fix output rownames

AllenInstitute · Mar 18, 2023 · 1a58164 · 1a58164
1 parent 484ecc3
commit 1a58164
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/loadTaxonomy.R b/R/loadTaxonomy.R
@@ -28,7 +28,7 @@ loadTaxonomy = function(refFolder,
     ## Convert count data into a matrix
     countsReference = as.matrix(countsReference[,names(countsReference)!=gene_id])
     rownames(countsReference) = colnames(datReference)
-    countsReference = t(countsReference)
+    countsReference = Matrix::t(countsReference)
   }else{
     countsReference = NULL
   }
@@ -97,10 +97,10 @@ loadTaxonomy = function(refFolder,
       }
     )
   }
+
   # This next bit should NOT be needed, but the anndata crashes without it
   if(is_tibble(umap.coords)){
     umap.coords = as.data.frame(umap.coords)
-    print(class(umap.coords))
     rownames(umap.coords) = umap.coords[,sample_id]
   }
 

diff --git a/R/taxonomy_mapping.R b/R/taxonomy_mapping.R
@@ -45,6 +45,7 @@ taxonomy_mapping = function(AIT.anndata, query.data, corr.map=TRUE, tree.map=TRU
     #############
     ## Combine mapping results
     mappingAnno = Reduce(cbind, mappingResults)
+    rownames(mappingAnno) = colnames(query.data) ## Add query sample names to mapping results
 
     #############
     ## ---- Convert cell type mappings to subclass, neighborhood (if available), and class -------------------------------