Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
view DiffExpAnal/DESeqTools/clusterPlot.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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# clusterPlot # dendrogram of sample clustering # input : counts, outputName, type of data (raw or norm) # output : dendrogram (jpeg) # created Sept 13th, 2012 # modified Oct 30th, 2012 # Marie-Agnes Dillies clusterPlot <- function( cds, OUT_clusterPlot, type = "raw", out = TRUE ){ if (out) png( file=OUT_clusterPlot ) if (type == "norm"){ cdsblind <- estimateDispersions( cds, method="blind" ) vsd <- getVarianceStabilizedData( cdsblind ) } else { vsd <- counts(cds) } hc <- hclust( dist(t(vsd)), method="ward" ) plot( hc, xlab = "Euclidean distance, Ward criterion", main=paste("Cluster Dendrogram, ", type, " data", sep="") ) if (out) dev.off() }