--- a
+++ b/heatmap_scripts/heatmap_mutation.R
@@ -0,0 +1,71 @@
+library(gplots)
+library(RColorBrewer)
+
+args <- commandArgs(trailingOnly = TRUE)
+# print(args[1])
+# print(args[2])
+
+
+#########################################################
+### reading in data and transform it to matrix format
+#########################################################
+
+data <- read.csv(args[1], comment.char="#")
+rnames <- data[,1]                            # assign labels in column 1 to "rnames"
+mat_data <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
+rownames(mat_data) <- rnames                  # assign row names
+
+
+
+#########################################################
+### customizing and plotting heatmap
+#########################################################
+
+
+offset <- -13
+offset <- -40
+offset <- -10
+
+
+colors=NULL
+
+
+# color_map <- colorRampPalette(c("blue","red"))(n = 500)
+# colors = c(seq(-1,0,length=100),seq(0.001,1,length=100)) # for yellow\
+
+color_map <- bluered
+# color_map <- colorRampPalette(c("white","red"))(n = 39)
+
+
+
+png(file = args[2], units="in", width=11, height=8.5, res=300)
+
+heatmap.2(t(mat_data),
+	# cellnote = t(mat_data),
+	Rowv=NULL,
+	Colv="NA",
+	srtCol=0,
+	labRow = "",
+	col = color_map,
+  breaks = colors,
+	scale="none",
+	margins=c(3,0), # ("margin.Y", "margin.X")
+	trace='none',
+	symkey=FALSE,
+	symbreaks=FALSE,
+	dendrogram='none',
+	offsetCol = offset,
+	cexCol=0.9,
+  key=FALSE, #change to turn on
+  density.info=NULL,
+  denscol="black",
+	keysize=1,
+  #( "bottom.margin", "left.margin", "top.margin", "left.margin" )
+  key.par=list(mar=c(3.5,0,3,0)),
+  # lmat -- added 2 lattice sections (5 and 6) for padding
+  lmat=rbind(c(5, 4, 2), c(6, 1, 3)), lhei=c(2.5, 5), lwid=c(1, 10, 1)
+  )
+
+
+
+dev.off()