Mercurial > repos > greg > ideas_genome_tracks

comparison create_heatmap.R @ 81:dcd4be407063 draft

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author greg
date Thu, 04 Jan 2018 12:31:46 -0500
parents efbc9e58c4eb
children cf0a62d084dc
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80:6d97ef6bf7b7 81:dcd4be407063
5 # based on the received data_frame which was created 5 # based on the received data_frame which was created
6 # by reading the .para file. 6 # by reading the .para file.
7 num_columns = dim(data_frame)[2]; 7 num_columns = dim(data_frame)[2];
8 num_rows = dim(data_frame)[1]; 8 num_rows = dim(data_frame)[1];
9 p = (sqrt(9 + 8 * (num_columns-1)) - 3) / 2; 9 p = (sqrt(9 + 8 * (num_columns-1)) - 3) / 2;
10 data_matrix = as.matrix(data_frame[,1+1:p] / data_frame[,1]); 10 data_matrix = as.matrix(data_frame[,1+1:p]/data_frame[,1]);
11 colnames(data_matrix) = colnames(data_frame)[1+1:p]; 11 colnames(data_matrix) = colnames(data_frame)[1+1:p];
12 histone_marks = colnames(data_matrix); 12 histone_marks = colnames(data_matrix);
13 rownames(data_matrix) = paste(1:num_rows-1, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep=""); 13 rownames(data_matrix) = paste(1:num_rows-1, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep="");
14 if (!is.null(output_file_name)) { 14 if (!is.null(output_file_name)) {
15 # Open the output PDF file. 15 # Open the output PDF file.
24 defpalette = palette(my_palette); 24 defpalette = palette(my_palette);
25 # Plot the heatmap for the current .para / .state combination. 25 # Plot the heatmap for the current .para / .state combination.
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); 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);
27 axis(1, at=1:p-0.5, labels=colnames(data_matrix), las=2); 27 axis(1, at=1:p-0.5, labels=colnames(data_matrix), las=2);
28 axis(4, at=1:num_rows-0.5, labels=rownames(data_matrix), las=2); 28 axis(4, at=1:num_rows-0.5, labels=rownames(data_matrix), las=2);
29 color = round((t(data_matrix) - min_max_vector[1]) / (min_max_vector[2] - min_max_vector[1]) * 100); 29 col = round((t(data_matrix) - min_max_vector[1]) / (min_max_vector[2] - min_max_vector[1]) * 100);
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=color); 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);
31 histone_mark_color = t(col2rgb(terrain.colors(ceiling(p))[1:p])); 31 histone_mark_color = t(col2rgb(terrain.colors(ceiling(p))[1:p]));
32 32
33 # Specify a color for common feature names like "h3k4me3". 33 # Specify a color for common feature names like "h3k4me3".
34 # These are histone marks frequently used to identify 34 # These are histone marks frequently used to identify
35 # promoter activities in a cell, and are often displayed 35 # promoter activities in a cell, and are often displayed