comparison create_heatmap.R @ 135:fc94a1ce21eb draft

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134:91db24a1384d

#!/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

    # 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));

    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)) {

135:fc94a1ce21eb

#!/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

    # 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]);
    colnames(data_matrix) = colnames(data_frame)[1+1:p];
    marks = colnames(data_matrix);
    rownames(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));

    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, num_rows), 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:num_rows-0.5, labels=rownames(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)) {