.688628197\n",
"16 2.135017 -4.512797 -3.1149621 -0.6912211 2.36023521 -3.102366447\n",
"17 6.150630 -2.117392 -7.6357203 -1.1690760 2.25795364 -0.003877617\n",
"18 2.312166 -5.685179 -2.8385687 -0.8936508 3.65207744 -2.871114254\n",
"19 2.429922 -4.932943 -2.6174059 -0.8195862 2.17509794 -2.780509472\n",
"20 2.254678 -4.960459 -2.8935974 -0.6894010 4.19933748 -2.056086540\n",
"21 2.205649 -5.913129 -6.9990859 -4.5424247 -0.84446913 -4.734327316\n",
"22 1.810154 -5.327662 -7.9744616 -5.6502333 -1.02558923 -6.010929585\n",
"23 4.685986 -5.116011 -3.1311259 0.8566008 -3.44091296 -8.548442841\n",
"24 4.453277 -2.539899 -5.8208671 -0.8443363 0.69092727 1.077887058\n",
"25 2.527725 -5.494924 -3.1933997 -0.8952646 4.07469130 -3.641104221\n",
"26 3.103855 -6.742973 -3.5297267 -2.0476065 6.32211161 -2.486951590\n",
"27 5.988764 -6.884144 -3.9173372 2.5298469 -4.67566061 -9.430804253\n",
"28 4.379490 -2.066716 -5.8044329 -0.9604352 1.19236827 0.312468559\n",
"29 4.342060 -4.860115 -2.9849405 1.1048417 -2.97053623 -8.818906784\n",
"30 3.050938 -3.352108 -4.2128959 -0.2189043 0.17008510 0.643936157\n",
"⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ \n",
"71 4.568026 -1.580006 -5.7653575 -1.2712021 1.4136478901 -0.15090951 \n",
"72 4.638977 -2.231600 -6.1335502 -0.6928905 1.4882037640 0.57408309 \n",
"73 2.554769 -5.719078 -3.5181692 -0.5363890 3.1886093616 -4.29229975 \n",
"74 6.997326 -5.011719 0.8019572 -2.3327296 -0.0902997032 -4.05709743 \n",
"75 2.108623 -7.906268 -12.8760176 -10.1564293 -0.3261828423 -5.45073509 \n",
"76 5.739309 -5.118634 -0.7052121 -1.9376416 -0.1254920661 -4.34498072 \n",
"77 4.352842 -2.290206 -6.0016479 -0.6265063 1.2788192034 -0.59810448 \n",
"78 8.203038 -6.737101 0.6308022 -2.6791546 0.0331112072 -4.44884872 \n",
"79 9.683000 -2.138233 -10.8349619 -2.0128343 3.7677421570 -0.62864161 \n",
"80 5.065584 -4.819563 -1.1874355 -1.6336071 -0.3672036529 -5.05415821 \n",
"81 8.155322 -6.406314 0.7154618 -2.7522581 0.0002044067 -3.99534893 \n",
"82 2.037210 -5.748902 -7.2167077 -3.8441615 -0.8778251410 -5.02795029 \n",
"83 2.549152 -5.778267 -2.5680861 -0.8840805 3.4824593067 -2.21734452 \n",
"84 3.290432 -7.053134 -3.6329198 -1.1331015 4.9401106834 -2.90880346 \n",
"85 2.088002 -5.836352 -8.4787912 -5.4655275 -1.2730693817 -5.26897335 \n",
"86 4.730251 -5.462926 -3.5259504 1.5797091 -3.4017002583 -8.72756290 \n",
"87 2.519696 -6.206445 -3.4693151 -0.5791476 3.6860020161 -3.09619904 \n",
"88 3.051261 -6.164137 -3.0902605 -1.2714670 4.5201320648 -2.99722004 \n",
"89 1.073783 -4.613420 -6.3512692 -3.8319449 -1.1131196022 -5.25494576 \n",
"90 3.049418 -6.526370 -3.3531973 -1.5409517 5.9906334877 -3.15830564 \n",
"91 2.299257 -6.576549 -11.1815224 -8.6209688 -0.3008396626 -5.88015747 \n",
"92 1.978040 -5.101249 -6.9519877 -4.3321543 -0.9555765390 -4.55864906 \n",
"93 7.351749 -1.355803 -8.2382669 -1.1935792 1.7584133148 0.17264697 \n",
"94 3.614705 -1.751079 -4.6328015 -0.8231169 0.8779423833 0.08133652 \n",
"95 2.115447 -6.168517 -8.7798109 -6.1212263 -0.8637107611 -5.51797819 \n",
"96 3.559060 -4.317487 -3.0177283 0.3407646 -1.9263570309 -8.09674168 \n",
"97 4.570605 -5.248532 -3.4832544 0.7583200 -3.1959526539 -8.19375896 \n",
"98 4.472492 -4.890934 -2.8845019 1.1547174 -2.7677462101 -8.72113419 \n",
"99 3.624304 -7.847561 -4.0640669 -2.0619318 6.9316506386 -2.27580905 \n",
"100 5.600024 -6.079413 -3.2682271 2.0289369 -4.1170182228 -8.73837376 \n",
" V7 V8 V9 V10 V11 V12 \n",
"1 8.110886574 -12.86491 -3.4131663 -5.428276 1.327641 0.8208714\n",
"2 -0.336862415 -18.69882 -0.8183411 -11.961297 -4.329017 1.4387116\n",
"3 5.656763077 -15.47860 -1.7644137 -14.102664 4.162706 -2.7230189\n",
"4 4.338903904 -19.56525 2.5292537 -10.912452 2.073539 1.2014283\n",
"5 0.063670896 -18.75797 -0.7224302 -12.040921 -2.402636 1.0178714\n",
"6 -0.200865120 -17.53624 -0.6945462 -12.145635 -3.268605 1.0533069\n",
"7 5.575583935 -14.51855 -1.6430770 -13.642753 3.455180 -2.6348953\n",
"8 6.261950016 -15.05157 -1.5113701 -13.822030 3.711386 -2.7433469\n",
"9 2.773021221 -16.90816 3.2329519 -8.983538 2.222119 0.7351513\n",
"10 0.274122059 -16.74387 -1.4031473 -10.049000 -3.127479 2.0756233\n",
"11 7.615598679 -13.31031 -2.9576387 -6.647234 1.821403 1.0560647\n",
"12 8.112017632 -13.83120 -3.7243154 -6.103724 2.105867 -0.1509407\n",
"13 5.301970005 -15.46400 -1.5542859 -14.349189 5.744266 -2.0513182\n",
"14 0.131115586 -18.77938 -0.7902449 -12.933554 -2.872724 2.4071269\n",
"15 2.346898317 -15.45988 3.3585019 -7.827687 1.389345 2.1458004\n",
"16 -0.125342697 -18.72714 -0.6737446 -12.904139 -4.015753 1.3522795\n",
"17 4.861887932 -14.79570 -1.4861823 -14.267993 4.918198 -3.7151437\n",
"18 0.681894660 -20.18568 -0.8540531 -13.591594 -2.791981 1.6250285\n",
"19 0.045440339 -17.16429 -1.3006248 -11.506498 -4.298565 2.3186226\n",
"20 0.432444483 -18.75689 -0.8170811 -12.882384 -3.683805 1.2375404\n",
"21 7.841816425 -11.71596 -3.4425547 -5.544622 3.152965 0.6267796\n",
"22 7.475661755 -12.04173 -3.7144790 -5.123187 2.177110 1.4698161\n",
"23 1.476135373 -12.91754 -3.0472486 -9.819015 4.450594 4.3443832\n",
"24 4.765635014 -13.51657 -0.8940221 -13.050684 5.226885 -1.9341412\n",
"25 0.292647034 -19.27273 -0.9903327 -13.815386 -3.444628 2.1892321\n",
"26 0.005822206 -18.06101 -0.7176652 -12.309981 -3.116259 1.8818451\n",
"27 2.601134062 -11.58389 -3.3441653 -9.453644 4.865941 4.1122088\n",
"28 5.911241055 -15.86650 -2.0005322 -13.652694 4.565659 -3.5513661\n",
"29 2.848891973 -15.38535 -2.5427375 -10.871824 4.184150 2.9246807\n",
