Mercurial > repos > greg > ideas

comparison create_heatmaps.R @ 159:04db93e8566b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 12 Jan 2018 14:14:38 -0500
parents 08e77c105188
children 19142fc18b2d
comparison
equal deleted inserted replaced
158:c996089f1747 159:04db93e8566b
3 suppressPackageStartupMessages(library("optparse")) 3 suppressPackageStartupMessages(library("optparse"))
4 4
5 option_list <- list( 5 option_list <- list(
6 make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"), 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"), 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") 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")
9 ) 10 )
10 11
11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list); 12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
12 args <- parse_args(parser, positional_arguments=TRUE); 13 args <- parse_args(parser, positional_arguments=TRUE);
13 opt <- args$options; 14 opt <- args$options;
14 15
15 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/"); 16 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/");
16 source(heatmap_path); 17 source(heatmap_path);
17 18
18 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE); 19 if (opt$in_training_mode) {
20 ext <- ".para";
21 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE);
22 } else {
23 ext <- ".para0";
24 para_files <- list.files(path=opt$input_dir, pattern="\\.para0$", full.names=TRUE);
25 }
19 for (i in 1:length(para_files)) { 26 for (i in 1:length(para_files)) {
20 para_file <- para_files[i]; 27 para_file <- para_files[i];
21 para_file_base_name <- strsplit(para_file, split="/")[[1]][2]; 28 para_file_base_name <- strsplit(para_file, split="/")[[1]][2];
22 output_file_base_name <- gsub(".para", "", para_file_base_name); 29 output_file_base_name <- gsub(ext, "", para_file_base_name);
23 output_file_name <- paste(output_file_base_name, "state", i, "pdf", sep="."); 30 output_file_name <- paste(output_file_base_name, "state", i, "pdf", sep=".");
24 output_file_path <- paste(opt$output_dir, output_file_name, sep="/"); 31 output_file_path <- paste(opt$output_dir, output_file_name, sep="/");
25 data_frame <- read.table(para_file, comment="!", header=T); 32 data_frame <- read.table(para_file, comment="!", header=T);
26 create_heatmap(data_frame, output_file_path); 33 create_heatmap(data_frame, output_file_path);
27 } 34 }