Mercurial > repos > elixir-it > vinyl_pca

annotate PCA.R @ 1:460883beb10c draft default tip

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author elixir-it
date Wed, 15 Jul 2020 07:55:07 +0000
parents 0011da72f65a
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elixir-it
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1 args <- commandArgs(trailingOnly = TRUE)
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elixir-it
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2 fileIn=args[1]
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elixir-it
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3 nhealth=args[2]
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elixir-it
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4 ndis=args[3]
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elixir-it
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5 fileO=args[4]
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elixir-it
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6 Final_D=read.table(fileIn,header=T,row.names=1)
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elixir-it
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7 PCA=prcomp(t(Final_D))
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elixir-it
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8 M=PCA$x
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elixir-it
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9 png(fileO,width=1800,height=1800,res=160)
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elixir-it
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10 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)
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elixir-it
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11 legend(min(M[,1]),min(M[,2])*0.8,fill=c("orange","purple"),legend=c("affected","unaffected"),cex=1.5)
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elixir-it
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12 dev.off()