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b/Figures/clonevol/clonevol_P42_141118.R |
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library(dplyr) |
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library(plyr) |
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library(clonevol) |
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library(fishplot) |
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library(reshape) |
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####coverage: from reseq BAM files |
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####step1: Using mpileup to extract coverage for each site. (Prepared 27/10/18), default parameter |
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####step2: Prepare input for pyclone, using segments from ASCAT |
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####step3: Run Pyclone twice. The first run is to identify founding cluster, |
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#### the second run adding --tumour_content based on the cellular prevalence for each biopsy (29/10/18) |
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###step4: using clonevol to build evolution tree and model (in this script) (30/10/18) |
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### using Fishplot to visulaize |
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### using Fishplot to visulaize |
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###P42, 3 biopsies, hist_transform |
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#T1:LN_left_axilla |
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#T2:LN_left_neck |
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#T3:LN_left_inguinal |
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setwd("G:/FL_resequncing/FL_exome_final/fl_latest/11_pyclone/BED_bam/counts_new/pyclone_output_301018") |
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pyclone_out<- read.table(file="ouput_pyclone/output_200X_i2/P42_200X_i2/tables/loci.tsv",sep="\t",header=T) |
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mutations<-cast(pyclone_out[,1:4], mutation_id~sample_id, value="cellular_prevalence") |
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id<-unique(pyclone_out[, c(1,3)] ) |
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P_case<- merge(id, mutations,by="mutation_id") |
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vafs = data.frame(cluster=P_case$cluster_id, |
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T1_vaf=(P_case$`GCF0150-0042-T01`/2)*100, |
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T2_vaf=(P_case$`GCF0150-0042-T02`/2)*100, |
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T3_vaf=(P_case$`GCF0150-0042-T03`/2)*100, |
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stringsAsFactors=F) |
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vafs$cluster<- vafs$cluster+1 |
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samples<-c("P42_1","P42_2", "P42_3") |
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samples1<-c("P42_1\nPrimary","P42_2\nRelapsed_1","P42_3\nRelapsed_2" ) |
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samples2<-c("P42_1\nPrimary\nLN_left_axilla","P42_2\nRelapsed_1\nLN_left_neck","P42_3\nRelapsed_2\nLN_left_inguinal" ) |
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max_id<- max(vafs$cluster)+1 |
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vafs$cluster[vafs$cluster==1]<-max_id |
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vafs$cluster[vafs$cluster==4]<-1 |
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vafs$cluster[vafs$cluster==max_id]<-4 |
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###needs manully check density plot to identify which cluster is founding cluster |
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##clonevol requires founding cluster=1 |
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names(vafs)[2:4] = samples |
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##step 2: run infer.clonal.models, run twice: 1. include all cluster. |
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###########2. manual review density plot and exlcude cluster with small number of mutations |
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##step 2: run infer.clonal.models, run twice: 1. include all cluster. |
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###########2. manual review density plot and exlcude cluster with small number of mutations |
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dir.create("./clonevol/P42") |
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## |
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##first: use all clusters, no consensus models |
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#vafs$P31_3[vafs$cluster=="1"]<-vafs$P31_3[vafs$cluster=="1"]+ 0.5 |
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#vafs$P27_2[vafs$cluster=="1"]<-vafs$P27_2[vafs$cluster=="1"]+ 0.5 |
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#vafs$P27_3[vafs$cluster=="3"]<-vafs$P27_3[vafs$cluster=="3"]+1 |
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res = infer.clonal.models(variants=vafs, cluster.col.name="cluster", vaf.col.names=samples, |
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subclonal.test="bootstrap", subclonal.test.model="non-parametric", |
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founding.cluster=1, |
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cluster.center="mean", num.boots=1000, |
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min.cluster.vaf=0.01, sum.p=0.01, alpha=0.01) |
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res = infer.clonal.models(variants=vafs, cluster.col.name="cluster", vaf.col.names=samples, |
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subclonal.test="bootstrap", subclonal.test.model="non-parametric", |
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founding.cluster=1,ignore.clusters = c(7,9,10), |
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cluster.center="mean", num.boots=1000, |
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min.cluster.vaf=0.01, sum.p=0.01, alpha=0.01) |
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vafs_used<- subset(vafs, !cluster %in% c(7,9,10)) |
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vafs_used$cluster[vafs_used$cluster==8]<-7 |
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res = infer.clonal.models(variants=vafs_used, cluster.col.name="cluster", vaf.col.names=samples, |
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subclonal.test="bootstrap", subclonal.test.model="non-parametric", |
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founding.cluster=1, |
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cluster.center="mean", num.boots=1000, |
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min.cluster.vaf=0.01, sum.p=0.01, alpha=0.01) |
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res<-convert.consensus.tree.clone.to.branch(res, branch.scale = 'sqrt') |
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pdf("./clonevol/P42/P42_trees.pdf", useDingbats = FALSE) |
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plot.all.trees.clone.as.branch(res, branch.width = 0.5, node.size = 1, node.label.size = 0.5) |
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dev.off() |
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plot.clonal.models(res, |
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# box plot parameters |
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box.plot = TRUE, |
