Mercurial > repos > elixir-it > vinyl_pca

diff PCA.R @ 0:0011da72f65a draft

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author elixir-it
date Tue, 09 Jun 2020 16:11:33 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PCA.R	Tue Jun 09 16:11:33 2020 +0000
@@ -0,0 +1,12 @@
+args <- commandArgs(trailingOnly = TRUE)
+fileIn=args[1]
+nhealth=args[2]
+ndis=args[3]
+fileO=args[4]
+Final_D=read.table(fileIn,header=T,row.names=1)
+PCA=prcomp(t(Final_D))
+M=PCA$x
+png(fileO,width=1800,height=1800,res=160)
+plot(M[,1],M[,2],col=rep(c("orange","purple"),c(nhealth,ndis)),main="PCA of gene scores",xlab="PC1",ylab="PC2",cex.main=2,cex.lab=2,pch=20,cex.axis=1.5,cex=1.5)
+legend(min(M[,1]),min(M[,2])*0.8,fill=c("orange","purple"),legend=c("affected","unaffected"),cex=1.5)
+dev.off()