Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
comparison DiffExpAnal/DESeqTools/plotDispEstimates.R @ 0:63799b789162 draft
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| author | yufei-luo |
|---|---|
| date | Tue, 22 Jan 2013 10:07:03 -0500 |
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| -1:000000000000 | 0:63799b789162 |
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| 1 # Marie-Anges Dillies | |
| 2 # plotDispEstimates | |
| 3 # scatter plots representing dispersion estimates vs mean expression | |
| 4 | |
| 5 # input : cds, OUT_plotDispEstimatesName | |
| 6 # output : scatterplot (png) | |
| 7 | |
| 8 plotDispEstimates <- function( cds, OUT_plotDispEstimatesName, out = TRUE ){ | |
| 9 | |
| 10 if (out) png( file=OUT_plotDispEstimatesName ) | |
| 11 | |
| 12 plot( | |
| 13 rowMeans( counts(cds, normalized=T) ), | |
| 14 fitInfo(cds)$perGeneDispEsts, | |
| 15 pch=".", log="xy", | |
| 16 xlab = "Mean expression strength", ylab = "Dispersion estimate" ) | |
| 17 | |
| 18 xg <- 10^seq(-.5, 5, length.out=300) | |
| 19 lines( xg, fitInfo(cds)$dispFun(xg), col="red" ) | |
| 20 | |
| 21 if (out) dev.off() | |
| 22 } |