modify one_metric_df function and update meta.yml in propd

modules/nf-core/propr/propd/meta.yml

@@ -52,8 +52,16 @@ output:
       pattern: "*.propd.tsv"
   - fdr:
       type: file
-      description: (optional) propr fdr table
+      description: (optional) propd fdr table
       pattern: "*.fdr.tsv"
+  - adj:
+      type: file
+      description: (optional) propd adj table
+      pattern: "*.adj.csv"
+  - warnings:
+      type: file
+      description: propd warnings
+      pattern: "*.warnings.txt"
   - session_info:
       type: file
       description: dump of R SessionInfo

modules/nf-core/propr/propd/templates/propd.R

@@ -67,24 +67,27 @@ read_delim_flexible <- function(file, header = TRUE, row.names = 1, check.names
 #'
 #' @param object propd object
 one_metric_df <- function(object){
-    result <- getResults(object)
-    genes <- unique(c(result\$Pair, result\$Partner))
-
-    empty_matrix <- matrix(NA, nrow = length(genes), ncol = length(genes), dimnames = list(genes, genes))
-
-    if (object@active == "theta_d"){
-    metric <- "theta"
-    }else{
-    metric <- object@active
-    }
-
-    for (i in 1:nrow(result)) {
-        row_name <- result\$Pair[i]
-        col_name <- result\$Partner[i]
-        empty_matrix[row_name, col_name] <- result[[metric]][i]
-        empty_matrix[col_name, row_name] <- result[[metric]][i]
-        }
-    return(empty_matrix)
+    results <- getResults(object)
+    #keep only the metric of interest
+    one_metric <- cbind(results\$Partner, results\$Pair, results\$theta)
+    colnames(one_metric) <- c("Partner", "Pair", "theta")
+    one_metric <- as.data.frame(one_metric)
+
+    # Extract the unique gene names
+    gene_names <- sort(unique(c(one_metric\$Partner, one_metric\$Pair)))
+    # Initialize a square matrix with NA
+    square_matrix <- matrix(NA, nrow = length(gene_names), ncol = length(gene_names))
+    rownames(square_matrix) <- gene_names
+    colnames(square_matrix) <- gene_names
+
+    # Use the `match` function to get the row and column indices
+    row_indices <- match(one_metric\$Partner, gene_names)
+    col_indices <- match(one_metric\$Pair, gene_names)
+    # Use these indices to populate the matrix
+    square_matrix[cbind(row_indices, col_indices)] <- one_metric[["theta"]]
+    # Populate the reverse pairs to ensure symmetry
+    square_matrix[cbind(col_indices, row_indices)] <- one_metric[["theta"]]
+    return(square_matrix)
 }
 
 #' Extract the differential proportionality cutoff for a specified FDR value.

modules/nf-core/propr/propd/tests/main.nf.test.snap

@@ -14,7 +14,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:55:35.703293"
+        "timestamp": "2024-05-23T13:10:06.778954"
     },
     "Test propr/propd using theta_e and boxcox permutation - results": {
         "content": [
@@ -31,7 +31,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:59:33.28078"
+        "timestamp": "2024-05-23T13:13:35.158486"
     },
     "Test propr/propd using theta_e permutation - results": {
         "content": [
@@ -48,7 +48,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:57:24.038188"
+        "timestamp": "2024-05-23T13:12:03.500722"
     },
     "versions": {
         "content": [
@@ -60,7 +60,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:53:45.165637"
+        "timestamp": "2024-05-23T13:07:07.588326"
     },
     " - results": {
         "content": [
@@ -77,7 +77,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T14:13:47.602525"
+        "timestamp": "2024-05-23T13:16:44.428551"
     },
     " Test propr/propd using default boxcox permutation - results": {
         "content": [
@@ -94,7 +94,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:55:32.476341"
+        "timestamp": "2024-05-23T13:10:02.25738"
     },
     "Test propr/propd using default permutation - results": {
         "content": [
@@ -111,7 +111,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T11:53:43.056295"
+        "timestamp": "2024-05-23T13:07:04.720183"
     },
     "Test propr/propd with adjacency matrix - adj": {
         "content": [
@@ -120,14 +120,14 @@
                     {
                         "id": "test"
                     },
-                    "test.adj.csv:md5,f9d19255f9400e6c4daa01f86d74f017"
+                    "test.adj.csv:md5,9da907136fba72b0e098c7fbacbeb837"
                 ]
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-16T14:13:47.427246"
+        "timestamp": "2024-05-23T13:16:38.527389"
     }
 }