Create heatmap.R

heatmap.R

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+args  <- commandArgs(TRUE)
+input <- args[1]
+out   <- args[2]
+
+library('gplots')
+a = read.table(input, sep = "\t", header = T, check.names = F)
+lie  = ncol(a)
+hang = nrow(a)
+high_pre = hang/10
+high = round(high_pre, digits = 0)
+high = high + 10
+high = ifelse(high < 7, 7, ifelse(high>200, 200, high))
+x = a[,2:lie]
+y = as.matrix(x)
+y = log10(y+1)
+rownames(y) = a[,1]
+scale = ifelse(ncol(y)>2, "row", "none")
+pdf(file = out,height=high)
+par(oma = c(3,3,3,5))
+heatmap.2(y, 
+          Colv=NA,dendrogram=('row'), # make x axis clusterting
+          col=colorRampPalette(c("navy","white","firebrick3")),
+          trace = "none",
+          cexCol=1,
+          srtCol=45,
+          scale = scale,
+          cexRow = 0.6,
+          lhei=c(10,100)
+        )#,labRow=F)