Mercurial > repos > spficklin > aurora_wgcna

comparison aurora_wgcna_render.R @ 2:9e8788803adc draft

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author spficklin
date Fri, 22 Nov 2019 19:45:39 -0500
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children 66fe92fa79f7
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1:c18d0db68d51 2:9e8788803adc
1 # ------------------------------------------------------------------
2 # Set options and load libraries.
3 # ------------------------------------------------------------------
4
5 # setup R error handline to go to stderr
6 options(show.error.messages=FALSE, error=function() {
7 cat(geterrmessage(), file=stderr())
8 quit("no", 1, F)
9 })
10
11 # We need to not crash galaxy with an UTF8 error on German LC settings.
12 loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
13
14 options(warn = -1)
15 args = commandArgs(trailingOnly=TRUE)
16
17 suppressPackageStartupMessages({
18 library(rmarkdown)
19 library(getopt)
20 library(WGCNA)
21 library(caret)
22 library(ggplot2)
23 library(reshape2)
24 # Uncomment for HTML-based reports.
25 #library(DT)
26 #library(htmltools)
27 })
28
29
30 # ------------------------------------------------------------------
31 # Handle arguments from command line
32 # ------------------------------------------------------------------
33
34 # Get the tool arguments.
35 spec = matrix(c(
36 # Input Files
37 'trait_data', 't', 2, 'character',
38 'expression_data', 'e', 1, 'character',
39
40 # Input Arguments
41 'missing_value1', 'i', 1, 'character',
42 'missing_value2', 'o', 2, 'character',
43 'sname_col', 'c', 2, 'integer',
44 'min_cluster_size', 's', 1, 'integer',
45 'height_cut', 'h', 2, 'double',
46 'power', 'p', 2, 'double',
47 'block_size', 'b', 1, 'integer',
48 'hard_threshold', 'j', 1, 'double',
49 'one_hot_cols', 'y', 2, 'character',
50 'ignore_cols', 'x', 2, 'character',
51
52 # Output Files
53 'gene_module_file', 'k', 1, 'character',
54 'network_edges_file', 'w', 1, 'character',
55 'gene_association_file', 'g', 2, 'character',
56 'module_association_file', 'm', 2, 'character',
57 'module_association_report', 'q', 2, 'character',
58 'network_construction_report', 'r', 1, 'character',
59 'updated_trait_matrix', 'z', 2, 'character',
60 'r_data', 'a', 1, 'character',
61 'render_log_file', 'l', 1, 'character',
62 'filtered_GEM', 'd', 1, 'character'
63 ),
64 byrow=TRUE, ncol=4)
65
66 opt = getopt(spec)
67
68 # We have to have values for the one_hot_cols and ignore_cols but the
69 # fact these are optional means that we might not get a value for them and the
70 # getopt function will then leave them out. So, we need to make sure they are
71 # there.
72 if (!"one_hot_cols" %in% names(opt)) {
73 opt[["one_hot_cols"]] <- ''
74 }
75 if (!"ignore_cols" %in% names(opt)) {
76 opt[["ignore_cols"]] <- ''
77 }
78
79 # Define environment variables for all input values. This will allow use
80 # of the input arguments in the Rmarkdown template file.
81 do.call(Sys.setenv, opt[-1])
82
83 # ------------------------------------------------------------------
84 # Render Rmd files
85 # ------------------------------------------------------------------
86 tool_directory = Sys.getenv('TOOL_INSTALL_DIR')
87
88
89 # We don't want the Rmarkdown STDOUT to show up in Galaxy, so save it to a file.
90 zz = file(opt$render_log_file)
91 sink(zz)
92 sink(zz, type = 'message')
93
94 # Print the options
95 print(opt)
96
97 # Next render the R markdown template file.
98 system(command = paste0('cp ', tool_directory, '/aurora_wgcna.Rmd ./'))
99 render(input = 'aurora_wgcna.Rmd', output_file = opt$network_construction_report)
100
101 # If the trait data was provided then we'll continue the
102 # analysis.
103 if (!is.null(opt$trait_data)) {
104 system(command = paste0('cp ', tool_directory, '/aurora_wgcna_trait.Rmd ./'))
105 render(input = 'aurora_wgcna_trait.Rmd', output_file = opt$module_association_report)
106 }
107
108 sink()