Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
diff DiffExpAnal/DESeqTools/plotDispEstimates.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/plotDispEstimates.R Tue Jan 22 10:07:03 2013 -0500 @@ -0,0 +1,22 @@ +# Marie-Anges Dillies +# plotDispEstimates +# scatter plots representing dispersion estimates vs mean expression + +# input : cds, OUT_plotDispEstimatesName +# output : scatterplot (png) + +plotDispEstimates <- function( cds, OUT_plotDispEstimatesName, out = TRUE ){ + + if (out) png( file=OUT_plotDispEstimatesName ) + + plot( + rowMeans( counts(cds, normalized=T) ), + fitInfo(cds)$perGeneDispEsts, + pch=".", log="xy", + xlab = "Mean expression strength", ylab = "Dispersion estimate" ) + + xg <- 10^seq(-.5, 5, length.out=300) + lines( xg, fitInfo(cds)$dispFun(xg), col="red" ) + + if (out) dev.off() +}