Mercurial > repos > iuc > cemitool

annotate CEMiTool.R @ 2:9d93999d9028 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit f5a9be967de99a62addf6b3c7c01a10ba3572466
author iuc
date Thu, 22 Aug 2024 17:49:08 +0000
parents 81bffdf16b71
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
1 # Load all required libraries
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
2 library(CEMiTool, quietly = TRUE, warn.conflicts = FALSE)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
3 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
4 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
5 # setup R error handling to go to stderr
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
6 options(
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
7 show.error.messages = FALSE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
8 error = function() {
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
9 cat(geterrmessage(), file = stderr())
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
10 q("no", 1, FALSE)
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
11 }
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
12 )
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
13
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
14 # we need that to not crash galaxy with an UTF8 error on German LC settings.
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
16
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
17 ################################################################################
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
18 ### Input Processing
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
19 ################################################################################
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
20
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
21 # Collect arguments from command line
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
22 args <- commandArgs(trailingOnly = TRUE)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
23
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
24 # Get options, using the spec as defined by the enclosed list.
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
25 # Read the options from the default: commandArgs(TRUE).
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
26 spec <- matrix(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
27 c(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
28 "expressionMatrix", "M", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
29 "sampleAnnotation", "A", 2, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
30 "pathwayList", "P", 2, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
31 "interactions", "I", 2, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
32 "set_beta", "B", 1, "integer",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
33 "filter", "f", 1, "logical",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
34 "filter_pval", "i", 1, "numeric",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
35 "apply_vst", "a", 1, "logical",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
36 "n_genes", "n", 1, "integer",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
37 "eps", "e", 1, "numeric",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
38 "cor_method", "c", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
39 "cor_function", "y", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
40 "network_type", "x", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
41 "tom_type", "t", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
42 "merge_similar", "m", 1, "logical",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
43 "rank_method", "r", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
44 "min_ngen", "g", 1, "integer",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
45 "diss_thresh", "d", 1, "numeric",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
46 "center_func", "h", 1, "character",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
47 "ora_pval", "o", 1, "numeric",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
48 "gsea_scale", "l", 1, "logical",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
49 "gsea_min_size", "w", 1, "integer",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
50 "gsea_max_size", "z", 1, "integer",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
51 "sample_column_name", "v", 1, "character"
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
52 ),
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
53 byrow = TRUE, ncol = 4
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
54 )
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
55
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
56 opt <- getopt(spec)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
57 counts <- read.table(
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
58 opt$expressionMatrix,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
59 header = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
60 sep = "\t",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
61 strip.white = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
62 stringsAsFactors = FALSE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
63 check.names = FALSE
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
64 )
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
65
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
66
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
67 # Run CEMiTool
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
68
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
69 if (is.null(opt$sampleAnnotation)) {
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
70 cem <- cemitool(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
71 counts,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
72 filter = opt$filter,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
73 filter_pval = opt$filter_pval,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
74 apply_vst = opt$apply_vst,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
75 n_genes = opt$n_genes,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
76 eps = opt$eps,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
77 cor_method = opt$cor_method,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
78 cor_function = opt$cor_function,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
79 network_type = opt$network_type,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
80 tom_type = opt$tom_type,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
81 merge_similar = opt$merge_similar,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
82 min_ngen = opt$min_ngen,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
83 diss_thresh = opt$diss_thresh,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
84 center_func = opt$center_func,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
85 verbose = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
86 ora_pval = opt$ora_pval,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
87 set_beta = opt$set_beta
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
88 )
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
89 } else {
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
90 annotation <- read.table(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
91 opt$sampleAnnotation,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
92 header = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
93 sep = "\t",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
94 strip.white = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
95 stringsAsFactors = FALSE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
96 check.names = FALSE
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
97 )
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
98 cem <- cemitool(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
99 counts,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
100 annotation,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
101 filter = opt$filter,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
102 filter_pval = opt$filter_pval,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
103 apply_vst = opt$apply_vst,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
104 n_genes = opt$n_genes,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
105 eps = opt$eps,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
106 cor_method = opt$cor_method,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
107 cor_function = opt$cor_function,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
108 network_type = opt$network_type,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
109 tom_type = opt$tom_type,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
110 merge_similar = opt$merge_similar,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
111 min_ngen = opt$min_ngen,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
112 diss_thresh = opt$diss_thresh,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
113 center_func = opt$center_func,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
114 verbose = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
115 ora_pval = opt$ora_pval,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
116 sample_name_column = opt$sample_column_name,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
117 class_column = "Class",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
118 order_by_class = TRUE
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
119 )
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
120 cem <- mod_gsea(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
121 cem,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
122 gsea_scale = opt$gsea_scale,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
123 gsea_min_size = opt$gsea_min_size,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
124 gsea_max_size = opt$gsea_max_size,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
125 rank_method = opt$rank_method
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
126 )
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
127 cem <- plot_gsea(cem)
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
128 }
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
129
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
130 if (!is.null(opt$pathwayList)) {
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
131 gmt_in <- read_gmt(opt$pathwayList)
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
132 cem <- mod_ora(cem, gmt_in)
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
133 cem <- plot_ora(cem)
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
134 }
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
135
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
136 if (!is.null(opt$interactions)) {
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
137 interactions <- read.table(
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
138 opt$interactions,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
139 header = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
140 sep = "\t",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
141 strip.white = TRUE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
142 stringsAsFactors = FALSE,
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
143 check.names = FALSE
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
144 )
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
145 interactions_data(cem) <- interactions # add interactions
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
146 cem <- plot_interactions(cem)
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
147 }
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
148
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
149 ## Write analysis results into files
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
150 write_files(cem,
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
151 directory = "./Tables",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
152 force = TRUE
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
153 )
0
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
154
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
155 generate_report(cem)
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
156
3f9ff31c88bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 07372bcbc3a94f886436a7263f4cfcb01981c7f3
iuc
parents:
diff changeset
157 save_plots(cem,
1
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
158 value = "all",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
159 directory = "./Plots",
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
160 force = TRUE
81bffdf16b71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
iuc
parents: 0
diff changeset
161 )