"30 5.411861897 -12.82839 -1.6516005 -12.974924 4.789909 -2.1248729\n",
"⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ \n",
"71 5.92859268 -17.53403 -1.8591350 -16.006456 4.7152524 -3.3079474\n",
"72 5.57630920 -15.55637 -1.7714077 -14.134931 3.8968377 -2.5810466\n",
"73 1.61574495 -21.29429 -1.2954823 -13.825887 -2.5001032 2.3772862\n",
"74 2.32674885 -13.16608 2.8190386 -6.616040 2.3638618 1.8632438\n",
"75 8.47327328 -14.24173 -3.3009071 -6.392434 2.1642957 1.1111578\n",
"76 2.72932315 -15.68990 3.2943606 -8.407866 1.0114187 1.7510997\n",
"77 5.52771187 -15.34131 -1.5754925 -14.513073 4.1602216 -2.3213527\n",
"78 3.04271936 -16.22462 3.3452938 -9.058146 0.8915003 1.7142127\n",
"79 6.15969086 -15.54685 -1.8161896 -15.213776 5.6375279 -2.4573510\n",
"80 3.50948167 -16.78403 2.8720467 -8.697453 1.2968588 1.0252613\n",
"81 0.79592109 -14.30064 3.7953365 -7.784212 1.5141768 1.3084570\n",
"82 7.20830011 -10.12536 -3.5305285 -3.485076 2.4987838 1.0515349\n",
"83 0.30072370 -17.59094 -1.5749041 -10.843613 -2.8605871 1.0696204\n",
"84 -0.44940862 -17.51407 -1.0047024 -11.673330 -4.0656734 -0.2132214\n",
"85 7.97211409 -13.41879 -3.0513813 -6.089839 1.7254858 1.8032290\n",
"86 2.15470767 -12.69422 -2.9002886 -10.065287 3.1706443 2.9299498\n",
"87 -0.09280834 -17.92822 -1.1767925 -12.469215 -2.6421485 2.1279385\n",
"88 0.18775597 -16.98655 -0.7562402 -11.177454 -3.5248618 0.9328425\n",
"89 7.46743917 -12.47251 -3.2143519 -5.923545 1.8268092 0.2752512\n",
"90 -0.49258718 -16.15066 -1.0405034 -10.777252 -2.7216291 2.3298395\n",
"91 6.96856928 -12.34746 -3.4155140 -6.228897 2.2964327 1.7340368\n",
"92 7.44492292 -13.12647 -3.4570978 -5.639615 1.2233088 0.1023000\n",
"93 6.06365252 -17.30200 -2.4722471 -15.670676 5.4404073 -1.9588546\n",
"94 5.52687597 -14.87722 -1.1260140 -14.548677 3.7598212 -2.1644452\n",
"95 7.84722757 -12.17093 -3.2496598 -5.268707 1.7024575 0.5100074\n",
"96 1.70674980 -11.62743 -2.7164323 -9.439749 3.9634116 3.7463126\n",
"97 2.27919364 -10.96759 -2.8234141 -8.845697 3.2261248 4.1440792\n",
"98 1.92387354 -10.56394 -3.1129119 -7.769747 4.6511006 3.7833085\n",
"99 0.33176556 -19.14009 -1.1348858 -11.961175 -1.9076225 1.2473679\n",
"100 3.27058840 -13.87365 -2.9598057 -9.943305 4.3723140 4.5461845\n",
" V13 V14 V15 \n",
"1 4.85717201 1.830986 -6.8246655\n",
"2 2.34280133 -5.000385 -1.2720186\n",
"3 3.05050159 -3.451958 -5.3215613\n",
"4 5.25957203 -7.206652 -3.0671186\n",
"5 -0.03812202 -7.610836 1.0129657\n",
"6 0.36909178 -6.418007 -0.4841153\n",
"7 2.54848194 -3.242677 -6.6115537\n",
"8 3.76614356 -3.393880 -5.3013635\n",
"9 4.32916212 -7.979029 -3.2727027\n",
"10 1.02622116 -7.171580 -0.6122004\n",
"11 5.72816753 1.565586 -7.4634547\n",
"12 4.77471638 3.423587 -7.0119233\n",
"13 2.37798476 -2.994759 -5.0165834\n",
"14 1.14506173 -7.564617 -1.2979107\n",
"15 4.89003038 -8.474400 -3.9662571\n",
"16 1.21443474 -6.400146 -0.3348852\n",
"17 2.21812177 -1.412993 -5.3857493\n",
"18 0.64879322 -7.775698 -0.2633811\n",
"19 1.95389259 -7.208811 -0.7329761\n",
"20 0.45104983 -7.683989 -0.6559558\n",
"21 5.87554359 2.998562 -5.5737910\n",
"22 4.98864174 2.221669 -6.5479803\n",
"23 -1.29453611 -3.905795 -1.7515311\n",
"24 2.98280501 -2.753903 -5.2867203\n",
"25 1.76097059 -7.238525 -0.6136954\n",
"26 -0.58147472 -6.959402 2.5841742\n",
"27 -1.13433194 -4.462288 -3.2808540\n",
"28 2.80084538 -1.744902 -5.3310199\n",
"29 -2.52695537 -2.322521 -3.4124339\n",
"30 3.62720108 -3.038718 -5.1394057\n",
"⋮ ⋮ ⋮ ⋮ \n",
"71 2.3683727 -1.749003 -4.7701387\n",
"72 2.6179118 -3.479542 -6.4095054\n",
"73 1.2030927 -8.640922 -0.2206428\n",
"74 4.5743742 -8.239238 -3.0091286\n",
"75 5.8463268 1.772806 -6.6452203\n",
"76 5.0616970 -6.371283 -2.7987578\n",
"77 2.8614898 -3.471461 -5.9957261\n",
"78 5.5755992 -7.383893 -4.1187649\n",
"79 2.4149096 -2.970704 -4.3525071\n",
"80 5.0780172 -6.404398 -3.5434029\n",
"81 5.5818005 -6.562686 -2.9888823\n",
"82 4.9519787 2.422310 -5.8234034\n",
"83 0.6033388 -7.399768 -0.1852023\n",
"84 0.4301564 -5.902227 -0.5074827\n",
"85 4.8907895 1.325236 -8.4227810\n",
"86 -2.1684637 -3.836938 -3.5421708\n",
"87 1.2929267 -8.515422 -0.6013060\n",
"88 0.8078923 -6.104471 0.8842458\n",
"89 4.5594120 2.688883 -7.2799592\n",
"90 1.3262671 -7.742356 0.7600487\n",
"91 5.5737391 1.621253 -6.8108306\n",
"92 4.9460096 2.714372 -6.9929123\n",
"93 2.0936201 -3.130454 -5.1776347\n",
"94 3.2774484 -3.430882 -6.0524898\n",
"95 4.9548903 2.214145 -7.7204466\n",
"96 -1.9930896 -5.052331 -3.1405520\n",
"97 -0.9228735 -4.618789 -3.9137733\n",
"98 -1.6304593 -5.594076 -2.5928376\n",
"99 0.5517591 -8.137267 0.6829665\n",
"100 -1.0018466 -4.417732 -3.1890416"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"factorization"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"cl <- as.matrix(read.table(\"../data/simulations_20210329212141/equal/5/c.txt\", \n",
" sep=\"\\t\",header=FALSE))"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" V1\n",
" [1,] 4\n",
" [2,] 1\n",
" [3,] 2\n",
" [4,] 3\n",
" [5,] 1\n",
" [6,] 1\n",
" [7,] 2\n",
" [8,] 2\n",
" [9,] 3\n",
" [10,] 1\n",
" [11,] 4\n",
" [12,] 4\n",
" [13,] 2\n",
" [14,] 1\n",
" [15,] 3\n",
" [16,] 1\n",
" [17,] 2\n",
" [18,] 1\n",
" [19,] 1\n",
" [20,] 1\n",
" [21,] 4\n",
" [22,] 4\n",
" [23,] 0\n",
" [24,] 2\n",
" [25,] 1\n",
" [26,] 1\n",
" [27,] 0\n",
" [28,] 2\n",
" [29,] 0\n",
" [30,] 2\n",
" [31,] 4\n",
" [32,] 2\n",
" [33,] 3\n",
" [34,] 3\n",
" [35,] 1\n",
" [36,] 1\n",
" [37,] 4\n",
" [38,] 2\n",
" [39,] 2\n",
" [40,] 4\n",
" [41,] 0\n",
" [42,] 1\n",
" [43,] 3\n",
" [44,] 3\n",
