I want to use pairs function and get a matrix of scatterplots with the correlations in the upper panel and the ordinary scatterplots in the lower panel.
Moreover, I want to have points colored in five differet ways in the lower panel, because I have five subgroups.
In order to do that I tried to combine examples on pairs function help.
I got a colored matrix using hints on iris dataset.
I got a black and white matrix with correlations using function panel.cor, exactly as it is in the example.
Unfortunately, the line:
jpeg(filename="/home/valeria/Thesis/lung/fig/scatterplotcolnames.jpg")
pairs(aggiunta[,1: 6],labels=c("ALCAM","ITGB5","MSN","CSTB","DHCR24","TRIM29"), main = "Scatterplots selected genes",pch=21,
bg = c("red", "green3", "blue", "brown","orange")[aggiunta[,7]],upper.panel=panel.cor)
dev.off()
doesn't allow me to get the desidered matrix with colors and correlations.
I also tried to create a function panel.col for the lower.panel:
## put colors on the lower panels
panel.col <- function(datiepheno)
{
usr <- par("usr"); on.exit(par(usr))
par(bg = c("red", "green3", "blue", "brown","orange")[datiepheno[,7]],pch=21, usr = c(0, 1, 0, 1))
}
but it doesn't work as well. Any idea? I hope I'll be precise but not too much precise! Thank you very much Valeria
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