#!/usr/bin/env Rscript

suppressPackageStartupMessages(library("optparse"))

option_list <- list(
    make_option(c("-i", "--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
    make_option(c("-o", "--output_dir"), action="store", dest="output_dir", help="PDF output directory")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
args <- parse_args(parser, positional_arguments=TRUE)
opt <- args$options

state_color <- function(statemean, markcolor=NULL)
{    
    if(length(markcolor) == 0) {
        markcolor = rep("", dim(statemean)[2]);
        markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:dim(statemean)[2]-1) / dim(statemean)[2], 1, 1);
        markcolor = t(col2rgb(markcolor));
    }

    rg = apply(statemean, 1, range);
    mm = NULL;
    for(i in 1:dim(statemean)[1]) {
        mm = rbind(mm, (statemean[i,] - rg[1,i] + 1e-10) / (rg[2,i] - rg[1,i] + 1e-10));
    }
    mm = mm^6;
    if(dim(mm)[2] > 1) {
        mm = mm / (apply(mm, 1, sum) + 1e-10);
    }
    mycol = mm%*%markcolor;
    s = apply(statemean, 1, max);
    s = (s - min(s)) / (max(s) - min(s) + 1e-10);
    h = t(apply(mycol, 1, function(x){rgb2hsv(x[1], x[2], x[3])}));
    h[,2] = h[,2] * s;
    h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])});
    rt = cbind(apply(t(col2rgb(h)), 1, function(x){paste(x, collapse=",")}) ,h);
    return(rt);
}

create_heatmap<-function(data_frame, output_file_name, statecolor=NULL, markcolor=NULL, cols=c("white","dark blue")) {
    k = dim(data_frame)[2];
    l = dim(data_frame)[1];
    p = (sqrt(9 + 8 * (k - 1)) - 3) / 2;
    data_matrix = as.matrix(data_frame[,1+1:p] / data_frame[,1]);
    colnames(data_matrix) = colnames(data_frame)[1+1:p];
    marks = colnames(data_matrix);
    rownames(data_matrix) = paste(1:l," (", round(data_frame[,1] / sum(data_frame[,1]) * 10000) / 100, "%)", sep="");
    pdf(file=output_file_name);
    par(mar=c(6, 1, 1, 6));
    rg = range(data_matrix);
    colors = 0:100 / 100 * (rg[2] - rg[1]) + rg[1];
    my_palette = colorRampPalette(cols)(n=100);
    defpalette = palette(my_palette);

    plot(NA, NA, xlim=c(0,p+0.7), ylim=c(0,l), xaxt="n", yaxt="n", xlab=NA, ylab=NA, frame.plot=F);
    axis(1, at=1:p-0.5, labels=colnames(data_matrix), las=2);
    axis(4, at=1:l-0.5, labels=rownames(data_matrix), las=2);
    rect(rep(1:p-1,l), rep(1:l-1,each=p), rep(1:p,l), rep(1:l,each=p), col=round((t(data_matrix)-rg[1])/(rg[2]-rg[1])*100));

    if(length(statecolor)==0) {
        if(length(markcolor)==0) {
            markcolor=t(col2rgb(terrain.colors(ceiling(p))[1:p]));
            for(i in 1:length(marks)) {
                if(regexpr("h3k4me3",tolower(marks[i]))>0) {
                    markcolor[i,]=c(255,0,0);
                }
                if(regexpr("h3k4me2",tolower(marks[i]))>0) {
                    markcolor[i,]=c(250,100,0);
                }
                if(regexpr("h3k4me1",tolower(marks[i]))>0) {
                    markcolor[i,]=c(250,250,0);
                }
                if(regexpr("h3k36me3",tolower(marks[i]))>0) {
                    markcolor[i,]=c(0,150,0);
                }
                if(regexpr("h2a",tolower(marks[i]))>0) {
                    markcolor[i,]=c(0,150,150);
                }
                if(regexpr("dnase",tolower(marks[i]))>0) {
                    markcolor[i,]=c(0,200,200);
                }
                if(regexpr("h3k9ac",tolower(marks[i]))>0) {
                    markcolor[i,]=c(250,0,200);
                }
                if(regexpr("h3k9me3",tolower(marks[i]))>0) {
                    markcolor[i,]=c(100,100,100);
                }
                if(regexpr("h3k27ac",tolower(marks[i]))>0) {
                    markcolor[i,]=c(250,150,0);
                }
                if(regexpr("h3k27me3",tolower(marks[i]))>0) {
                    markcolor[i,]=c(0,0,200);
                }
                if(regexpr("h3k79me2",tolower(marks[i]))>0) {
                    markcolor[i,]=c(200,0,200);
                }
                if(regexpr("h4k20me1",tolower(marks[i]))>0) {
                    markcolor[i,]=c(50,200,50);
                }
                if(regexpr("ctcf",tolower(marks[i]))>0) {
                    markcolor[i,]=c(200,0,250);
                }
            }
        }
        sc = state_color(data_matrix, markcolor)[,2];
    }
    rect(rep(p+0.2,l), 1:l-0.8, rep(p+0.8,l), 1:l-0.2, col=sc);
    palette(defpalette);
    dev.off();
}

# Read the inputs.
para_files <- list.files(path=input_dir, pattern="*.para", full.names=TRUE);
for (i in 1:length(para_files) {
    para_file <- para_files[i];
    para_file_base_name <- strsplit(para_file, ".para", fixed=TRUE)[1];
    output_file_name <- paste(opt$output_dir, "/", para_file_base_name, ".pdf", sep="");
    data_frame <- read.table(para_file, comment="!", header=T);
    create_heatmap(data_frame, output_file_name);
}