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Alex Rivera
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I would like to color points in a pairs plot based of certain row indexes. Here is the code I used for plotting 1 variable against another. cases<-which(rownames(data_no_na) %in% colnames(tumor_data)) controls<-which(rownames(data_no_na) %in% colnames(control_data)) plot(y=range(pca[,1]),x=range(pca[,2]),type='n',xlab="Principle Component 2",ylab="Principle Component 1", main="Iterative Thresholding Sparse PCA") points(y=pca[cases,1], x=pca[cases,2], col = 'red' ) points(y=pca[controls,1], x=pca[controls,2], col = 'blue' ); A simple pairs plot is something like: pairs(pca[,1:3]) EDIT: EXAMPLE: cases<-1:10 controls<-11:20 pca<-matrix(c(rnorm(3*10,0,1),rnorm(3*10,5,1)),nrow=20,ncol=3)
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