comparison aurora_wgcna_render.R @ 14:4ec9d51ed4e0 draft

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13:2c8beaaa2374

})

# 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(getopt)
  library(tools)
  library(WGCNA)
})

# Load libraries
library(rmarkdown)
library(WGCNA)
library(DT)
library(htmltools)
library(ggplot2)
library(reshape2)
library(caret)

# ------------------------------------------------------------------
# Handle arguments from command line
# ------------------------------------------------------------------

    # Input Files
    'trait_data',                  't', 2, 'character',
    'expression_data',             'e', 1, 'character',

    # Input Arguments
    'missing_value',               'i', 1, 'character',
    'sname_col',                   'c', 2, 'integer',
    'min_cluster_size',            's', 1, 'integer',
    'height_cut',                  'h', 2, 'double',
    'power',                       'p', 2, 'double',
    'block_size',                  'b', 1, 'integer',

    'network_edges_file',          'w', 1, 'character',
    'gene_association_file',       'g', 2, 'character',
    'module_association_file',     'm', 2, 'character',
    'module_association_report',   'q', 2, 'character',
    'network_construction_report', 'r', 1, 'character',
    'r_data',                      'a', 1, 'character',
    'render_log_file',             'l', 1, 'character'
  ),
  byrow=TRUE, ncol=4)

opt = getopt(spec)

14:4ec9d51ed4e0

})

# We need  to not crash galaxy with an UTF8 error on German LC settings.
loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

options(warn = -1)
args = commandArgs(trailingOnly=TRUE)

suppressPackageStartupMessages({
  library(rmarkdown)
  library(getopt)
  library(WGCNA)
  library(caret)
  library(ggplot2)
  library(reshape2)
  # Uncomment for HTML-based reports.
  #library(DT)  
  #library(htmltools)
})


# ------------------------------------------------------------------
# Handle arguments from command line
# ------------------------------------------------------------------

    # Input Files
    'trait_data',                  't', 2, 'character',
    'expression_data',             'e', 1, 'character',

    # Input Arguments
    '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',
    'power',                       'p', 2, 'double',
    'block_size',                  'b', 1, 'integer',

    'network_edges_file',          'w', 1, 'character',
    'gene_association_file',       'g', 2, 'character',
    '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',
    'filtered_GEM',                'd', 1, 'character'
  ),
  byrow=TRUE, ncol=4)

opt = getopt(spec)