" [45,] 2\n",
" [46,] 1\n",
" [47,] 1\n",
" [48,] 3\n",
" [49,] 4\n",
" [50,] 3\n",
" [51,] 0\n",
" [52,] 3\n",
" [53,] 0\n",
" [54,] 3\n",
" [55,] 0\n",
" [56,] 4\n",
" [57,] 1\n",
" [58,] 4\n",
" [59,] 3\n",
" [60,] 3\n",
" [61,] 4\n",
" [62,] 4\n",
" [63,] 2\n",
" [64,] 0\n",
" [65,] 3\n",
" [66,] 3\n",
" [67,] 2\n",
" [68,] 1\n",
" [69,] 0\n",
" [70,] 0\n",
" [71,] 2\n",
" [72,] 2\n",
" [73,] 1\n",
" [74,] 3\n",
" [75,] 4\n",
" [76,] 3\n",
" [77,] 2\n",
" [78,] 3\n",
" [79,] 2\n",
" [80,] 3\n",
" [81,] 3\n",
" [82,] 4\n",
" [83,] 1\n",
" [84,] 1\n",
" [85,] 4\n",
" [86,] 0\n",
" [87,] 1\n",
" [88,] 1\n",
" [89,] 4\n",
" [90,] 1\n",
" [91,] 4\n",
" [92,] 4\n",
" [93,] 2\n",
" [94,] 2\n",
" [95,] 4\n",
" [96,] 0\n",
" [97,] 0\n",
" [98,] 0\n",
" [99,] 1\n",
"[100,] 0\n"
]
}
],
"source": [
"print(cl)"
]
},
{
"cell_type": "code",
"execution_count": 46,
"metadata": {},
"outputs": [],
"source": [
"cl <- as.matrix(read.table(\"../data/simulations_20210329212141/equal/5/clusters.txt\", \n",
" sep=\"\\t\", row.names=1, header=TRUE))"
]
},
{
"cell_type": "code",
"execution_count": 47,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<caption>A matrix: 100 × 2 of type chr</caption>\n",
"<thead>\n",
"\t<tr><th></th><th scope=col>subjects</th><th scope=col>cluster.id</th></tr>\n",
"</thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>1</th><td>subject1 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>2</th><td>subject2 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>3</th><td>subject3 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>4</th><td>subject4 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>5</th><td>subject5 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>6</th><td>subject6 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>7</th><td>subject7 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>8</th><td>subject8 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>9</th><td>subject9 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>10</th><td>subject10</td><td>1</td></tr>\n",
"\t<tr><th scope=row>11</th><td>subject11</td><td>4</td></tr>\n",
"\t<tr><th scope=row>12</th><td>subject12</td><td>4</td></tr>\n",
"\t<tr><th scope=row>13</th><td>subject13</td><td>2</td></tr>\n",
"\t<tr><th scope=row>14</th><td>subject14</td><td>1</td></tr>\n",
"\t<tr><th scope=row>15</th><td>subject15</td><td>3</td></tr>\n",
"\t<tr><th scope=row>16</th><td>subject16</td><td>1</td></tr>\n",
"\t<tr><th scope=row>17</th><td>subject17</td><td>2</td></tr>\n",
"\t<tr><th scope=row>18</th><td>subject18</td><td>1</td></tr>\n",
"\t<tr><th scope=row>19</th><td>subject19</td><td>1</td></tr>\n",
"\t<tr><th scope=row>20</th><td>subject20</td><td>1</td></tr>\n",
"\t<tr><th scope=row>21</th><td>subject21</td><td>4</td></tr>\n",
"\t<tr><th scope=row>22</th><td>subject22</td><td>4</td></tr>\n",
"\t<tr><th scope=row>23</th><td>subject23</td><td>5</td></tr>\n",
"\t<tr><th scope=row>24</th><td>subject24</td><td>2</td></tr>\n",
"\t<tr><th scope=row>25</th><td>subject25</td><td>1</td></tr>\n",
"\t<tr><th scope=row>26</th><td>subject26</td><td>1</td></tr>\n",
"\t<tr><th scope=row>27</th><td>subject27</td><td>5</td></tr>\n",
"\t<tr><th scope=row>28</th><td>subject28</td><td>2</td></tr>\n",
"\t<tr><th scope=row>29</th><td>subject29</td><td>5</td></tr>\n",
"\t<tr><th scope=row>30</th><td>subject30</td><td>2</td></tr>\n",
"\t<tr><th scope=row>⋮</th><td>⋮</td><td>⋮</td></tr>\n",
"\t<tr><th scope=row>71</th><td>subject71 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>72</th><td>subject72 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>73</th><td>subject73 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>74</th><td>subject74 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>75</th><td>subject75 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>76</th><td>subject76 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>77</th><td>subject77 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>78</th><td>subject78 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>79</th><td>subject79 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>80</th><td>subject80 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>81</th><td>subject81 </td><td>3</td></tr>\n",
"\t<tr><th scope=row>82</th><td>subject82 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>83</th><td>subject83 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>84</th><td>subject84 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>85</th><td>subject85 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>86</th><td>subject86 </td><td>5</td></tr>\n",
"\t<tr><th scope=row>87</th><td>subject87 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>88</th><td>subject88 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>89</th><td>subject89 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>90</th><td>subject90 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>91</th><td>subject91 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>92</th><td>subject92 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>93</th><td>subject93 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>94</th><td>subject94 </td><td>2</td></tr>\n",
"\t<tr><th scope=row>95</th><td>subject95 </td><td>4</td></tr>\n",
"\t<tr><th scope=row>96</th><td>subject96 </td><td>5</td></tr>\n",
"\t<tr><th scope=row>97</th><td>subject97 </td><td>5</td></tr>\n",
"\t<tr><th scope=row>98</th><td>subject98 </td><td>5</td></tr>\n",
"\t<tr><th scope=row>99</th><td>subject99 </td><td>1</td></tr>\n",
