Mercurial > repos > ppericard > mixomics_blocksplsda

comparison circleCor_wrapper.R @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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children b0ab97ffc2a1
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2:655d1fbcd3e6 3:0a3c83f2197a
1 #!/usr/bin/env Rscript
2
3 # Setup R error handling to go to stderr
4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
5
6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
8
9 ## Get parameters ##
10 suppressPackageStartupMessages(require(argparse))
11
12 parser <- ArgumentParser(description='Run the circleCor function')
13
14 parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file")
15 parser$add_argument('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector")
16 parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables")
17 parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min")
18 parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max")
19 parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min")
20 parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max")
21 parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file")
22 parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file")
23
24 args <- parser$parse_args()
25
26 ## Print parameters
27 print("Input RData:")
28 print(args$input_rdata)
29 print("Blocks vector:")
30 print(args$blocks_vec)
31 print("Response variables:")
32 print(args$responses_var)
33 print("X min:")
34 print(args$x_min)
35 print("X max:")
36 print(args$x_max)
37 print("Y min:")
38 print(args$y_min)
39 print("Y max:")
40 print(args$y_max)
41 print("Output variables file:")
42 print(args$output_var)
43 print("Output PDF file:")
44 print(args$output_pdf)
45
46 ## Loading libraries
47 suppressPackageStartupMessages(require(ellipse))
48 suppressPackageStartupMessages(require(grDevices))
49 suppressPackageStartupMessages(require(RColorBrewer))
50 # suppressPackageStartupMessages(require(mixOmics))
51
52
53 # R script call
54 source_local <- function(fname)
55 {
56 argv <- commandArgs(trailingOnly = FALSE)
57 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
58 source(paste(base_dir, fname, sep="/"))
59 }
60 ## Loading local functions
61 source_local("Integration_block_splsda_fonc.R")
62
63 load(args$input_rdata)
64
65 blocks_vector = strsplit(args$blocks_vec, ",")[[1]]
66 response_variables = strsplit(args$responses_var, ",")[[1]]
67
68
69 print("liste_vec_indice_blockSelect:")
70 print(liste_vec_indice_blockSelect)
71 print("liste_vec_blocks:")
72 print(liste_vec_blocks)
73 print("Mat cor comp1:")
74 print(mat_cor_comp1)
75 print("blocks_vector:")
76 print(blocks_vector)
77
78
79
80 pdf(args$output_pdf, width=12, height=9)
81
82 varSelect = circleCor(liste_dataframe_cor_comp_var_global = liste_dataframe_cor_comp_var_global,
83 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
84 mat_cor_comp1 = mat_cor_comp1,
85 mat_cor_comp2 = mat_cor_comp2,
86 vec_blocks = blocks_vector,
87 nomsVarReponses = response_variables,
88 min.X = args$x_min,
89 max.X = args$x_max,
90 min.Y = args$y_min,
91 max.Y = args$y_max,
92 cutoff = 0.85,
93 rad.in = 0.5,
94 cex = 0.7,
95 cex_legend = 0.8,
96 pos = c(1.2, 0),
97 pch = 20,
98 inset = c(-0.25, 0))
99
100 dev.off()
101
102 write(varSelect, file=args$output_var, ncolumns=1)