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comparison CEMiTool.R @ 1:53230429a90c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool commit 90f5b1b6df8661779e097330e1f11346c6f388fc
author iuc
date Mon, 19 Aug 2024 10:47:06 +0000
parents a081fc047ccb
children
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0:a081fc047ccb 1:53230429a90c
2 library(CEMiTool, quietly = TRUE, warn.conflicts = FALSE) 2 library(CEMiTool, quietly = TRUE, warn.conflicts = FALSE)
3 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE) 3 library(ggplot2, quietly = TRUE, warn.conflicts = FALSE)
4 library(getopt, quietly = TRUE, warn.conflicts = FALSE) 4 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
5 # setup R error handling to go to stderr 5 # setup R error handling to go to stderr
6 options( 6 options(
7 show.error.messages = FALSE, 7 show.error.messages = FALSE,
8 error = function() { 8 error = function() {
9 cat(geterrmessage(), file = stderr()) 9 cat(geterrmessage(), file = stderr())
10 q("no", 1, FALSE) 10 q("no", 1, FALSE)
11 } 11 }
12 ) 12 )
13 13
14 # we need that to not crash galaxy with an UTF8 error on German LC settings. 14 # we need that to not crash galaxy with an UTF8 error on German LC settings.
15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") 15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
16 16
21 # Collect arguments from command line 21 # Collect arguments from command line
22 args <- commandArgs(trailingOnly = TRUE) 22 args <- commandArgs(trailingOnly = TRUE)
23 23
24 # Get options, using the spec as defined by the enclosed list. 24 # Get options, using the spec as defined by the enclosed list.
25 # Read the options from the default: commandArgs(TRUE). 25 # Read the options from the default: commandArgs(TRUE).
26 spec <- matrix(c( 26 spec <- matrix(
27 "expressionMatrix", "M", 1, "character", 27 c(
28 "sampleAnnotation", "A", 2, "character", 28 "expressionMatrix", "M", 1, "character",
29 "pathwayList", "P", 2, "character", 29 "sampleAnnotation", "A", 2, "character",
30 "interactions", "I", 2, "character", 30 "pathwayList", "P", 2, "character",
31 "filter", "f", 1, "logical", 31 "interactions", "I", 2, "character",
32 "filter_pval", "i", 1, "numeric", 32 "set_beta", "B", 1, "integer",
33 "apply_vst", "a", 1, "logical", 33 "filter", "f", 1, "logical",
34 "n_genes", "n", 1, "integer", 34 "filter_pval", "i", 1, "numeric",
35 "eps", "e", 1, "numeric", 35 "apply_vst", "a", 1, "logical",
36 "cor_method", "c", 1, "character", 36 "n_genes", "n", 1, "integer",
37 "cor_function", "y", 1, "character", 37 "eps", "e", 1, "numeric",
38 "network_type", "x", 1, "character", 38 "cor_method", "c", 1, "character",
39 "tom_type", "t", 1, "character", 39 "cor_function", "y", 1, "character",
40 "merge_similar", "m", 1, "logical", 40 "network_type", "x", 1, "character",
41 "rank_method", "r", 1, "character", 41 "tom_type", "t", 1, "character",
42 "min_ngen", "g", 1, "integer", 42 "merge_similar", "m", 1, "logical",
43 "diss_thresh", "d", 1, "numeric", 43 "rank_method", "r", 1, "character",
44 "center_func", "h", 1, "character", 44 "min_ngen", "g", 1, "integer",
45 "ora_pval", "o", 1, "numeric", 45 "diss_thresh", "d", 1, "numeric",
46 "gsea_scale", "l", 1, "logical", 46 "center_func", "h", 1, "character",
47 "gsea_min_size", "w", 1, "integer", 47 "ora_pval", "o", 1, "numeric",
48 "gsea_max_size", "z", 1, "integer", 48 "gsea_scale", "l", 1, "logical",
49 "sample_column_name", "v", 1, "character"), 49 "gsea_min_size", "w", 1, "integer",
50 byrow = TRUE, ncol = 4 50 "gsea_max_size", "z", 1, "integer",
51 "sample_column_name", "v", 1, "character"
52 ),
53 byrow = TRUE, ncol = 4
51 ) 54 )
52 55
53 opt <- getopt(spec) 56 opt <- getopt(spec)
54 counts <- read.table( 57 counts <- read.table(
55 opt$expressionMatrix, 58 opt$expressionMatrix,
56 header = TRUE, 59 header = TRUE,
57 sep = "\t", 60 sep = "\t",
58 strip.white = TRUE, 61 strip.white = TRUE,
59 stringsAsFactors = FALSE, 62 stringsAsFactors = FALSE,
60 check.names = FALSE 63 check.names = FALSE
61 ) 64 )
62 65
63 66
64 # Run CEMiTool 67 # Run CEMiTool
65 68
66 if (is.null(opt$sampleAnnotation)) { 69 if (is.null(opt$sampleAnnotation)) {
67 cem <- cemitool( 70 cem <- cemitool(
68 counts, 71 counts,
69 filter = opt$filter, 72 filter = opt$filter,
