--- a
+++ b/heatmap_scripts/heatmap_temporal.R
@@ -0,0 +1,96 @@
+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
+#########################################################
+
+# creates a own color palette from red to green
+my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
+
+# (optional) defines the color breaks manually for a "skewed" color transition
+col_breaks = c(seq(-1,0,length=100),  # for red
+  seq(0.001,0.7,length=100),              # for yellow
+  seq(0.71,1,length=100))              # for green
+
+# creates a 5 x 5 inch image
+# png("h1_simple.png",
+#   width = 5*300,        # 5 x 300 pixels
+#   height = 5*300,
+#   res = 300,            # 300 pixels per inch
+#   pointsize = 8)        # smaller font size
+
+# heatmap.2(t(mat_data),
+#   cellnote = t(mat_data),  # same data set for cell labels
+#   #notecol="black",      # change font color of cell labels to black
+#   #density.info="none",  # turns off density plot inside color legend
+#   trace="none",         # turns off trace lines inside the heat map
+#   margins =c(12,9),     # widens margins around plot
+#   col=my_palette,       # use on color palette defined earlier
+#   breaks=col_breaks,    # enable color transition at specified limits
+#   dendrogram="none",     # only draw a row dendrogram
+
+if(length(args) < 3){
+  offset <- -13
+} else {
+  offset <- as.integer(args[3])
+}
+
+if(length(args) < 4){
+  color_map <- bluered
+  colors = c(seq(0,0.5,length=20),seq(0.501,1,length=20)) #TODO change for certain graphs
+} else {
+  color_map <- colorRampPalette(c("white","red"))(n = 39)
+  # colors = c(seq(0,0.05,length=20),seq(0.501,1,length=20)) #TODO change for certain graphs
+  colors=NULL
+}
+
+
+
+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()