--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fonctions_auxiliaires.R	Wed Jul 10 15:20:11 2024 +0000
@@ -0,0 +1,158 @@
+#--------------------------------------------------------------------------------------------------------------------------------------------------------------
+check_features <- function(M1, M2) {
+  #M1/M2 = data.frame containing sampleMetadata or variableMetadata
+  #check the variables in the 2 matrices .
+  #returns the names of the columns in the two metadata
+
+  colnames_1 <- colnames(M1)
+  colnames_2 <- colnames(M2)
+  samecolumns <- intersect(colnames_1, colnames_2)
+
+  if (is.null(samecolumns)) {
+    cat("\nWarning: There are no features in common \n")
+  }
+
+  return(samecolumns)
+}
+
+#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+compare_same_columns <- function(M1, M2, same, choice_keep, Keep, tab1, tab2) {
+
+  #M1/M2 = data.frame containing sampleMetadata or variableMetadata
+  #same = list of column names with the same name in M1 and M2
+  #choice_keep = choice of keeping columns with the same no or keeping just one
+  #keep = keep the column in M1 or M2
+  #tab1/tab2 = Suffix for Metadata 1/2
+
+  #Check that the variables in the 2 matrices have the same values and
+  #If not, they are renamed or deleted according to the parameters chosen by the user.
+  #returns the two modified metadata
+
+  compare_results <- list()
+  non_identical_columns_v <- c()
+
+
+  #Creation of 2 sub-tables with shared individuals and variables
+  common_individuals <- intersect(M1[, 1], M2[, 1])
+  common_columns <- intersect(colnames(M1), colnames(M2))
+
+  M1_common <- subset(M1, M1[, 1] %in% common_individuals)
+  M2_common <- subset(M2, M2[, 1] %in% common_individuals)
+
+
+  M1_common <- M1_common[, common_columns]
+  M2_common <- M2_common[, common_columns]
+
+
+
+  common_columns <- common_columns[-1]# delete id column
+
+
+  for (col_name in common_columns) {
+    #Check that the columns are identical, then delete them from M2
+    if (!identical(M1_common[[col_name]], M2_common[[col_name]])) {
+
+      non_identical_columns_v <- c(non_identical_columns_v, col_name)
+
+      #otherwise store the columns where the values are not the same in non_identical_columns
+    } else {
+      M2 <- M2[, -which(colnames(M2) == col_name)]
+    }
+
+  }
+
+  #if the list of columns that do not take the same values is null, we return M1/M2
+  if (is.null(non_identical_columns_v)) {
+
+    result <- list(M1 = M1, M2 = M2)
+
+    return(result)
+
+
+  } else {
+
+    for (non_identical_columns in non_identical_columns_v) {
+
+      #If we decide to keep the 2 columns and they do not take the same values, we change their names by adding a suffix.
+
+      if (choice_keep == "yes") {#keep both columns and give them a new name
+
+        new_name <- paste(tab1, non_identical_columns, sep = "_")
+        colnames(M1)[colnames(M1) == non_identical_columns] <- new_name
+
+        new_name <- paste(tab2, non_identical_columns, sep = "_")
+        colnames(M2)[colnames(M2) == non_identical_columns] <- new_name
+
+      }
+
+      if (choice_keep == "no") {#Keep only one and delete the other
+        if (Keep == 1) {
+          M2 <- M2[, -which(colnames(M2) == non_identical_columns)]
+          new_name <- paste(tab1, non_identical_columns, sep = "_")
+          colnames(M1)[colnames(M1) == non_identical_columns] <- new_name
+
+        }
+        if (Keep == 2) {
+          M1 <- M1[, -which(colnames(M1) == non_identical_columns)]
+          new_name <- paste(tab2, non_identical_columns, sep = "_")
+          colnames(M2)[colnames(M2) == non_identical_columns] <- new_name
+        }
+
+      }
+    }
+  }
+
+
+  result <- list(M1 = M1, M2 = M2)
+  return(result)
+
+}
+#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+match2_bis <- function(Metadata_1, Metadata_2, Mtype) {
+
+
+  #Metadata1/Metadata2 = data.frame containing sampleMetadata or variableMetadata
+  #Mtype = "sample" or "variable" depending on Metadata content
+  #To check if metadata1 and metadata2  match regarding identifiers
+  #returns a vector containing an error message if the identifiers are not all the same in the two metadatas
+  err.stock <- NULL#error vector
+
+
+  id2 <- Metadata_1[, 1]
+  id1 <- Metadata_2[, 1]
+
+  if (length(which(id1 %in% id2)) != length(id1) || length(which(id2 %in% id1)) != length(id2)) {
+    err.stock <- c("\n", Mtype, "Metadata_1 and ", Mtype, "Metadata_2 do not match regarding Metadata_2 identifiers.")
+    if (length(which(id1 %in% id2)) != length(id1)) {
+      if (length(which(! (id1 %in% id2))) < 4) {
+        err.stock <- c(err.stock, "\n    The ")
+      } else {
+        err.stock <- c(err.stock, "\n    For example, the ")
+      }
+      err.stock <- c(err.stock, "following identifiers found in the ", Mtype, "Metadata_1 file\n",
+                     "    do not appear in the ", Mtype, " Metadata_2 file:\n")
+      identif <- id1[which(! (id1 %in% id2))][seq_len(min(3, length(which(! (id1 %in% id2)))))]
+      err.stock <- c(err.stock, "    ", paste(identif, collapse = "\n    "), "\n")
+    }
+    if (length(which(id2 %in% id1)) != length(id2)) {
+      if (length(which(! (id2 %in% id1))) < 4) {
+        err.stock <- c(err.stock, "\n    The ")
+      } else {
+        err.stock <- c(err.stock, "\n    For example, the ")
+      }
+      err.stock <- c(err.stock, "following identifiers found in the ", Mtype, " Metadata_2 file\n",
+                     "    do not appear in the", Mtype, " Metadata_1 file:\n")
+      identif <- id2[which(! (id2 %in% id1))][seq_len(min(3, length(which(! (id2 %in% id1)))))]
+      err.stock <- c(err.stock, "    ", paste(identif, collapse = "\n    "), "\n")
+    }
+    err.stock <- c(err.stock, "\nPlease check your data.\n")
+  }
+
+  return(err.stock)
+
+}