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fancy.boxplot = TRUE, |
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fancy.variant.boxplot.highlight = 'is.driver', |
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fancy.variant.boxplot.highlight.shape = 21, |
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fancy.variant.boxplot.highlight.fill.color = 'red', |
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fancy.variant.boxplot.highlight.color = 'black', |
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fancy.variant.boxplot.highlight.note.col.name = 'gene', |
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fancy.variant.boxplot.highlight.note.color = 'blue', |
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fancy.variant.boxplot.highlight.note.size = 2, |
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fancy.variant.boxplot.jitter.alpha = 1, |
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fancy.variant.boxplot.jitter.center.color = 'grey50', |
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fancy.variant.boxplot.base_size = 12, |
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fancy.variant.boxplot.plot.margin = 1, |
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fancy.variant.boxplot.vaf.suffix = '.VAF', |
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# bell plot parameters |
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clone.shape = 'bell', |
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bell.event = TRUE, |
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bell.event.label.color = 'blue', |
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bell.event.label.angle = 60, |
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clone.time.step.scale = 1, |
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bell.curve.step = 2, |
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# node-based consensus tree parameters |
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merged.tree.plot = TRUE, |
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tree.node.label.split.character = NULL, |
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tree.node.shape = 'circle', |
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tree.node.size = 30, |
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tree.node.text.size = 0.5, |
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merged.tree.node.size.scale = 1.25, |
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merged.tree.node.text.size.scale = 2, |
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merged.tree.cell.frac.ci = FALSE, |
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# branch-based consensus tree parameters |
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merged.tree.clone.as.branch = TRUE, |
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mtcab.event.sep.char = ',', |
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mtcab.branch.text.size = 1, |
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mtcab.branch.width = 0.75, |
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mtcab.node.size = 3, |
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mtcab.node.label.size = 1, |
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mtcab.node.text.size = 1.5, |
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# cellular population parameters |
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cell.plot = TRUE, |
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num.cells = 100, |
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cell.border.size = 0.25, |
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cell.border.color = 'black', |
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clone.grouping = 'horizontal', |
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#meta-parameters |
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scale.monoclonal.cell.frac = TRUE, |
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show.score = FALSE, |
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cell.frac.ci = TRUE, |
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disable.cell.frac = FALSE, |
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# output figure parameters |
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out.dir = './clonevol/P42/', |
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out.format = 'pdf', |
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overwrite.output = TRUE, |
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width = 10, |
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height = 4, |
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# vector of width scales for each panel from left to right |
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panel.widths = c(1.5,2.5,1.5,2.5,2)) |
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###removing cell.frac annotation |
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plot.clonal.models(res, |
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# box plot parameters |
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box.plot = TRUE, |
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fancy.boxplot = TRUE, |
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fancy.variant.boxplot.highlight = 'is.driver', |
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fancy.variant.boxplot.highlight.shape = 21, |
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fancy.variant.boxplot.highlight.fill.color = 'red', |
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fancy.variant.boxplot.highlight.color = 'black', |
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fancy.variant.boxplot.highlight.note.col.name = 'gene', |
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fancy.variant.boxplot.highlight.note.color = 'blue', |
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fancy.variant.boxplot.highlight.note.size = 2, |
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fancy.variant.boxplot.jitter.alpha = 1, |
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fancy.variant.boxplot.jitter.center.color = 'grey50', |
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fancy.variant.boxplot.base_size = 12, |
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fancy.variant.boxplot.plot.margin = 1, |
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fancy.variant.boxplot.vaf.suffix = '.VAF', |
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# bell plot parameters |
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clone.shape = 'bell', |
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bell.event = TRUE, |
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bell.event.label.color = 'blue', |
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bell.event.label.angle = 60, |
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clone.time.step.scale = 1, |
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bell.curve.step = 2, |
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# node-based consensus tree parameters |
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merged.tree.plot = TRUE, |
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tree.node.label.split.character = NULL, |
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tree.node.shape = 'circle', |
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tree.node.size = 30, |
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tree.node.text.size = 0.5, |
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merged.tree.node.size.scale = 1.25, |
