Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
diff DiffExpAnal/DESeqTools/pairwiseScatterPlots.R @ 0:63799b789162 draft
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author | yufei-luo |
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date | Tue, 22 Jan 2013 10:07:03 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R Tue Jan 22 10:07:03 2013 -0500 @@ -0,0 +1,31 @@ +# pairwiseScatterPlots +# scatter plots for pairwise comparaisons of log counts + +# input : counts, target, outputName +# output : scatter plots (pdf: allows multiple figures in one file) + +# created Feb 21th, 2012 +# modified Sept 27th, 2012 (pdf output file) +# modified Oct 30th, 2012 (png) +# Marie-Agnes Dillies + + +pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){ + + if (out & !pdffile) png( OUT_scatterPlot ) + if (pdffile) pdf( OUT_scatterPlot ) + + conds <- unique(target$group) + # colnames(counts) <- target$label + + for (i in 1:(length(conds)-1)){ + for (j in (i+1):length(conds)){ + cond1 <- conds[i]; cond2 <- conds[j] + pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1), + pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") ) + } + } + + if (pdffile) dev.off() + if (out) dev.off() +}