Develop

r.scripts/StressCompare.R

+library(methods)
+library(optparse)
+library(Seurat)
+library(readr)
+library(fBasics)
+library(pastecs)
+library(qusage)
+library(RColorBrewer)
+
+load("./analysis/sc10x.Stress.Rda")
+sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="ALL")
+gene.exp <- as.data.frame(as.matrix(sc10x.Stress@raw.data[,colnames(sc10x.Stress@data)]))
+genes.stress <- read_csv("./genesets/DEG_C2.CGP.M10970.txt")
+genes.stress <- genes.stress[2:nrow(genes.stress),]
+genes.stress <- as.list(genes.stress)
+
+gene.stress.pct <- apply(gene.exp,2,function(x) sum(x[rownames(gene.exp) %in% unlist(genes.stress)])/sum(x))
+
+histo <- hist(gene.stress.pct,breaks=100,prob=TRUE,plot=TRUE,main="Distribution of Stress Gene Expression in Transcriptome",xlab="% of transcriptome associated to stress genes")
+abline(v=.00575,col="red")
+
+
+sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="ALL+Stress")
+cell.index.stress <- names(sc10x.Stress@ident[sc10x.Stress@ident=="Stress"])
+cell.index.stress <- which(colnames(gene.exp) %in% cell.index.stress)
+cell.index.ntstress <- names(sc10x.Stress@ident[sc10x.Stress@ident=="ALL"])
+cell.index.ntstress <- which(colnames(gene.exp) %in% cell.index.ntstress)
+