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merged.tree.node.text.size.scale = 2, |
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merged.tree.cell.frac.ci = FALSE, |
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# branch-based consensus tree parameters |
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merged.tree.clone.as.branch = TRUE, |
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mtcab.event.sep.char = ',', |
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mtcab.branch.text.size = 1, |
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mtcab.branch.width = 0.75, |
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mtcab.node.size = 3, |
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mtcab.node.label.size = 1, |
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mtcab.node.text.size = 1.5, |
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# cellular population parameters |
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cell.plot = TRUE, |
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num.cells = 100, |
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cell.border.size = 0.25, |
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cell.border.color = 'black', |
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clone.grouping = 'horizontal', |
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#meta-parameters |
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scale.monoclonal.cell.frac = TRUE, |
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show.score = FALSE, |
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cell.frac.ci = TRUE, |
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disable.cell.frac = TRUE, |
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# output figure parameters |
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out.dir = './clonevol/P42/', |
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out.format = 'pdf', |
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overwrite.output = TRUE, |
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width = 10, |
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height = 4, |
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# vector of width scales for each panel from left to right |
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panel.widths = c(1.5,2.5,1.5,2.5,2)) |
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##generating fish plot |
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f<- generateFishplotInputs(results = res) |
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fishes=createFishPlotObjects(f) |
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pdf('./clonevol/P42/P42_fish_200x_pyclone_anno_loc.pdf', width=14, height=7) |
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for (i in 1:(length(fishes))){ |
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fish = layoutClones(fishes[[i]]) |
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fish = setCol(fish,f$clonevol.clone.colors) |
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fishPlot(fish,shape="spline", cex.title=0.7,cex.vlab = 1.4, |
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vlines=seq(1, length(samples2)), vlab=samples2, pad.left=0.5) |
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} |
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dev.off() |
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pdf("./clonevol/P42/P42_box.pdf", width=3, height=3,useDingbats = FALSE, title='') |
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pp<-plot.variant.clusters(vafs_used, |
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cluster.col.name = 'cluster', |
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show.cluster.size = FALSE, |
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cluster.size.text.color = 'blue', |
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vaf.col.names = samples, |
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vaf.limits = 70, |
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sample.title.size = 20, |
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violin = FALSE, |
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box = FALSE, |
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jitter = TRUE, |
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jitter.shape = 1, |
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jitter.size = 3, |
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jitter.alpha = 1, |
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jitter.center.method = 'median', |
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jitter.center.size = 1, |
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jitter.center.color = 'darkgray', |
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jitter.center.display.value = 'none', |
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highlight = 'is.driver', |
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highlight.shape = 21, |
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highlight.color = 'blue', |
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highlight.fill.color = 'green', |
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highlight.note.col.name = 'gene', |
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highlight.note.size = 2, |
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order.by.total.vaf = FALSE) |
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dev.off() |
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plot.pairwise(vafs_used, col.names = samples, |
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out.prefix = './clonevol/P42/P42_variants.pairwise.plot') |
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pdf('./clonevol/P42/P42_flow.pdf') |
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plot.cluster.flow(vafs, vaf.col.names = samples, |
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sample.names = c('Primary', 'Relapsed', "Transformed")) |
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dev.off() |
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####checking coverage |
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Pcase<-do.call("rbind", lapply( list.files("input_pyclone_271018_newpara/200X/GCF0150-0042-N01_200X/",full=TRUE), |
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read.table, header=TRUE, sep="\t")) |
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######## |
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#min (dp) =min(c1inP4_1$var_counts+c1inP4_1$ref_counts)=273 |
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#max (dp) =max(c1inP4_1$var_counts+c1inP4_1$ref_counts)=648 |
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#median (dp) =median(c1inP4_1$var_counts+c1inP4_1$ref_counts)=380 |
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#mean (dp) =mean(c1inP4_1$var_counts+c1inP4_1$ref_counts)=417 |
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library(ggplot2) |
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pdf("clonevol/P42/coverage.pdf") |
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ggplot(Pcase, aes(x=(var_counts+ref_counts)))+ |
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geom_histogram(position="dodge")+ |
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facet_grid(~sample) |
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dev.off() |
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save.image("G:/FL_resequncing/FL_exome_final/fl_latest/11_pyclone/BED_bam/counts_new/pyclone_output_301018/P42.RData") |
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