--- a
+++ b/heatmap_scripts/heatmap_visualizations.R
@@ -0,0 +1,112 @@
+library(gridGraphics)
+library(grid)
+library(gplots)
+library(RColorBrewer)
+
+grab_grob <- function(){
+  grid.echo()
+  grid.grab()
+}
+
+
+
+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_data1 <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
+rownames(mat_data1) <- rnames
+
+
+data <- read.csv(args[1], comment.char="#")
+rnames <- data[,1]                            # assign labels in column 1 to "rnames"
+mat_data2 <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
+rownames(mat_data2) <- rnames
+
+data <- read.csv(args[1], comment.char="#")
+rnames <- data[,1]                            # assign labels in column 1 to "rnames"
+mat_data3 <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
+rownames(mat_data3) <- rnames
+
+
+data <- read.csv(args[1], comment.char="#")
+rnames <- data[,1]                            # assign labels in column 1 to "rnames"
+mat_data4 <- data.matrix(data[,2:ncol(data)])  # transform column 2-5 into a matrix
+rownames(mat_data4) <- rnames
+
+
+arr <- list(mat_data1,mat_data2,mat_data3,mat_data4)
+
+
+png(file = args[2], units="in", width=11, height=8.5, res=300)
+
+
+
+
+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
+
+attach(mtcars)
+par(mfrow=c(1,2))
+
+heatmap.2(t(mat_data1),
+	# 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,
+  # dendrogram='none',
+  density.info='histogram',
+  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)
+  )
+
+
+
+heatmap.2(t(mat_data2),
+	# 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,
+  # dendrogram='none',
+  density.info='histogram',
+  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)
+  )