Mercurial > repos > ppericard > viscorvar

annotate additional_functions_block_splsda.R @ 0:d0b77b926863 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
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children e93350dc99f1
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1 #' @title Check if a block contains missing values
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2 #' @description Check if a block contains missing values
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3 #' @param list_X type : list of matrix. This list is used to perform the data integration.
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4 #' @details This function checks if a block contains missing values.
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5 #' @return type : boolean. If at least one block contains missing values,
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6 #' this function returns TRUE, otherwise this function returns FALSE.
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7 #' @examples
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8 #' X1 = matrix(1:9, nrow = 3, ncol = 3)
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9 #' X2 = matrix(10:18, nrow = 3, ncol = 3)
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10 #' list_X = list()
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11 #' list_X[[1]] = X1
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12 #' list_X[[2]] = X2
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13 #' names(list_X) = c("X1", "X2")
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14 #' boolean_block_missing_values = blockMissingValues(list_X)
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15 #' @export
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16 blockMissingValues <-function(list_X)
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17 {
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18 name_blocks = names(list_X)
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19 name_blocks_missing_values = c()
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20 boolean_block_missing_values = FALSE
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22 for(i in 1:length(list_X))
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23 {
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24 X_i = list_X[[i]]
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25 name_block_i = name_blocks[i]
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27 vec = sapply(1:dim(X_i)[2], FUN = function(j){
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28 res = any(is.na(X_i[, j]))
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30 return(res)
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31 })
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33 if(any(vec))
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34 {
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35 name_blocks_missing_values = c(name_blocks_missing_values, name_block_i)
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37 }
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39 } # End for(i in 1:length(list_X)).
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41 if(length(name_blocks_missing_values) != 0)
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42 {
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43 stop(paste("The data integration can not be performed if a block contains missing values : ", paste(name_blocks_missing_values, collapse = ", "), " contains missing values. "))
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44 boolean_block_missing_values = TRUE
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46 }
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48 return(boolean_block_missing_values)
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50 }
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53 #' @title Determination of selected variables for all components
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54 #' @description The function unionSelectBlockVariables determines, for each block, the selected block variables
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55 #' for all components.
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56 #' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function
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57 #' mixOmics.
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58 #' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for
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59 #' at least one component. Otherwise, this function returns 0.
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60 #' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with
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61 #' this block variable. Otherwise the value 0 is associated with this block variable.
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62 #' @examples
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63 #' data(res_data_integration)
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64 #' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration)
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65 #' @export
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66 unionSelectBlockVariables <-function(res_block_splsda)
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67 {
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68 ncomp = res_block_splsda$ncomp[1]
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70 names_blocks = names(res_block_splsda$loadings)
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71 index_Y = which(names_blocks == "Y")
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72 names_blocks = names_blocks[ - index_Y]
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73 list_select_block_variables = list()
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75 for(i in 1:length(names_blocks))
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76 {
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77 mat_loadings_i = res_block_splsda$loadings[[i]]
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78 index_i = c()
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80 for(j in 1:ncomp)
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81 {
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82 loadings_i_j = mat_loadings_i[, j]
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83 index_i_j = which(loadings_i_j != 0)
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85 index_i = c(index_i, index_i_j)
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87 } # End for(j 1:ncomp).
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88
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89 index_i = unique(index_i)
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90
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91 mat_select_block_variables = matrix(0,
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92 nrow = dim(mat_loadings_i)[1],
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93 ncol = 1)
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94 mat_select_block_variables[index_i, 1] = rep(1, length(index_i))
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95 rownames(mat_select_block_variables) = rownames(mat_loadings_i)
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96
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97 list_select_block_variables[[i]] = mat_select_block_variables
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98
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99 } # End for(i in 1:length(names_blocks)).
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100
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101 names(list_select_block_variables) = names_blocks
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102
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103 return(list_select_block_variables)
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104 }