Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/DESeqTools/clusterPlot.R @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 # clusterPlot | |
| 2 # dendrogram of sample clustering | |
| 3 | |
| 4 # input : counts, outputName, type of data (raw or norm) | |
| 5 # output : dendrogram (jpeg) | |
| 6 | |
| 7 # created Sept 13th, 2012 | |
| 8 # modified Oct 30th, 2012 | |
| 9 # Marie-Agnes Dillies | |
| 10 | |
| 11 | |
| 12 clusterPlot <- function( cds, OUT_clusterPlot, type = "raw", out = TRUE ){ | |
| 13 | |
| 14 if (out) png( file=OUT_clusterPlot ) | |
| 15 | |
| 16 if (type == "norm"){ | |
| 17 cdsblind <- estimateDispersions( cds, method="blind" ) | |
| 18 vsd <- getVarianceStabilizedData( cdsblind ) | |
| 19 } | |
| 20 else { | |
| 21 vsd <- counts(cds) | |
| 22 } | |
| 23 hc <- hclust( dist(t(vsd)), method="ward" ) | |
| 24 plot( hc, xlab = "Euclidean distance, Ward criterion", main=paste("Cluster Dendrogram, ", type, " data", sep="") ) | |
| 25 | |
| 26 if (out) dev.off() | |
| 27 } |