From 1521cc708282a6f1f15c1e38ffa6d89e3f90270e Mon Sep 17 00:00:00 2001 From: svarona Date: Wed, 14 Aug 2024 16:39:25 +0200 Subject: [PATCH] Created option to pass date specific order --- .../time_series_differential_expression.R | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/time_series_differential_expression.R b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/time_series_differential_expression.R index 57d1725f..ce5b964e 100644 --- a/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/time_series_differential_expression.R +++ b/bu_isciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/time_series_differential_expression.R @@ -41,7 +41,8 @@ option_list <- list( make_option(c("-c", "--clinical_data" ), type="character" , default='../clinical_data.txt' , metavar="path" , help="Path to clinical data file" ), make_option(c("-g", "--group_col" ), type="character" , default='Group' , metavar="string" , help="Colname with the sample classes in sample_data of the experiment for the DE." ), make_option(c("-n", "--norm_counts" ), type="logical" , default=FALSE , metavar="boolean", help="Create table with normalized counts" ), - make_option(c("-q", "--quality_plots" ), type="logical" , default=TRUE , metavar="boolean", help="Create quality plots or not." ) + make_option(c("-q", "--quality_plots" ), type="logical" , default=TRUE , metavar="boolean", help="Create quality plots or not." ), + make_option(c("-t", "--time_order" ), type="character" , default=NULL , metavar="string" , help="Order to plot the dates as list, eg: 15D,45D,3M." ) ) opt_parser <- OptionParser(option_list=option_list) @@ -51,6 +52,14 @@ cat(blue$bold("########################\nRunning analysis with the following par cat(blue("-Path to RNAseq input folder: ")) + cat(blue(opt$rnaseq_dir))+cat(blue("\n")) cat(blue("-Path to samples clinical data: ")) + cat(blue(opt$clinical_data))+cat(blue("\n")) cat(blue("-Column with the group info: ")) + cat(blue(opt$group_col))+cat(blue("\n")) + +if (is.null(opt$time_order)) { + print_help(opt_parser) + stop("You need to specify the order for the dates.", call.=FALSE) +} else { + time_order <- unlist(strsplit(opt$time_order, ",")) +} + if (opt$norm_counts) { cat(blue("-Saving normalized counts to file\n")) } else{ @@ -62,6 +71,7 @@ if (opt$quality_plots) { cat(blue("-Skipping quality plots\n")) } +cat(blue("Time order: ")) + cat(blue(time_order)) +cat(blue("\n")) ################################################ ################################################