diff mixomics_blocksplsda_additional_funct.R @ 2:c8533e9298e5 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_blocksplsda_additional_funct.R	Fri Oct 23 10:15:56 2020 +0000
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+#' @title Determination of selected variables for all components
+#' @description The function unionSelectBlockVariables determines, for each block, the selected block variables
+#' for all components.
+#' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function 
+#' mixOmics.
+#' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for
+#' at least one component. Otherwise, this function returns 0.
+#' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with 
+#' this block variable. Otherwise the value 0 is associated with this block variable. 
+#' @examples 
+#' data(res_data_integration)
+#' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration)
+#' @export
+unionSelectBlockVariables <-function(res_block_splsda)
+{
+  ncomp = res_block_splsda$ncomp[1]
+  
+  names_blocks = names(res_block_splsda$loadings)
+  index_Y = which(names_blocks == "Y")
+  names_blocks = names_blocks[ - index_Y]
+  list_select_block_variables = list()
+  
+  for(i in 1:length(names_blocks))
+  {
+    mat_loadings_i = res_block_splsda$loadings[[i]]
+    index_i = c()
+    
+    for(j in 1:ncomp)
+    {
+      loadings_i_j = mat_loadings_i[, j]
+      index_i_j = which(loadings_i_j != 0)
+      
+      index_i = c(index_i, index_i_j)
+      
+    } # End for(j 1:ncomp).
+    
+    index_i = unique(index_i)
+    
+    mat_select_block_variables = matrix(0,
+                                        nrow = dim(mat_loadings_i)[1],
+                                        ncol = 1)
+    mat_select_block_variables[index_i, 1] = rep(1, length(index_i))
+    rownames(mat_select_block_variables) = rownames(mat_loadings_i)
+    
+    list_select_block_variables[[i]] = mat_select_block_variables
+    
+  } # End for(i in 1:length(names_blocks)).
+  
+  names(list_select_block_variables) = names_blocks
+  
+  return(list_select_block_variables)
+}