Mercurial > repos > ppericard > viscorvar
comparison circleCor_wrapper.R @ 1:e93350dc99f1 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
| author | ppericard |
|---|---|
| date | Thu, 15 Oct 2020 12:22:25 +0000 |
| parents | d0b77b926863 |
| children |
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| 0:d0b77b926863 | 1:e93350dc99f1 |
|---|---|
| 56 # suppressPackageStartupMessages(require(grDevices)) | 56 # suppressPackageStartupMessages(require(grDevices)) |
| 57 # suppressPackageStartupMessages(require(RColorBrewer)) | 57 # suppressPackageStartupMessages(require(RColorBrewer)) |
| 58 # suppressPackageStartupMessages(require(mixOmics)) | 58 # suppressPackageStartupMessages(require(mixOmics)) |
| 59 ## Loading local functions | 59 ## Loading local functions |
| 60 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") | 60 # source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") |
| 61 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) | 61 install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.5.tar.gz", repos=NULL) |
| 62 suppressPackageStartupMessages(require(visCorVar)) | 62 suppressPackageStartupMessages(require(visCorVar)) |
| 63 print("visCorVar has been loaded") | 63 print("visCorVar has been loaded") |
| 64 | 64 |
| 65 # R script call | 65 # R script call |
| 66 source_local <- function(fname) | 66 source_local <- function(fname) |
| 100 print("list_cor_comp_selected_var_resp_var:") | 100 print("list_cor_comp_selected_var_resp_var:") |
| 101 print(list_cor_comp_selected_var_resp_var) | 101 print(list_cor_comp_selected_var_resp_var) |
| 102 print("res_compute_cor_var_interest:") | 102 print("res_compute_cor_var_interest:") |
| 103 print(res_compute_cor_var_interest) | 103 print(res_compute_cor_var_interest) |
| 104 | 104 |
| 105 # Open output pdf file | 105 # Open output pdf file |
| 106 pdf(args$output_pdf, width=8, height=7) | 106 pdf(args$output_pdf, width=8, height=7) |
| 107 mar = c(5, 5, 2, 8) | 107 mar = c(5, 5, 2, 8) |
| 108 par(mar = mar) | 108 par(mar = mar) |
| 109 | 109 |
| 110 selected_variables = circleCor(list_dataframe_cor_comp_var_global = list_cor_comp_selected_var_resp_var, | 110 selected_variables = circleCor(list_dataframe_cor_comp_var_global = list_cor_comp_selected_var_resp_var, |
| 112 mat_cor_comp1 = mat_cor_comp1, | 112 mat_cor_comp1 = mat_cor_comp1, |
| 113 mat_cor_comp2 = mat_cor_comp2, | 113 mat_cor_comp2 = mat_cor_comp2, |
| 114 names_blocks = names_blocks, | 114 names_blocks = names_blocks, |
| 115 names_response_variables = names_response_variables, | 115 names_response_variables = names_response_variables, |
| 116 comp = comp, | 116 comp = comp, |
| 117 cutoff = 0.85, | 117 cutoff = 0.80, |
| 118 min.X = args$x_min, | 118 min.X = args$x_min, |
| 119 max.X = args$x_max, | 119 max.X = args$x_max, |
| 120 min.Y = args$y_min, | 120 min.Y = args$y_min, |
| 121 max.Y = args$y_max, | 121 max.Y = args$y_max, |
| 122 # vec_col = vec_col, | 122 # vec_col = vec_col, |