Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
comparison
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 # pairwiseScatterPlots | |
| 2 # scatter plots for pairwise comparaisons of log counts | |
| 3 | |
| 4 # input : counts, target, outputName | |
| 5 # output : scatter plots (pdf: allows multiple figures in one file) | |
| 6 | |
| 7 # created Feb 21th, 2012 | |
| 8 # modified Sept 27th, 2012 (pdf output file) | |
| 9 # modified Oct 30th, 2012 (png) | |
| 10 # Marie-Agnes Dillies | |
| 11 | |
| 12 | |
| 13 pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){ | |
| 14 | |
| 15 if (out & !pdffile) png( OUT_scatterPlot ) | |
| 16 if (pdffile) pdf( OUT_scatterPlot ) | |
| 17 | |
| 18 conds <- unique(target$group) | |
| 19 # colnames(counts) <- target$label | |
| 20 | |
| 21 for (i in 1:(length(conds)-1)){ | |
| 22 for (j in (i+1):length(conds)){ | |
| 23 cond1 <- conds[i]; cond2 <- conds[j] | |
| 24 pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1), | |
| 25 pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") ) | |
| 26 } | |
| 27 } | |
| 28 | |
| 29 if (pdffile) dev.off() | |
| 30 if (out) dev.off() | |
| 31 } |