Mercurial > repos > ppericard > viscorvar

comparison circleCor_wrapper.R @ 1:e93350dc99f1 draft

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"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,