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()