bugfix previous commit

modules/local/spacemarkers.nf

@@ -31,22 +31,26 @@ process SPACEMARKERS {
     """
     mkdir "${prefix}"
     Rscript -e 'library("SpaceMarkers");
-      #load spatial coordinates from tissue positions
-      coords <- load10XCoords("$data");
-      features <- getSpatialFeatures("$cogapsResult");
-      spPatterns <- merge(coords, features, by.x = "barcode", by.y = "row.names");
+      #load spatial coords from tissue positions, deconvolved patterns, and expression
+      coords <- load10XCoords("$data")
+      features <- getSpatialFeatures("$cogapsResult")
+      dataMatrix <- load10XExpr("$data")
+
+      #add spatial coordinates to deconvolved data, only use barcodes present in data
+      spPatterns <- merge(coords, features, by.x = "barcode", by.y = "row.names")
+      spPatterns <- spPatterns[which(spPatterns[,"barcode"] %in% colnames(dataMatrix)),]
       saveRDS(spPatterns, file = "${prefix}/spPatterns.rds");
 
-      #load expression data, rm low expression genes, rm barcodes w/o spatial
-      dataMatrix <- load10XExpr("$data");
-      keepGenes <- which(apply(dataMatrix, 1, sum) > 10);
-      keepBarcodes <- which(colnames(dataMatrix) %in% spPatterns["barcode"]);
-      dataMatrix <- dataMatrix[keepGenes, keepBarcodes];
-      
+      #remove genes with low expression, only barcodes present in spatial data
+      keepGenes <- which(apply(dataMatrix, 1, sum) > 10)
+      keepBarcodes <- which(colnames(dataMatrix) %in% spPatterns[,"barcode"])
+      dataMatrix <- dataMatrix[keepGenes, keepBarcodes]
+
       #compute optimal parameters for spatial patterns
       optParams <- getSpatialParameters(spPatterns);
       saveRDS(optParams, file = "${prefix}/optParams.rds");
 
+      #find genes that are differentially expressed in spatial patterns
       spaceMarkers <- getInteractingGenes(data = dataMatrix, \
                                           optParams = optParams, \
                                           spPatterns = spPatterns, \