Mercurial > repos > melpetera > corr_table
comparison CorrTable/Corr_wrap.r @ 1:29ec7e3afdd4 draft
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| author | melpetera |
|---|---|
| date | Thu, 01 Aug 2019 11:30:58 -0400 |
| parents | b22c453e4cf4 |
| children | 2173ad5e7750 |
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| 0:b22c453e4cf4 | 1:29ec7e3afdd4 |
|---|---|
| 2 | 2 |
| 3 ################################################################################################ | 3 ################################################################################################ |
| 4 # WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE) # | 4 # WRAPPER FOR Corr_Script_samples_row.R (CORRELATION TABLE) # |
| 5 # # | 5 # # |
| 6 # Author: Ophelie BARBET # | 6 # Author: Ophelie BARBET # |
| 7 # Maintainer: Melanie PETERA # | |
| 7 # User: Galaxy # | 8 # User: Galaxy # |
| 8 # Original data: used with Corr_Script_samples_row.R # | 9 # Original data: used with Corr_Script_samples_row.R # |
| 9 # Starting date: # | 10 # Starting date: # |
| 10 # V-1: First version of wrapper # | 11 # V-1: First version of wrapper # |
| 12 # V-2: Corresponds to XML version 1.0.0 # | |
| 11 # # | 13 # # |
| 12 # # | 14 # # |
| 13 # Input files: 2 tables with common samples file # | 15 # Input files: 2 tables with common samples file # |
| 14 # Output files: Correlation table ; Heatmap file # | 16 # Output files: Correlation table ; Heatmap file # |
| 15 # # | 17 # # |
| 54 } | 56 } |
| 55 | 57 |
| 56 type_classes <- NULL | 58 type_classes <- NULL |
| 57 reg_class_value <- NULL | 59 reg_class_value <- NULL |
| 58 irreg_class_vect <- NULL | 60 irreg_class_vect <- NULL |
| 61 if(args$plot_choice == "none"){args$color_heatmap <- "no"; args$heatmap_out <- NULL} | |
| 59 if(args$color_heatmap == "yes"){ | 62 if(args$color_heatmap == "yes"){ |
| 60 type_classes <- args$type_classes | 63 type_classes <- args$type_classes |
| 61 if(type_classes == "regular"){ | 64 if(type_classes == "regular"){ |
| 62 reg_class_value <- args$reg_class_value | 65 reg_class_value <- args$reg_class_value |
| 63 } else if(type_classes == "irregular"){ | 66 } else if(type_classes == "irregular"){ |
| 65 } | 68 } |
| 66 } | 69 } |
| 67 | 70 |
| 68 | 71 |
| 69 correlation.tab(args$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, | 72 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$heatmap_out) | 73 args$reorder_var, args$plot_choice, args$color_heatmap, type_classes, reg_class_value, irreg_class_vect, args$tabcorr_out, args$heatmap_out) |
| 71 | 74 |
| 72 | 75 |
| 73 cat('\n--------------------------------------------------------------------', | 76 cat('\n--------------------------------------------------------------------', |
| 74 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n') | 77 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n') |
| 75 sessionInfo() | 78 sessionInfo() |