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66
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1 #!/usr/bin/env Rscript
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2
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3 create_heatmap<-function(data_frame, output_file_name=NULL) {
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4 # Plot a heatmap for a .para / .state combination
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5 # based on the received data_frame which was created
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6 # by reading the .para file.
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7 num_columns = dim(data_frame)[2];
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8 num_rows = dim(data_frame)[1];
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9 p = (sqrt(9 + 8 * (num_columns-1)) - 3) / 2;
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82
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10 data_matrix = as.matrix(data_frame[,1+1:p] / data_frame[,1]);
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11 colnames(data_matrix) = colnames(data_frame)[1+1:p];
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12 histone_marks = colnames(data_matrix);
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13 rownames(data_matrix) = paste(1:num_rows-1, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep="");
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14 if (!is.null(output_file_name)) {
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15 # Open the output PDF file.
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16 pdf(file=output_file_name);
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17 }
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18 # Set graphical parameters.
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19 par(mar=c(6, 1, 1, 6));
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20 # Create a vector containing the minimum and maximum values in data_matrix.
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21 min_max_vector = range(data_matrix);
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22 # Create a color palette.
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23 my_palette = colorRampPalette(c("white", "dark blue"))(n=100);
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24 defpalette = palette(my_palette);
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25 # Plot the heatmap for the current .para / .state combination.
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26 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);
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27 axis(1, at=1:p-0.5, labels=colnames(data_matrix), las=2);
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28 axis(4, at=1:num_rows-0.5, labels=rownames(data_matrix), las=2);
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29 col = round((t(data_matrix) - min_max_vector[1]) / (min_max_vector[2] - min_max_vector[1]) * 100);
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30 rect(rep(1:p-1, num_rows), rep(1:num_rows-1, each=p), rep(1:p, num_rows), rep(1:num_rows, each=p), col=col);
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31 histone_mark_color = t(col2rgb(terrain.colors(ceiling(p))[1:p]));
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32
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33 # Specify a color for common feature names like "h3k4me3".
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34 # These are histone marks frequently used to identify
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35 # promoter activities in a cell, and are often displayed
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36 # in shades of red.
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37 for(i in 1:length(histone_marks)) {
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38 if(regexpr("h3k4me3", tolower(histone_marks[i])) > 0) {
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39 histone_mark_color[i,] = c(255, 0, 0);
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40 }
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41 if(regexpr("h3k4me2", tolower(histone_marks[i])) > 0) {
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42 histone_mark_color[i,] = c(250, 100, 0);
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43 }
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44 if(regexpr("h3k4me1", tolower(histone_marks[i])) > 0) {
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45 histone_mark_color[i,] = c(250, 250, 0);
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46 }
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47 if(regexpr("h3k36me3", tolower(histone_marks[i]))>0) {
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48 histone_mark_color[i,] = c(0, 150, 0);
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49 }
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50 if(regexpr("h2a", tolower(histone_marks[i])) > 0) {
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51 histone_mark_color[i,] = c(0, 150, 150);
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52 }
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53 if(regexpr("dnase", tolower(histone_marks[i])) > 0) {
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54 histone_mark_color[i,] = c(0, 200, 200);
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55 }
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56 if(regexpr("h3k9ac", tolower(histone_marks[i])) > 0) {
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57 histone_mark_color[i,] = c(250, 0, 200);
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58 }
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59 if(regexpr("h3k9me3", tolower(histone_marks[i])) > 0) {
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60 histone_mark_color[i,] = c(100, 100, 100);
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61 }
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62 if(regexpr("h3k27ac", tolower(histone_marks[i])) > 0) {
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63 histone_mark_color[i,] = c(250, 150, 0);
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64 }
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65 if(regexpr("h3k27me3", tolower(histone_marks[i])) > 0) {
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66 histone_mark_color[i,] = c(0, 0, 200);
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67 }
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68 if(regexpr("h3k79me2", tolower(histone_marks[i])) > 0) {
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69 histone_mark_color[i,] = c(200, 0, 200);
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70 }
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71 if(regexpr("h4k20me1", tolower(histone_marks[i])) > 0) {
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72 histone_mark_color[i,] = c(50, 200, 50);
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73 }
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74 if(regexpr("ctcf", tolower(histone_marks[i])) > 0) {
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75 histone_mark_color[i,] = c(200, 0, 250);
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76 }
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82
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77 state_color = get_state_color(data_matrix, histone_mark_color)[,2];
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66
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78 }
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82
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79 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);
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80 palette(defpalette);
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81 if (!is.null(output_file_name)) {
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82 dev.off();
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83 }
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84 return(state_color);
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85 }
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86
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87 get_state_color <- function(data_matrix, histone_mark_color) {
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88 range_vector = apply(data_matrix, 1, range);
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89 mm = NULL;
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90 for(i in 1:dim(data_matrix)[1]) {
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91 range_val1 = range_vector[1, i] + 1e-10;
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92 range_val2 = range_vector[2, i];
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93 mm = rbind(mm, (data_matrix[i,] - range_val1) / (range_val2 - range_val1));
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94 }
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95 mm = mm^5;
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96 if(dim(mm)[2] > 1) {
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97 mm = mm / (apply(mm, 1, sum) + 1e-10);
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98 }
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99 state_color = mm%*%histone_mark_color;
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100 s = apply(data_matrix, 1, max);
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101 s = (s - min(s)) / (max(s) - min(s) + 1e-10);
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102 state_color = round(255 - (255 - state_color) * s/0.5);
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103 state_color[state_color<0] = 0;
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104 rt = paste(state_color[,1], state_color[,2], state_color[,3], sep=",");
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105 h = t(apply(state_color, 1, function(x){rgb2hsv(x[1], x[2], x[3])}));
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106 h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])});
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107 rt = cbind(rt, h);
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108 return(rt);
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109 }
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