Hotfix createGiottoVisiumObject with custom h5 path

ameliazug · May 15, 2023 · 88ca31f · 88ca31f
1 parent 22241fb
commit 88ca31f
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/R/data_evaluation.R b/R/data_evaluation.R
@@ -140,6 +140,8 @@ evaluate_cell_metadata = function(metadata,
                      Setting temporary NA values'))
     # set temporary NA values
     metadata[, cell_ID := NA_character_]
+    # re-order so that cell_ID is the first column
+    data.table::setcolorder(metadata, neworder = "cell_ID")
 
   }
 

diff --git a/R/giotto.R b/R/giotto.R
@@ -1856,13 +1856,17 @@ createGiottoVisiumObject = function(visium_dir = NULL,
     } else {
       visium_png_list = NULL
     }
+
+    # Create cell_ID column for metadata
+    cell_ID = NULL
+    colnames(spatial_results)[colnames(spatial_results) == "barcode"] = "cell_ID"
 
     # create Giotto object
     giotto_object = createGiottoObject(expression = raw_matrix,
                                        expression_feat = 'rna',
                                        spatial_locs = spatial_locs,
                                        instructions = instructions,
-                                       cell_metadata = list('cell' = list('rna' = spatial_results[,.(in_tissue, array_row, array_col)])),
+                                       cell_metadata = list('cell' = list('rna' = spatial_results[,.(cell_ID, in_tissue, array_row, array_col)])),
                                        images = visium_png_list)
     return(giotto_object)