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annotate fonctions_auxiliaires.R @ 0:c577f13705f2 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
author workflow4metabolomics
date Wed, 10 Jul 2024 15:20:11 +0000
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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1 #--------------------------------------------------------------------------------------------------------------------------------------------------------------
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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2 check_features <- function(M1, M2) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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3 #M1/M2 = data.frame containing sampleMetadata or variableMetadata
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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4 #check the variables in the 2 matrices .
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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5 #returns the names of the columns in the two metadata
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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7 colnames_1 <- colnames(M1)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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8 colnames_2 <- colnames(M2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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9 samecolumns <- intersect(colnames_1, colnames_2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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11 if (is.null(samecolumns)) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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12 cat("\nWarning: There are no features in common \n")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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13 }
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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15 return(samecolumns)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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16 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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18 #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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20 #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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22 compare_same_columns <- function(M1, M2, same, choice_keep, Keep, tab1, tab2) {
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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24 #M1/M2 = data.frame containing sampleMetadata or variableMetadata
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25 #same = list of column names with the same name in M1 and M2
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26 #choice_keep = choice of keeping columns with the same no or keeping just one
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27 #keep = keep the column in M1 or M2
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28 #tab1/tab2 = Suffix for Metadata 1/2
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30 #Check that the variables in the 2 matrices have the same values and
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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31 #If not, they are renamed or deleted according to the parameters chosen by the user.
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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32 #returns the two modified metadata
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34 compare_results <- list()
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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35 non_identical_columns_v <- c()
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38 #Creation of 2 sub-tables with shared individuals and variables
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39 common_individuals <- intersect(M1[, 1], M2[, 1])
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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40 common_columns <- intersect(colnames(M1), colnames(M2))
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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42 M1_common <- subset(M1, M1[, 1] %in% common_individuals)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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43 M2_common <- subset(M2, M2[, 1] %in% common_individuals)
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46 M1_common <- M1_common[, common_columns]
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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47 M2_common <- M2_common[, common_columns]
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51 common_columns <- common_columns[-1]# delete id column
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54 for (col_name in common_columns) {
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55 #Check that the columns are identical, then delete them from M2
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56 if (!identical(M1_common[[col_name]], M2_common[[col_name]])) {
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58 non_identical_columns_v <- c(non_identical_columns_v, col_name)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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60 #otherwise store the columns where the values are not the same in non_identical_columns
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61 } else {
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62 M2 <- M2[, -which(colnames(M2) == col_name)]
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63 }
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65 }
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67 #if the list of columns that do not take the same values is null, we return M1/M2
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68 if (is.null(non_identical_columns_v)) {
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70 result <- list(M1 = M1, M2 = M2)
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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72 return(result)
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75 } else {
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77 for (non_identical_columns in non_identical_columns_v) {
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79 #If we decide to keep the 2 columns and they do not take the same values, we change their names by adding a suffix.
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81 if (choice_keep == "yes") {#keep both columns and give them a new name
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83 new_name <- paste(tab1, non_identical_columns, sep = "_")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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84 colnames(M1)[colnames(M1) == non_identical_columns] <- new_name
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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86 new_name <- paste(tab2, non_identical_columns, sep = "_")
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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87 colnames(M2)[colnames(M2) == non_identical_columns] <- new_name
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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89 }
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91 if (choice_keep == "no") {#Keep only one and delete the other
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92 if (Keep == 1) {
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93 M2 <- M2[, -which(colnames(M2) == non_identical_columns)]
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94 new_name <- paste(tab1, non_identical_columns, sep = "_")
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95 colnames(M1)[colnames(M1) == non_identical_columns] <- new_name
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96
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97 }
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98 if (Keep == 2) {
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99 M1 <- M1[, -which(colnames(M1) == non_identical_columns)]
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100 new_name <- paste(tab2, non_identical_columns, sep = "_")
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101 colnames(M2)[colnames(M2) == non_identical_columns] <- new_name
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102 }
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103
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104 }
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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105 }
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106 }
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107
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108
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109 result <- list(M1 = M1, M2 = M2)
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110 return(result)
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111
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112 }
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113 #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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114
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115 #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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116 match2_bis <- function(Metadata_1, Metadata_2, Mtype) {
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117
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118
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119 #Metadata1/Metadata2 = data.frame containing sampleMetadata or variableMetadata
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120 #Mtype = "sample" or "variable" depending on Metadata content
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121 #To check if metadata1 and metadata2 match regarding identifiers
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122 #returns a vector containing an error message if the identifiers are not all the same in the two metadatas
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123 err.stock <- NULL#error vector
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124
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125
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126 id2 <- Metadata_1[, 1]
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127 id1 <- Metadata_2[, 1]
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128
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129 if (length(which(id1 %in% id2)) != length(id1) || length(which(id2 %in% id1)) != length(id2)) {
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130 err.stock <- c("\n", Mtype, "Metadata_1 and ", Mtype, "Metadata_2 do not match regarding Metadata_2 identifiers.")
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131 if (length(which(id1 %in% id2)) != length(id1)) {
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132 if (length(which(! (id1 %in% id2))) < 4) {
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133 err.stock <- c(err.stock, "\n The ")
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134 } else {
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135 err.stock <- c(err.stock, "\n For example, the ")
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136 }
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137 err.stock <- c(err.stock, "following identifiers found in the ", Mtype, "Metadata_1 file\n",
c577f13705f2 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit eba1150dad55ad9eca5e93358d9f75e6b6dba2ec
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138 " do not appear in the ", Mtype, " Metadata_2 file:\n")
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139 identif <- id1[which(! (id1 %in% id2))][seq_len(min(3, length(which(! (id1 %in% id2)))))]
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140 err.stock <- c(err.stock, " ", paste(identif, collapse = "\n "), "\n")
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141 }
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142 if (length(which(id2 %in% id1)) != length(id2)) {
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143 if (length(which(! (id2 %in% id1))) < 4) {
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144 err.stock <- c(err.stock, "\n The ")
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145 } else {
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146 err.stock <- c(err.stock, "\n For example, the ")
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147 }
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148 err.stock <- c(err.stock, "following identifiers found in the ", Mtype, " Metadata_2 file\n",
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149 " do not appear in the", Mtype, " Metadata_1 file:\n")
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150 identif <- id2[which(! (id2 %in% id1))][seq_len(min(3, length(which(! (id2 %in% id1)))))]
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151 err.stock <- c(err.stock, " ", paste(identif, collapse = "\n "), "\n")
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152 }
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153 err.stock <- c(err.stock, "\nPlease check your data.\n")
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154 }
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155
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156 return(err.stock)
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157
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158 }