TCGA

TCGA unsupervised clustering

Author: Charleen D. Adams

setwd("C:/Users/chaadams/Dropbox/COH/BROAD")
load("./Data/TCGAheatmap.Rdata")
mypalette <- brewer.pal(11,"RdYlBu")
morecols <- colorRampPalette(mypalette)
heatmap.2(highly_variable_lcpm, 
          col=rev(morecols(50)),
          trace="none", 
          main="Top 500 most variable genes across samples",
          distfun=function(x) dist(x, method="euclidean"), 
          hclustfun=function(x) hclust(x, method="ward.D2"))

png(file="./Figures/High_var_genes.heatmap_EUdistance2.png")
heatmap.2(highly_variable_lcpm,col=rev(morecols(50)),
          trace="none", main="Top 500 most variable genes\nacross samples")
dev.off()

## png 
##   2

Note: includes Hispanics