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comparison create_heatmaps.R @ 0:b785bcfe5cd0 draft default tip

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author greg
date Mon, 12 Feb 2018 09:52:26 -0500
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-1:000000000000 0:b785bcfe5cd0
1 #!/usr/bin/env Rscript
2
3 suppressPackageStartupMessages(library("optparse"))
4
5 option_list <- list(
6 make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
7 make_option(c("--output_dir"), action="store", dest="output_dir", help="PDF output directory"),
8 make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
9 make_option(c("--in_training_mode"), action="store_true", dest="in_training_mode", default=FALSE, help="Flag for training mode")
10 )
11
12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
13 args <- parse_args(parser, positional_arguments=TRUE);
14 opt <- args$options;
15
16 heatmap_path = paste(opt$script_dir, "create_heatmap.R", sep="/");
17 source(heatmap_path);
18
19 if (opt$in_training_mode) {
20 ext = ".para0";
21 pattern = "\\.para0$";
22 } else {
23 ext = ".para";
24 pattern = "\\.para$"
25 }
26 para_files = list.files(path=opt$input_dir, pattern=pattern, full.names=TRUE);
27 for (i in 1:length(para_files)) {
28 para_file = para_files[i];
29 para_file_base_name = strsplit(para_file, split="/")[[1]][2];
30 output_file_base_name = gsub(ext, "", para_file_base_name);
31 output_file_name = paste(output_file_base_name, "state", i, "pdf", sep=".");
32 output_file_path = paste(opt$output_dir, output_file_name, sep="/");
33 data_frame = read.table(para_file, comment="!", header=T);
34 create_heatmap(data_frame, output_file_path);
35 }