"\t<tr><th scope=row>100</th><td>subject100</td><td>5</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"A matrix: 100 × 2 of type chr\n",
"\\begin{tabular}{r|ll}\n",
" & subjects & cluster.id\\\\\n",
"\\hline\n",
"\t1 & subject1 & 4\\\\\n",
"\t2 & subject2 & 1\\\\\n",
"\t3 & subject3 & 2\\\\\n",
"\t4 & subject4 & 3\\\\\n",
"\t5 & subject5 & 1\\\\\n",
"\t6 & subject6 & 1\\\\\n",
"\t7 & subject7 & 2\\\\\n",
"\t8 & subject8 & 2\\\\\n",
"\t9 & subject9 & 3\\\\\n",
"\t10 & subject10 & 1\\\\\n",
"\t11 & subject11 & 4\\\\\n",
"\t12 & subject12 & 4\\\\\n",
"\t13 & subject13 & 2\\\\\n",
"\t14 & subject14 & 1\\\\\n",
"\t15 & subject15 & 3\\\\\n",
"\t16 & subject16 & 1\\\\\n",
"\t17 & subject17 & 2\\\\\n",
"\t18 & subject18 & 1\\\\\n",
"\t19 & subject19 & 1\\\\\n",
"\t20 & subject20 & 1\\\\\n",
"\t21 & subject21 & 4\\\\\n",
"\t22 & subject22 & 4\\\\\n",
"\t23 & subject23 & 5\\\\\n",
"\t24 & subject24 & 2\\\\\n",
"\t25 & subject25 & 1\\\\\n",
"\t26 & subject26 & 1\\\\\n",
"\t27 & subject27 & 5\\\\\n",
"\t28 & subject28 & 2\\\\\n",
"\t29 & subject29 & 5\\\\\n",
"\t30 & subject30 & 2\\\\\n",
"\t⋮ & ⋮ & ⋮\\\\\n",
"\t71 & subject71 & 2\\\\\n",
"\t72 & subject72 & 2\\\\\n",
"\t73 & subject73 & 1\\\\\n",
"\t74 & subject74 & 3\\\\\n",
"\t75 & subject75 & 4\\\\\n",
"\t76 & subject76 & 3\\\\\n",
"\t77 & subject77 & 2\\\\\n",
"\t78 & subject78 & 3\\\\\n",
"\t79 & subject79 & 2\\\\\n",
"\t80 & subject80 & 3\\\\\n",
"\t81 & subject81 & 3\\\\\n",
"\t82 & subject82 & 4\\\\\n",
"\t83 & subject83 & 1\\\\\n",
"\t84 & subject84 & 1\\\\\n",
"\t85 & subject85 & 4\\\\\n",
"\t86 & subject86 & 5\\\\\n",
"\t87 & subject87 & 1\\\\\n",
"\t88 & subject88 & 1\\\\\n",
"\t89 & subject89 & 4\\\\\n",
"\t90 & subject90 & 1\\\\\n",
"\t91 & subject91 & 4\\\\\n",
"\t92 & subject92 & 4\\\\\n",
"\t93 & subject93 & 2\\\\\n",
"\t94 & subject94 & 2\\\\\n",
"\t95 & subject95 & 4\\\\\n",
"\t96 & subject96 & 5\\\\\n",
"\t97 & subject97 & 5\\\\\n",
"\t98 & subject98 & 5\\\\\n",
"\t99 & subject99 & 1\\\\\n",
"\t100 & subject100 & 5\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"A matrix: 100 × 2 of type chr\n",
"\n",
"| <!--/--> | subjects | cluster.id |\n",
"|---|---|---|\n",
"| 1 | subject1 | 4 |\n",
"| 2 | subject2 | 1 |\n",
"| 3 | subject3 | 2 |\n",
"| 4 | subject4 | 3 |\n",
"| 5 | subject5 | 1 |\n",
"| 6 | subject6 | 1 |\n",
"| 7 | subject7 | 2 |\n",
"| 8 | subject8 | 2 |\n",
"| 9 | subject9 | 3 |\n",
"| 10 | subject10 | 1 |\n",
"| 11 | subject11 | 4 |\n",
"| 12 | subject12 | 4 |\n",
"| 13 | subject13 | 2 |\n",
"| 14 | subject14 | 1 |\n",
"| 15 | subject15 | 3 |\n",
"| 16 | subject16 | 1 |\n",
"| 17 | subject17 | 2 |\n",
"| 18 | subject18 | 1 |\n",
"| 19 | subject19 | 1 |\n",
"| 20 | subject20 | 1 |\n",
"| 21 | subject21 | 4 |\n",
"| 22 | subject22 | 4 |\n",
"| 23 | subject23 | 5 |\n",
"| 24 | subject24 | 2 |\n",
"| 25 | subject25 | 1 |\n",
"| 26 | subject26 | 1 |\n",
"| 27 | subject27 | 5 |\n",
"| 28 | subject28 | 2 |\n",
"| 29 | subject29 | 5 |\n",
"| 30 | subject30 | 2 |\n",
"| ⋮ | ⋮ | ⋮ |\n",
"| 71 | subject71 | 2 |\n",
"| 72 | subject72 | 2 |\n",
"| 73 | subject73 | 1 |\n",
"| 74 | subject74 | 3 |\n",
"| 75 | subject75 | 4 |\n",
"| 76 | subject76 | 3 |\n",
"| 77 | subject77 | 2 |\n",
"| 78 | subject78 | 3 |\n",
"| 79 | subject79 | 2 |\n",
"| 80 | subject80 | 3 |\n",
"| 81 | subject81 | 3 |\n",
"| 82 | subject82 | 4 |\n",
"| 83 | subject83 | 1 |\n",
"| 84 | subject84 | 1 |\n",
"| 85 | subject85 | 4 |\n",
"| 86 | subject86 | 5 |\n",
"| 87 | subject87 | 1 |\n",
"| 88 | subject88 | 1 |\n",
"| 89 | subject89 | 4 |\n",
"| 90 | subject90 | 1 |\n",
"| 91 | subject91 | 4 |\n",
"| 92 | subject92 | 4 |\n",
"| 93 | subject93 | 2 |\n",
"| 94 | subject94 | 2 |\n",
"| 95 | subject95 | 4 |\n",
"| 96 | subject96 | 5 |\n",
"| 97 | subject97 | 5 |\n",
"| 98 | subject98 | 5 |\n",
"| 99 | subject99 | 1 |\n",
"| 100 | subject100 | 5 |\n",
"\n"
],
"text/plain": [
" subjects cluster.id\n",
"1 subject1 4 \n",
"2 subject2 1 \n",
"3 subject3 2 \n",
"4 subject4 3 \n",
"5 subject5 1 \n",
"6 subject6 1 \n",
"7 subject7 2 \n",
"8 subject8 2 \n",
"9 subject9 3 \n",
"10 subject10 1 \n",
"11 subject11 4 \n",
"12 subject12 4 \n",
"13 subject13 2 \n",
"14 subject14 1 \n",
"15 subject15 3 \n",
"16 subject16 1 \n",
"17 subject17 2 \n",
"18 subject18 1 \n",
"19 subject19 1 \n",
"20 subject20 1 \n",
"21 subject21 4 \n",
"22 subject22 4 \n",
"23 subject23 5 \n",
"24 subject24 2 \n",
"25 subject25 1 \n",
"26 subject26 1 \n",
"27 subject27 5 \n",
"28 subject28 2 \n",
"29 subject29 5 \n",
"30 subject30 2 \n",
"⋮ ⋮ ⋮ \n",
"71 subject71 2 \n",
"72 subject72 2 \n",
"73 subject73 1 \n",
"74 subject74 3 \n",
"75 subject75 4 \n",
"76 subject76 3 \n",
"77 subject77 2 \n",
"78 subject78 3 \n",
"79 subject79 2 \n",
"80 subject80 3 \n",
"81 subject81 3 \n",
"82 subject82 4 \n",
"83 subject83 1 \n",
"84 subject84 1 \n",
"85 subject85 4 \n",
"86 subject86 5 \n",
"87 subject87 1 \n",
"88 subject88 1 \n",
"89 subject89 4 \n",
"90 subject90 1 \n",
"91 subject91 4 \n",
"92 subject92 4 \n",
"93 subject93 2 \n",
"94 subject94 2 \n",
"95 subject95 4 \n",
"96 subject96 5 \n",
"97 subject97 5 \n",
"98 subject98 5 \n",
"99 subject99 1 \n",
"100 subject100 5 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"cl"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"myclusters_comparison <- function(factorizations, methods, in.folder, out.folder,number_cl) {\n",
"\n",
" ind <- 0\n",
" JI_final <- matrix(data=NA, nrow=number_cl, ncol=length(factorizations))\n",
" #cat(JI_final,\"\\n\")\n",
