Mercurial > repos > spficklin > aurora_wgcna
changeset 14:4ec9d51ed4e0 draft
Uploaded
| author | spficklin |
|---|---|
| date | Fri, 22 Nov 2019 21:42:39 +0000 |
| parents | 2c8beaaa2374 |
| children | 3ed8495d7df7 |
| files | aurora_wgcna_render.R |
| diffstat | 1 files changed, 12 insertions(+), 15 deletions(-) [+] |
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--- a/aurora_wgcna_render.R Fri Nov 22 21:42:31 2019 +0000 +++ b/aurora_wgcna_render.R Fri Nov 22 21:42:39 2019 +0000 @@ -11,27 +11,21 @@ # We need to not crash galaxy with an UTF8 error on German LC settings. loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") -# suppress warning options(warn = -1) - -options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) - args = commandArgs(trailingOnly=TRUE) suppressPackageStartupMessages({ + library(rmarkdown) library(getopt) - library(tools) library(WGCNA) + library(caret) + library(ggplot2) + library(reshape2) + # Uncomment for HTML-based reports. + #library(DT) + #library(htmltools) }) -# Load libraries -library(rmarkdown) -library(WGCNA) -library(DT) -library(htmltools) -library(ggplot2) -library(reshape2) -library(caret) # ------------------------------------------------------------------ # Handle arguments from command line @@ -44,7 +38,8 @@ 'expression_data', 'e', 1, 'character', # Input Arguments - 'missing_value', 'i', 1, 'character', + 'missing_value1', 'i', 1, 'character', + 'missing_value2', 'o', 2, 'character', 'sname_col', 'c', 2, 'integer', 'min_cluster_size', 's', 1, 'integer', 'height_cut', 'h', 2, 'double', @@ -61,8 +56,10 @@ 'module_association_file', 'm', 2, 'character', 'module_association_report', 'q', 2, 'character', 'network_construction_report', 'r', 1, 'character', + 'updated_trait_matrix', 'z', 2, 'character', 'r_data', 'a', 1, 'character', - 'render_log_file', 'l', 1, 'character' + 'render_log_file', 'l', 1, 'character', + 'filtered_GEM', 'd', 1, 'character' ), byrow=TRUE, ncol=4)