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plot_MA = function(featureNames, logCounts, logFoldChange, FDR, xlab="logCounts", ylab="logFC", title="MA plot", pch=20, top_gene_labels_show=20) {
plot(logCounts, logFoldChange, col=ifelse(FDR<=0.05, "red", "black"), xlab=xlab, ylab=ylab, main=title, pch=pch);;
text(logCounts[1:top_gene_labels_show], logFoldChange[1:top_gene_labels_show], labels=featureNames[1:top_gene_labels_show], cex= 0.7, pos=3)
}
plot_Volcano = function(featureNames, logFoldChange, FDR, xlab="logFC", ylab="-1*log10(FDR)", title="Volcano plot", pch=20, top_gene_labels_show=20) {
plot(logFoldChange, -1*log10(FDR), col=ifelse(FDR<=0.05, "red", "black"), xlab=xlab, ylab=ylab, main=title, pch=pch);
text(logFoldChange[1:top_gene_labels_show], (-1*log10(FDR))[1:top_gene_labels_show], labels=featureNames[1:top_gene_labels_show], cex= 0.7, pos=3)
}
plot_MA_and_Volcano = function(featureNames, logCounts, logFoldChange, FDR, xlab="logCounts", ylab="logFC", title="MA plot") {
def.par = par(no.readonly = TRUE) # save default, for resetting...
#gridlayout = matrix(c(1:4),nrow=2,ncol=2, byrow=TRUE);
#layout(gridlayout, widths=c(1,1,1,1), heights=c(1,1,1,1))
plot_MA(featureNames, logCounts, logFoldChange, FDR);
plot_Volcano(featureNames, logFoldChange, FDR);
# draw again, but use a smaller dot for data points
#plot_MA(logCounts, logFoldChange, FDR, pch='.');
#plot_Volcano(logFoldChange, FDR, pch='.');
par(def.par)
}
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