" # Read clusters imposed on simulated data \n",
" cl <- as.matrix(read.table(paste0(in.folder, \"clusters.txt\"), \n",
" sep=\"\\t\", row.names=1, header=TRUE))\n",
" #cat(\"cl:\",cl,\"\\t\")\n",
" cl2 <- as.matrix(as.numeric(cl[,2]))\n",
" cat(\"cl2:\",cl2[,1],\"\\n\")\n",
" rownames(cl2) <- cl[,1]\n",
" #print(length(factorizations))\n",
" # Assigning samples to cluster based on factors\n",
" for (i in 1:length(factorizations)) {\n",
" \n",
" if (methods[i]==\"iCluster\" || methods[i]==\"intNMF\") {\n",
" \n",
" } else {\n",
" \n",
" factors <- factorizations[[i]][[1]]\n",
" #print(factors)\n",
" # Clustering by Kmeans\n",
" JI_good <- numeric(0)\n",
" for (run in 1:1) {\n",
" kmeans.out <- kmeans(factors, centers=number_cl) \n",
" clust_iCluster <- as.matrix(kmeans.out$cluster)\n",
" cat(\"clust_iCluster:\",clust_iCluster,\"\\n\")\n",
" ######creation sets of samples\n",
" JI_mat <- numeric(0)\n",
" for (p in 1:number_cl) {\n",
" x1 <- rownames(clust_iCluster)[which(clust_iCluster[,1]==p)]\n",
" print(x1)\n",
" \n",
" row <- numeric(0)\n",
" for(j in 1:number_cl) {\n",
" x2 <- rownames(cl2)[which(cl2[,1]==j)]\n",
" cat(\"x2:\",x2,\"\\n\")\n",
" I <- length(intersect(x1,x2))#交集\n",
" cat(\"I:\",I,\"\\n\")\n",
" S <- I/(length(x1)+length(x2)-I)\n",
" cat(\"S:\",S,\"\\n\")\n",
" row <- cbind(row,S)\n",
" cat(\"row:\",row,\"\\n\")\n",
" }\n",
" JI_mat <- rbind(JI_mat,row)\n",
" cat(\"JI_mat:\",JI_mat,\"\\n\")\n",
" print(JI_mat)\n",
" \n",
" \n",
" }\n",
" JI_good <- rbind(JI_good,apply(JI_mat,1,max))\n",
" cat(\"JI_good:\",JI_good,\"\\n\")\n",
" }\n",
" JI_final[1:number_cl,i] <- apply(JI_good,2,mean)\n",
" }\n",
" }\n",
" \n",
" # Export JI values to a file \n",
" write.table(JI_final, paste0(out.folder,\"/JI.txt\"), sep=\"\\t\", row.names=FALSE, col.names=methods)\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"cl2: 4 7 3 1 5 4 3 3 10 4 5 5 9 3 10 5 6 8 2 2 1 7 3 1 1 5 9 10 3 2 8 2 8 1 10 2 8 9 6 8 2 6 8 6 5 2 7 4 4 1 5 8 6 1 3 2 6 9 1 1 9 1 4 6 8 6 1 9 8 1 10 1 4 5 2 10 6 8 6 4 3 10 3 9 5 4 9 9 9 5 1 7 10 1 7 10 4 10 3 2 \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"IOPub data rate exceeded.\n",
"The notebook server will temporarily stop sending output\n",
"to the client in order to avoid crashing it.\n",
"To change this limit, set the config variable\n",
"`--NotebookApp.iopub_data_rate_limit`.\n",
"\n",
"Current values:\n",
"NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)\n",
"NotebookApp.rate_limit_window=3.0 (secs)\n",
"\n"
]
}
],
"source": [
"number_cl=10\n",
"ind <- 0\n",
"JI_final <- matrix(data=NA, nrow=number_cl, ncol=1)\n",
"#cat(JI_final,\"\\n\")\n",
"# Read clusters imposed on simulated data \n",
"cl <- as.matrix(read.table(\"../data/simulations_20210329212141/equal/10/clusters.txt\", \n",
" sep=\"\\t\", row.names=1, header=TRUE))\n",
"#cat(\"cl:\",cl,\"\\t\")\n",
"cl2 <- as.matrix(as.numeric(cl[,2]))\n",
"cat(\"cl2:\",cl2[,1],\"\\n\")\n",
"rownames(cl2) <- cl[,1]\n",
"\n",
"#factorization=read.table(\"../data/simulations_20210329212141/equal/10/AE_FAETC_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"#factorization=read.table(\"../data/simulations_20210329212141/equal/10/AE_FCTAE_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"#factorization=read.table(\"../data/simulations_20210329212141/equal/10/DAE_FAETC_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"factorization=read.table(\"../data/simulations_20210329212141/equal/10/DAE_FCTAE_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"#factorization=read.table(\"../data/simulations_20210329212141/equal/10/VAE_FCTAE_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"#factorization=read.table(\"../data/simulations_20210329212141/equal/10/LSTMVAE_FCTAE_EM.txt\", sep=\" \", row.names=cl[,1],header=FALSE)\n",
"\n",
"\n",
"\n",
"factors <- factorization\n",
"#factors <- factorizations[[i]][[1]]\n",
"\n",
"#print(factors)\n",
"# Clustering by Kmeans\n",
"JI_good <- numeric(0)\n",
"for (run in 1:1000) {\n",
"kmeans.out <- kmeans(factors, centers=number_cl) \n",
"clust_iCluster <- as.matrix(kmeans.out$cluster)\n",
"cat(\"clust_iCluster:\",clust_iCluster,\"\\n\")\n",
"######creation sets of samples\n",
"JI_mat <- numeric(0)\n",
"for (p in 1:number_cl) {\n",
" x1 <- rownames(clust_iCluster)[which(clust_iCluster[,1]==p)]\n",
" print(x1)\n",
"\n",
" row <- numeric(0)\n",
" for(j in 1:number_cl) {\n",
" x2 <- rownames(cl2)[which(cl2[,1]==j)]\n",
" cat(\"x2:\",x2,\"\\n\")\n",
" I <- length(intersect(x1,x2))#交集\n",
" cat(\"I:\",I,\"\\n\")\n",
" S <- I/(length(x1)+length(x2)-I)\n",
" cat(\"S:\",S,\"\\n\")\n",
" row <- cbind(row,S)\n",
" cat(\"row:\",row,\"\\n\")\n",
" }\n",
" JI_mat <- rbind(JI_mat,row)\n",
" cat(\"JI_mat:\",JI_mat,\"\\n\")\n",
" print(JI_mat)\n",
"\n",
"\n",
" }\n",
" JI_good <- rbind(JI_good,apply(JI_mat,1,max))\n",
" cat(\"JI_good:\",JI_good,\"\\n\")\n",
"}\n",
"JI_final[1:number_cl] <- apply(JI_good,2,mean)"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<caption>A matrix: 10 × 1 of type dbl</caption>\n",
"<tbody>\n",
"\t<tr><td>0.8219333</td></tr>\n",
"\t<tr><td>0.8166000</td></tr>\n",
"\t<tr><td>0.8121667</td></tr>\n",
"\t<tr><td>0.8264000</td></tr>\n",
"\t<tr><td>0.8163333</td></tr>\n",
"\t<tr><td>0.8122667</td></tr>\n",
"\t<tr><td>0.8235000</td></tr>\n",
"\t<tr><td>0.8115667</td></tr>\n",
"\t<tr><td>0.8183000</td></tr>\n",
"\t<tr><td>0.8188286</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"A matrix: 10 × 1 of type dbl\n",
"\\begin{tabular}{l}\n",
"\t 0.8219333\\\\\n",
"\t 0.8166000\\\\\n",
"\t 0.8121667\\\\\n",