70 filter_pval = opt$filter_pval, 73 filter_pval = opt$filter_pval,
71 apply_vst = opt$apply_vst, 74 apply_vst = opt$apply_vst,
72 n_genes = opt$n_genes, 75 n_genes = opt$n_genes,
73 eps = opt$eps, 76 eps = opt$eps,
74 cor_method = opt$cor_method, 77 cor_method = opt$cor_method,
75 cor_function = opt$cor_function, 78 cor_function = opt$cor_function,
76 network_type = opt$network_type, 79 network_type = opt$network_type,
77 tom_type = opt$tom_type, 80 tom_type = opt$tom_type,
78 merge_similar = opt$merge_similar, 81 merge_similar = opt$merge_similar,
79 min_ngen = opt$min_ngen, 82 min_ngen = opt$min_ngen,
80 diss_thresh = opt$diss_thresh, 83 diss_thresh = opt$diss_thresh,
81 center_func = opt$center_func, 84 center_func = opt$center_func,
82 verbose = TRUE, 85 verbose = TRUE,
83 ora_pval = opt$ora_pval 86 ora_pval = opt$ora_pval,
84 ) 87 set_beta = opt$set_beta
88 )
85 } else { 89 } else {
86 annotation <- read.table( 90 annotation <- read.table(
87 opt$sampleAnnotation, 91 opt$sampleAnnotation,
88 header = TRUE, 92 header = TRUE,
89 sep = "\t", 93 sep = "\t",
90 strip.white = TRUE, 94 strip.white = TRUE,
91 stringsAsFactors = FALSE, 95 stringsAsFactors = FALSE,
92 check.names = FALSE 96 check.names = FALSE
93 ) 97 )
94 cem <- cemitool( 98 cem <- cemitool(
95 counts, 99 counts,
96 annotation, 100 annotation,
97 filter = opt$filter, 101 filter = opt$filter,
98 filter_pval = opt$filter_pval, 102 filter_pval = opt$filter_pval,
99 apply_vst = opt$apply_vst, 103 apply_vst = opt$apply_vst,
100 n_genes = opt$n_genes, 104 n_genes = opt$n_genes,
101 eps = opt$eps, 105 eps = opt$eps,
102 cor_method = opt$cor_method, 106 cor_method = opt$cor_method,
103 cor_function = opt$cor_function, 107 cor_function = opt$cor_function,
104 network_type = opt$network_type, 108 network_type = opt$network_type,
105 tom_type = opt$tom_type, 109 tom_type = opt$tom_type,
106 merge_similar = opt$merge_similar, 110 merge_similar = opt$merge_similar,
107 min_ngen = opt$min_ngen, 111 min_ngen = opt$min_ngen,
108 diss_thresh = opt$diss_thresh, 112 diss_thresh = opt$diss_thresh,
109 center_func = opt$center_func, 113 center_func = opt$center_func,
110 verbose = TRUE, 114 verbose = TRUE,
111 ora_pval = opt$ora_pval, 115 ora_pval = opt$ora_pval,
112 sample_name_column = opt$sample_column_name, 116 sample_name_column = opt$sample_column_name,
113 class_column = "Class", 117 class_column = "Class",
114 order_by_class = TRUE 118 order_by_class = TRUE
115 ) 119 )
116 cem <- mod_gsea( 120 cem <- mod_gsea(
117 cem, 121 cem,
118 gsea_scale = opt$gsea_scale, 122 gsea_scale = opt$gsea_scale,
119 gsea_min_size = opt$gsea_min_size, 123 gsea_min_size = opt$gsea_min_size,
120 gsea_max_size = opt$gsea_max_size, 124 gsea_max_size = opt$gsea_max_size,
121 rank_method = opt$rank_method 125 rank_method = opt$rank_method
122 ) 126 )
123 cem <- plot_gsea(cem) 127 cem <- plot_gsea(cem)
124 } 128 }
125 129
126 if (!is.null(opt$pathwayList)) { 130 if (!is.null(opt$pathwayList)) {
127 gmt_in <- read_gmt(opt$pathwayList) 131 gmt_in <- read_gmt(opt$pathwayList)
128 cem <- mod_ora(cem, gmt_in) 132 cem <- mod_ora(cem, gmt_in)
129 cem <- plot_ora(cem) 133 cem <- plot_ora(cem)
130 } 134 }
131 135
132 if (!is.null(opt$interactions)) { 136 if (!is.null(opt$interactions)) {
133 interactions <- read.table( 137 interactions <- read.table(
134 opt$interactions, 138 opt$interactions,
135 header = TRUE, 139 header = TRUE,
136 sep = "\t", 140 sep = "\t",
137 strip.white = TRUE, 141 strip.white = TRUE,
138 stringsAsFactors = FALSE, 142 stringsAsFactors = FALSE,
139 check.names = FALSE 143 check.names = FALSE
140 ) 144 )
141 interactions_data(cem) <- interactions # add interactions 145 interactions_data(cem) <- interactions # add interactions
142 cem <- plot_interactions(cem) 146 cem <- plot_interactions(cem)
143 } 147 }
144 148
145 ## Write analysis results into files 149 ## Write analysis results into files
146 write_files(cem, 150 write_files(cem,
147 directory = "./Tables", 151 directory = "./Tables",
148 force = TRUE) 152 force = TRUE
153 )
149 154
150 generate_report(cem) 155 generate_report(cem)
151 156
152 save_plots(cem, 157 save_plots(cem,
153 value = "all", 158 value = "all",
154 directory = "./Plots", 159 directory = "./Plots",
155 force = TRUE) 160 force = TRUE
161 )