--- a
+++ b/Fig3_FigS3_MDSsignature.R
@@ -0,0 +1,76 @@
+GIT_HOME="/research/users/ppolonen/git_home/ImmunogenomicLandscape-BloodCancers/"
+source(file.path(GIT_HOME, "common_scripts/visualisation/plotting_functions.R"))
+source(file.path(GIT_HOME, "common_scripts/statistics/functions_statistics.R"))
+source(file.path(GIT_HOME, "common_scripts/statistics/statistics_wrappers.R"))
+source(file.path(GIT_HOME, "common_scripts/pathway_analysis/functions.GSEA.R"))
+source(file.path(GIT_HOME, "common_scripts/scRNA/functions.scRNA.analysis.R"))
+source(file.path(GIT_HOME, "common_scripts/statistics/useful_functions.R"))
+
+# cancermap coordinates:
+library(reshape2)
+library(gridExtra)
+library(GSVA)
+library(RColorBrewer)
+library(ggplot2)
+library(Rtsne)
+library(LPCM)
+
+# plotting function
+Plot_GSVA_scores=function(feat, data_plot, VALUE, SIZE, CLUSTER_CENTRE, coord, peaks){
+  
+  # Find specified feature(feat) from data_plot
+  data=data_plot[rownames(data_plot)%in%feat,]
+  
+  # Transform matrix to numeric. 
+  data=as.numeric(data)
+  
+  # Color vector for gradient colors from blue to red.
+  rbPal <- colorRampPalette(c('blue','red'))
+  
+  # Adjust data for gradient colors.
+  data=c(data, 2, -2) # adjust range
+  datCol <- rbPal(10)[as.numeric(cut(data,breaks = 10))]
+  datCol=datCol[-c(length(datCol)-1, length(datCol))]
+  data=data[-c(length(data)-1, length(data))]
+  
+  # Samples below cutoff colored grey.
+  datCol[abs(data)<VALUE]="grey75"
+  front=abs(data)>VALUE
+  
+  # Prepare coordinate data for plotting.
+  dat2show <- cbind(coord$x, coord$y)
+  df=as.data.frame(dat2show)
+  colnames(df) = c("X1","X2")
+  
+  # Generate plot title. 
+  cutoff=paste("GSVA score >", VALUE)
+  plotname=paste(feat, cutoff, sep="\n")
+  
+  # Call actual plotting function.
+  drawFig(df, CLUSTER_CENTRE, datCol, front, plotname, SIZE, peaks) 
+}
+
+load("MDS_genesets.Rdata")
+geneset=list("MDS_signature"=geneset$MDS_signature_all_filt)
+
+# go through each cohort and plot GSVA score:
+setwd("/research/groups/sysgen/PROJECTS/HEMAP_IMMUNOLOGY/petri_work/HEMAP_IMMUNOLOGY/Published_data_figures")
+
+files=list.files(path = ".", "subtypes.Rdata")
+names(files)=gsub("_subtypes.Rdata", "", files)
+
+files=files[grepl("AML", names(files))]
+
+p.all=lapply(files, function(f){
+  load(f)
+  
+  score=gsva(data.matrix(gexp), geneset, mx.diff=F, tau=0.25, parallel.sz=4)
+  
+  plot.val=t(scale(t(score)))
+  
+  a=Plot_GSVA_scores(feat = "MDS_signature", data_plot = t(scale(t(score))), VALUE = 0.5,SIZE = 1, coord = coordinates.subtype, peaks = NULL, CLUSTER_CENTRE = F)
+  
+})
+
+# Save PDF figure (A4) with multiple panels
+ggsave("Figure3E_FigureS3D.pdf", do.call(marrangeGrob, list(grobs=p.all, nrow=4, ncol=3)), width = 210, height = 297, units = "mm", dpi=150)