"\t 0.8264000\\\\\n",
"\t 0.8163333\\\\\n",
"\t 0.8122667\\\\\n",
"\t 0.8235000\\\\\n",
"\t 0.8115667\\\\\n",
"\t 0.8183000\\\\\n",
"\t 0.8188286\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"A matrix: 10 × 1 of type dbl\n",
"\n",
"| 0.8219333 |\n",
"| 0.8166000 |\n",
"| 0.8121667 |\n",
"| 0.8264000 |\n",
"| 0.8163333 |\n",
"| 0.8122667 |\n",
"| 0.8235000 |\n",
"| 0.8115667 |\n",
"| 0.8183000 |\n",
"| 0.8188286 |\n",
"\n"
],
"text/plain": [
" [,1] \n",
" [1,] 0.8219333\n",
" [2,] 0.8166000\n",
" [3,] 0.8121667\n",
" [4,] 0.8264000\n",
" [5,] 0.8163333\n",
" [6,] 0.8122667\n",
" [7,] 0.8235000\n",
" [8,] 0.8115667\n",
" [9,] 0.8183000\n",
"[10,] 0.8188286"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"JI_final"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" subjects cluster.id\n",
"1 \"subject1\" \"4\" \n",
"2 \"subject2\" \"1\" \n",
"3 \"subject3\" \"2\" \n",
"4 \"subject4\" \"3\" \n",
"5 \"subject5\" \"1\" \n",
"6 \"subject6\" \"1\" \n",
"7 \"subject7\" \"2\" \n",
"8 \"subject8\" \"2\" \n",
"9 \"subject9\" \"3\" \n",
"10 \"subject10\" \"1\" \n",
"11 \"subject11\" \"4\" \n",
"12 \"subject12\" \"4\" \n",
"13 \"subject13\" \"2\" \n",
"14 \"subject14\" \"1\" \n",
"15 \"subject15\" \"3\" \n",
"16 \"subject16\" \"1\" \n",
"17 \"subject17\" \"2\" \n",
"18 \"subject18\" \"1\" \n",
"19 \"subject19\" \"1\" \n",
"20 \"subject20\" \"1\" \n",
"21 \"subject21\" \"4\" \n",
"22 \"subject22\" \"4\" \n",
"23 \"subject23\" \"5\" \n",
"24 \"subject24\" \"2\" \n",
"25 \"subject25\" \"1\" \n",
"26 \"subject26\" \"1\" \n",
"27 \"subject27\" \"5\" \n",
"28 \"subject28\" \"2\" \n",
"29 \"subject29\" \"5\" \n",
"30 \"subject30\" \"2\" \n",
"31 \"subject31\" \"4\" \n",
"32 \"subject32\" \"2\" \n",
"33 \"subject33\" \"3\" \n",
"34 \"subject34\" \"3\" \n",
"35 \"subject35\" \"1\" \n",
"36 \"subject36\" \"1\" \n",
"37 \"subject37\" \"4\" \n",
"38 \"subject38\" \"2\" \n",
"39 \"subject39\" \"2\" \n",
"40 \"subject40\" \"4\" \n",
"41 \"subject41\" \"5\" \n",
"42 \"subject42\" \"1\" \n",
"43 \"subject43\" \"3\" \n",
"44 \"subject44\" \"3\" \n",
"45 \"subject45\" \"2\" \n",
"46 \"subject46\" \"1\" \n",
"47 \"subject47\" \"1\" \n",
"48 \"subject48\" \"3\" \n",
"49 \"subject49\" \"4\" \n",
"50 \"subject50\" \"3\" \n",
"51 \"subject51\" \"5\" \n",
"52 \"subject52\" \"3\" \n",
"53 \"subject53\" \"5\" \n",
"54 \"subject54\" \"3\" \n",
"55 \"subject55\" \"5\" \n",
"56 \"subject56\" \"4\" \n",
"57 \"subject57\" \"1\" \n",
"58 \"subject58\" \"4\" \n",
"59 \"subject59\" \"3\" \n",
"60 \"subject60\" \"3\" \n",
"61 \"subject61\" \"4\" \n",
"62 \"subject62\" \"4\" \n",
"63 \"subject63\" \"2\" \n",
"64 \"subject64\" \"5\" \n",
"65 \"subject65\" \"3\" \n",
"66 \"subject66\" \"3\" \n",
"67 \"subject67\" \"2\" \n",
"68 \"subject68\" \"1\" \n",
"69 \"subject69\" \"5\" \n",
"70 \"subject70\" \"5\" \n",
"71 \"subject71\" \"2\" \n",
"72 \"subject72\" \"2\" \n",
"73 \"subject73\" \"1\" \n",
"74 \"subject74\" \"3\" \n",
"75 \"subject75\" \"4\" \n",
"76 \"subject76\" \"3\" \n",
"77 \"subject77\" \"2\" \n",
"78 \"subject78\" \"3\" \n",
"79 \"subject79\" \"2\" \n",
"80 \"subject80\" \"3\" \n",
"81 \"subject81\" \"3\" \n",
"82 \"subject82\" \"4\" \n",
"83 \"subject83\" \"1\" \n",
"84 \"subject84\" \"1\" \n",
"85 \"subject85\" \"4\" \n",
"86 \"subject86\" \"5\" \n",
"87 \"subject87\" \"1\" \n",
"88 \"subject88\" \"1\" \n",
"89 \"subject89\" \"4\" \n",
"90 \"subject90\" \"1\" \n",
"91 \"subject91\" \"4\" \n",
"92 \"subject92\" \"4\" \n",
"93 \"subject93\" \"2\" \n",
"94 \"subject94\" \"2\" \n",
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"[1] \"factors:\"\n",
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"subject100 -0.054739884 0.175063171 0.017107780 -0.0267241288 0.061461970\n",
"clust_iCluster: 4 1 2 1 1 1 2 2 1 1 4 4 2 1 1 1 2 1 1 1 4 4 5 2 1 1 3 2 5 2 4 2 1 1 1 1 4 2 2 4 5 1 1 1 2 1 1 1 4 1 5 1 5 1 5 4 1 4 1 1 4 4 2 3 1 1 2 1 5 5 2 2 1 1 4 1 2 1 2 1 1 4 1 1 4 5 1 1 4 1 4 4 2 2 4 5 5 5 1 3 \n",
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"[19] \"subject42\" \"subject43\" \"subject44\" \"subject46\" \"subject47\" \"subject48\"\n",
"[25] \"subject50\" \"subject52\" \"subject54\" \"subject57\" \"subject59\" \"subject60\"\n",
"[31] \"subject65\" \"subject66\" \"subject68\" \"subject73\" \"subject74\" \"subject76\"\n",
"[37] \"subject78\" \"subject80\" \"subject81\" \"subject83\" \"subject84\" \"subject87\"\n",
"[43] \"subject88\" \"subject90\" \"subject99\"\n",
"x2: subject2 subject5 subject6 subject10 subject14 subject16 subject18 subject19 subject20 subject25 subject26 subject35 subject36 subject42 subject46 subject47 subject57 subject68 subject73 subject83 subject84 subject87 subject88 subject90 subject99 \n",
"I: 25 \n",
"S: 0.5555556 \n",
"row: 0.5555556 \n",
"x2: subject3 subject7 subject8 subject13 subject17 subject24 subject28 subject30 subject32 subject38 subject39 subject45 subject63 subject67 subject71 subject72 subject77 subject79 subject93 subject94 \n",
"I: 0 \n",
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"row: 0.5555556 0 \n",
"x2: subject4 subject9 subject15 subject33 subject34 subject43 subject44 subject48 subject50 subject52 subject54 subject59 subject60 subject65 subject66 subject74 subject76 subject78 subject80 subject81 \n",
"I: 20 \n",
"S: 0.4444444 \n",
"row: 0.5555556 0 0.4444444 \n",
"x2: subject1 subject11 subject12 subject21 subject22 subject31 subject37 subject40 subject49 subject56 subject58 subject61 subject62 subject75 subject82 subject85 subject89 subject91 subject92 subject95 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0.5555556 0 0.4444444 0 \n",
