Mercurial > repos > melpetera > corr_table
comparison CorrTable/Corr_wrap.r @ 0:b22c453e4cf4 draft
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author | melpetera |
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date | Thu, 11 Oct 2018 05:35:55 -0400 |
parents | |
children | 29ec7e3afdd4 |
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-1:000000000000 | 0:b22c453e4cf4 |
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1 #!/usr/bin/Rscript --vanilla --slave --no-site-file | |
2 | |
3 ################################################################################################ | |
4 # WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE) # | |
5 # # | |
6 # Author: Ophelie BARBET # | |
7 # User: Galaxy # | |
8 # Original data: used with Corr_Script_samples_row.R # | |
9 # Starting date: # | |
10 # V-1: First version of wrapper # | |
11 # # | |
12 # # | |
13 # Input files: 2 tables with common samples file # | |
14 # Output files: Correlation table ; Heatmap file # | |
15 # # | |
16 ################################################################################################ | |
17 | |
18 | |
19 library(batch) #necessary for parseCommandArgs function | |
20 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects | |
21 | |
22 source_local <- function(...){ | |
23 argv <- commandArgs(trailingOnly = FALSE) | |
24 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
25 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))} | |
26 } | |
27 #Import the different functions | |
28 source_local("Corr_Script_samples_row.R") | |
29 | |
30 | |
31 if(length(args) < 10){ stop("NOT enough argument !!!") } | |
32 | |
33 | |
34 cat('\n--------------------------------------------------------------------', | |
35 '\nParameters used in "Between-table Correlation":\n\n') | |
36 print(args) | |
37 cat('--------------------------------------------------------------------\n\n') | |
38 | |
39 | |
40 risk_alpha <- NULL | |
41 correct_multi <- NULL | |
42 if(args$test_corr == "yes"){ | |
43 risk_alpha <- args$risk_alpha | |
44 correct_multi <- args$correct_multi | |
45 } | |
46 | |
47 filters_choice <- NULL | |
48 threshold <- NULL | |
49 if(args$filter == "yes"){ | |
50 filters_choice <- args$filters_choice | |
51 if(filters_choice == "filters_0_thr"){ | |
52 threshold <- args$threshold | |
53 } | |
54 } | |
55 | |
56 type_classes <- NULL | |
57 reg_class_value <- NULL | |
58 irreg_class_vect <- NULL | |
59 if(args$color_heatmap == "yes"){ | |
60 type_classes <- args$type_classes | |
61 if(type_classes == "regular"){ | |
62 reg_class_value <- args$reg_class_value | |
63 } else if(type_classes == "irregular"){ | |
64 irreg_class_vect <- eval(parse(text=paste0("c",args$irreg_class_vect))) | |
65 } | |
66 } | |
67 | |
68 | |
69 correlation.tab(args$tab1_in, args$tab2_in, args$tab1_samples, args$tab2_samples, args$corr_method, args$test_corr, risk_alpha, correct_multi, args$filter, filters_choice, threshold, | |
70 args$reorder_var, args$color_heatmap, type_classes, reg_class_value, irreg_class_vect, args$tabcorr_out, args$heatmap_out) | |
71 | |
72 | |
73 cat('\n--------------------------------------------------------------------', | |
74 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n') | |
75 sessionInfo() | |
76 cat('--------------------------------------------------------------------\n\n') | |
77 | |
78 | |
79 #delete the parameters to avoid the passage to the next tool in .RData image | |
80 rm(args) |