--- a/create_heatmap.R	Tue Dec 12 10:47:26 2017 -0500
+++ b/create_heatmap.R	Fri Dec 15 10:25:34 2017 -0500
@@ -11,112 +11,113 @@
 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));
+create_heatmap<-function(data_frame, output_file_name) {
+    # Plot a heatmap for a .para / .state combination
+    # based on the received data_frame which was created
+    # by reading the .para file.
+    num_columns = dim(data_frame)[2];
+    num_rows = dim(data_frame)[1];
+    p = (sqrt(9 + 8 * (num_columns - 1)) - 3) / 2;
+    data_matrix = as.matrix(data_frame[,1+1:p] / data_frame[,1]);
+    column_names(data_matrix) = column_names(data_frame)[1+1:p];
+    marks = column_names(data_matrix);
+    row_names(data_matrix) = paste(1:num_rows, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep="");
+
+    # Open the output PDF file.
+    pdf(file=output_file_name);
+    # Set graphical parameters.
+    par(mar=c(6, 1, 1, 6));
+    # Create a vector containing the minimum and maximum values in data_matrix.
+    min_max_vector = range(data_matrix);
+    # Define colors for the palette.
+    colors = 0:100 / 100 * (min_max_vector[2] - min_max_vector[1]) + min_max_vector[1];
+    # Create the color palette.
+    my_palette = colorRampPalette(c("white", "dark blue"))(n=100);
+    defpalette = palette(my_palette);
+    # Plot the heatmap for the current .para / .state combination.
+    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=column_names(data_matrix), las=2);
+    axis(4, at=1:num_rows-0.5, labels=row_names(data_matrix), las=2);
+    rect(rep(1:p-1, num_rows), rep(1:num_rows, each=p), rep(1:p, num_rows), rep(1:num_rows, each=p),
+            col=round((t(data_matrix)-min_max_vector[1])/(min_max_vector[2]-min_max_vector[1])*100));
+    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);
+        }
+        state_color = get_state_color(data_matrix, markcolor)[,2];
     }
+    rect(rep(p+0.2,num_rows), 1:num_rows-0.8, rep(p+0.8,num_rows), 1:num_rows-0.2, col=state_color);
+    palette(defpalette);
+    dev.off();
+}
 
-    rg = apply(statemean, 1, range);
-    mm = NULL;
+get_state_color<-function(statemean, 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 = rbind(mm, (statemean[i,]-rg[1,i]+1e-10)/(rg[2,i]-rg[1,i]+1e-10));
     }
-    mm = mm^6;
+    mm = mm^5;
     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);
+    s = (s-min(s)) / (max(s)-min(s) + 1e-10);
+    mycol = round(255-(255-mycol)*s/0.5);
+    mycol[mycol<0] = 0;
+    rt = paste(mycol[,1], mycol[,2], mycol[,3], sep=",");
     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);
+    rt = cbind(rt, 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=opt$input_dir, pattern="\\.para$", full.names=TRUE);
 for (i in 1:length(para_files)) {
     para_file <- para_files[i];
     para_file_base_name <- strsplit(para_file, split="/")[[1]][2]
     output_file_name <- gsub(".para", ".pdf", para_file_base_name)
-    output_file_path <- paste(opt$output_dir, "/", output_file_name, sep="");
+    output_file_path <- paste(opt$output_dir, output_file_name, sep="/");
     data_frame <- read.table(para_file, comment="!", header=T);
     create_heatmap(data_frame, output_file_path);
 }