"x2: subject23 subject27 subject29 subject41 subject51 subject53 subject55 subject64 subject69 subject70 subject86 subject96 subject97 subject98 subject100 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0.5555556 0 0.4444444 0 0 \n",
"JI_mat: 0.5555556 0 0.4444444 0 0 \n",
" S S S S S\n",
"[1,] 0.5555556 0 0.4444444 0 0\n",
" [1] \"subject3\" \"subject7\" \"subject8\" \"subject13\" \"subject17\" \"subject24\"\n",
" [7] \"subject28\" \"subject30\" \"subject32\" \"subject38\" \"subject39\" \"subject45\"\n",
"[13] \"subject63\" \"subject67\" \"subject71\" \"subject72\" \"subject77\" \"subject79\"\n",
"[19] \"subject93\" \"subject94\"\n",
"x2: subject2 subject5 subject6 subject10 subject14 subject16 subject18 subject19 subject20 subject25 subject26 subject35 subject36 subject42 subject46 subject47 subject57 subject68 subject73 subject83 subject84 subject87 subject88 subject90 subject99 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 \n",
"x2: subject3 subject7 subject8 subject13 subject17 subject24 subject28 subject30 subject32 subject38 subject39 subject45 subject63 subject67 subject71 subject72 subject77 subject79 subject93 subject94 \n",
"I: 20 \n",
"S: 1 \n",
"row: 0 1 \n",
"x2: subject4 subject9 subject15 subject33 subject34 subject43 subject44 subject48 subject50 subject52 subject54 subject59 subject60 subject65 subject66 subject74 subject76 subject78 subject80 subject81 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 1 0 \n",
"x2: subject1 subject11 subject12 subject21 subject22 subject31 subject37 subject40 subject49 subject56 subject58 subject61 subject62 subject75 subject82 subject85 subject89 subject91 subject92 subject95 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 1 0 0 \n",
"x2: subject23 subject27 subject29 subject41 subject51 subject53 subject55 subject64 subject69 subject70 subject86 subject96 subject97 subject98 subject100 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 1 0 0 0 \n",
"JI_mat: 0.5555556 0 0 1 0.4444444 0 0 0 0 0 \n",
" S S S S S\n",
"[1,] 0.5555556 0 0.4444444 0 0\n",
"[2,] 0.0000000 1 0.0000000 0 0\n",
"[1] \"subject27\" \"subject64\" \"subject100\"\n",
"x2: subject2 subject5 subject6 subject10 subject14 subject16 subject18 subject19 subject20 subject25 subject26 subject35 subject36 subject42 subject46 subject47 subject57 subject68 subject73 subject83 subject84 subject87 subject88 subject90 subject99 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 \n",
"x2: subject3 subject7 subject8 subject13 subject17 subject24 subject28 subject30 subject32 subject38 subject39 subject45 subject63 subject67 subject71 subject72 subject77 subject79 subject93 subject94 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 \n",
"x2: subject4 subject9 subject15 subject33 subject34 subject43 subject44 subject48 subject50 subject52 subject54 subject59 subject60 subject65 subject66 subject74 subject76 subject78 subject80 subject81 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 \n",
"x2: subject1 subject11 subject12 subject21 subject22 subject31 subject37 subject40 subject49 subject56 subject58 subject61 subject62 subject75 subject82 subject85 subject89 subject91 subject92 subject95 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 0 \n",
"x2: subject23 subject27 subject29 subject41 subject51 subject53 subject55 subject64 subject69 subject70 subject86 subject96 subject97 subject98 subject100 \n",
"I: 3 \n",
"S: 0.2 \n",
"row: 0 0 0 0 0.2 \n",
"JI_mat: 0.5555556 0 0 0 1 0 0.4444444 0 0 0 0 0 0 0 0.2 \n",
" S S S S S\n",
"[1,] 0.5555556 0 0.4444444 0 0.0\n",
"[2,] 0.0000000 1 0.0000000 0 0.0\n",
"[3,] 0.0000000 0 0.0000000 0 0.2\n",
" [1] \"subject1\" \"subject11\" \"subject12\" \"subject21\" \"subject22\" \"subject31\"\n",
" [7] \"subject37\" \"subject40\" \"subject49\" \"subject56\" \"subject58\" \"subject61\"\n",
"[13] \"subject62\" \"subject75\" \"subject82\" \"subject85\" \"subject89\" \"subject91\"\n",
"[19] \"subject92\" \"subject95\"\n",
"x2: subject2 subject5 subject6 subject10 subject14 subject16 subject18 subject19 subject20 subject25 subject26 subject35 subject36 subject42 subject46 subject47 subject57 subject68 subject73 subject83 subject84 subject87 subject88 subject90 subject99 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 \n",
"x2: subject3 subject7 subject8 subject13 subject17 subject24 subject28 subject30 subject32 subject38 subject39 subject45 subject63 subject67 subject71 subject72 subject77 subject79 subject93 subject94 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 \n",
"x2: subject4 subject9 subject15 subject33 subject34 subject43 subject44 subject48 subject50 subject52 subject54 subject59 subject60 subject65 subject66 subject74 subject76 subject78 subject80 subject81 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 \n",
"x2: subject1 subject11 subject12 subject21 subject22 subject31 subject37 subject40 subject49 subject56 subject58 subject61 subject62 subject75 subject82 subject85 subject89 subject91 subject92 subject95 \n",
"I: 20 \n",
"S: 1 \n",
"row: 0 0 0 1 \n",
"x2: subject23 subject27 subject29 subject41 subject51 subject53 subject55 subject64 subject69 subject70 subject86 subject96 subject97 subject98 subject100 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 1 0 \n",
"JI_mat: 0.5555556 0 0 0 0 1 0 0 0.4444444 0 0 0 0 0 0 1 0 0 0.2 0 \n",
" S S S S S\n",
"[1,] 0.5555556 0 0.4444444 0 0.0\n",
"[2,] 0.0000000 1 0.0000000 0 0.0\n",
"[3,] 0.0000000 0 0.0000000 0 0.2\n",
"[4,] 0.0000000 0 0.0000000 1 0.0\n",
" [1] \"subject23\" \"subject29\" \"subject41\" \"subject51\" \"subject53\" \"subject55\"\n",
" [7] \"subject69\" \"subject70\" \"subject86\" \"subject96\" \"subject97\" \"subject98\"\n",
"x2: subject2 subject5 subject6 subject10 subject14 subject16 subject18 subject19 subject20 subject25 subject26 subject35 subject36 subject42 subject46 subject47 subject57 subject68 subject73 subject83 subject84 subject87 subject88 subject90 subject99 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 \n",
"x2: subject3 subject7 subject8 subject13 subject17 subject24 subject28 subject30 subject32 subject38 subject39 subject45 subject63 subject67 subject71 subject72 subject77 subject79 subject93 subject94 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 \n",
"x2: subject4 subject9 subject15 subject33 subject34 subject43 subject44 subject48 subject50 subject52 subject54 subject59 subject60 subject65 subject66 subject74 subject76 subject78 subject80 subject81 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 \n",
"x2: subject1 subject11 subject12 subject21 subject22 subject31 subject37 subject40 subject49 subject56 subject58 subject61 subject62 subject75 subject82 subject85 subject89 subject91 subject92 subject95 \n",
"I: 0 \n",
"S: 0 \n",
"row: 0 0 0 0 \n",
"x2: subject23 subject27 subject29 subject41 subject51 subject53 subject55 subject64 subject69 subject70 subject86 subject96 subject97 subject98 subject100 \n",
"I: 12 \n",
"S: 0.8 \n",
"row: 0 0 0 0 0.8 \n",
"JI_mat: 0.5555556 0 0 0 0 0 1 0 0 0 0.4444444 0 0 0 0 0 0 0 1 0 0 0 0.2 0 0.8 \n",
" S S S S S\n",
"[1,] 0.5555556 0 0.4444444 0 0.0\n",
"[2,] 0.0000000 1 0.0000000 0 0.0\n",
"[3,] 0.0000000 0 0.0000000 0 0.2\n",
"[4,] 0.0000000 0 0.0000000 1 0.0\n",
"[5,] 0.0000000 0 0.0000000 0 0.8\n",
"JI_good: 0.5555556 1 0.2 1 0.8 \n"
]
}
],
"source": [
"clusters_comparison(out2$factorizations, out2$method, \"../data/simulations_20210329212141/equal/5/\", \"./\", 5)"
]
},
{
"cell_type": "code",
"execution_count": 94,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" RGCCA\n",
"1 0.00\n",
"2 0.35\n",
"3 0.50\n",
"4 0.00\n",
"5 1.00\n",
" RGCCA_EQ\n",
"1 0.00\n",
"2 0.35\n",
"3 0.50\n",
"4 0.00\n",
"5 1.00\n"
]
},
{
"data": {
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Guv75Bzho8ac8XokRecPah32WM3x/8u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\nrkJggg==",
"text/plain": [
"plot without title"
]
},
"metadata": {
"image/png": {
"height": 420,
"width": 420
},
"text/plain": {
"height": 420,
"width": 420
}
},
"output_type": "display_data"
}
],
"source": [
"eq_file <- paste0(\"JI.txt\")\n",
"if(exists(\"JI.final\")) rm(JI.final)\n",
" \n",
" # Load clusters (equal distribution)\n",
"if(file.exists(eq_file)) {\n",
" JI.final <- read.table(eq_file, sep=\"\\t\", header=TRUE)\n",
" print(JI.final)\n",
" names(JI.final) <- paste0(names(JI.final), \"_EQ\")\n",
" print(JI.final)\n",
"}\n",
"#par(mar=c(25,4,2,2)+.1)\n",
"boxplot(JI.final, xaxt=\"none\", cex.axis=3.5, \n",
" col=c('gray','gray','red','red','blue','blue','blueviolet','blueviolet','deeppink','deeppink','chocolate1','chocolate1','darkgoldenrod','darkgoldenrod','green','green','darkturquoise','darkturquoise'), \n",
" ann=FALSE, outline=FALSE)"
]
},
{
"cell_type": "code",
"execution_count": 86,
"metadata": {},
"outputs": [
{
"ename": "ERROR",
"evalue": "Error in parse(text = x, srcfile = src): <text>:16:3: unexpected string constant\n30: }\n31: }'\n ^\n",
"output_type": "error",
"traceback": [
"Error in parse(text = x, srcfile = src): <text>:16:3: unexpected string constant\n30: }\n31: }'\n ^\nTraceback:\n"
]
}
],
"source": [
"# Save all boxplots in a single PDF output file\n",
"pdf(file=paste0(results_folder, \"simulated_boxplots.pdf\"), width = 15, height = 15, onefile = TRUE)\n",
"\n",
"# Output files for each distribution\n",
" eq_file <- paste0(\"JI.txt\")\n",
" if(exists(\"JI.final\")) rm(JI.final)\n",
" \n",
" # Load clusters (equal distribution)\n",
" if(file.exists(eq_file)) {\n",
" JI.final <- read.table(eq_file, sep=\"\\t\", header=TRUE)\n",
" print(JI.final)\n",
" names(JI.final) <- paste0(names(JI.final), \"_EQ\") \n",
" }\n",
" \n",
" # Load clusters (heterogeneous distribution)\n",
"'''\n",
" if(file.exists(het_file)) {\n",
" JI.het <- read.table(het_file, sep=\"\\t\", header=TRUE)\n",
" names_methods <- names(JI.het)\n",
" names(JI.het) <- paste0(names(JI.het), \"_HET\")\n",
"\n",
" # Aggregate results\n",
" if(exists(\"JI.final\")) {\n",
" JI.final <- data.frame(JI.het, JI.final)\n",
" new_order <- apply(expand.grid(c(\"_HET\", \"_EQ\"), names_methods)[, c(2,1)], 1, paste, collapse=\"\")\n",
" JI.final <- JI.final[, new_order]\n",
" }\n",
" else {\n",
" JI.final <- JI.het\n",
" }\n",
" }'''\n",
" \n",
" # Plot results\n",
" par(mar=c(25,4,2,2)+.1)\n",
" boxplot(JI.final, xaxt=\"none\", cex.axis=3.5, \n",
" col=c('gray','gray','red','red','blue','blue','blueviolet','blueviolet','deeppink','deeppink','chocolate1','chocolate1','darkgoldenrod','darkgoldenrod','green','green','darkturquoise','darkturquoise'), \n",
" ann=FALSE, outline=FALSE)\n",
" matplot(1:ncol(JI.final), t(JI.final), col=\"black\", pch=16, xaxt=\"none\", cex=0.8, add=TRUE)\n",
" axis(1, at=1:ncol(JI.final), labels=names(JI.final), \n",
" las=2, srt=45, cex=0.8, cex.lab=3.5, cex.axis=3.5, cex.main=1.5, cex.sub=1.5) \n",
" title(main=paste(i,\"clusters\",sep=\" \"), \n",
" cex.lab=0.75, line = -2.5, adj=0, cex.main=3.5)\n",
"dev.off()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
Datasets
Models
