Merge pull request #138 from omnideconv/updateScaling

Update scaling function
omnideconv · Mar 15, 2024 · 67a3d35 · 67a3d35
2 parents eb36e11 + 9259e20
commit 67a3d35
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/R/scale_cell_counts.R b/R/scale_cell_counts.R
@@ -26,12 +26,14 @@ scale_cell_counts <- function(spe, value, cell_counts, resName = NULL) {
     resName <- paste0(value, "_absolute")
   }
 
-  if (any(is.na(match(rownames(colData(spe)), names(cell_densities))))) {
-    stop("Not all rownames in colData have a matching entry in cell_densities.")
+  if (cell_counts %in% colnames(colData(spe))) {
+    cell_densities <- colData(spe)[, cell_counts]
+  } else {
+    stop("Cell count data not available in the object")
   }
 
   # Calculate absolute cell densities
-  absoluteValues <- colData(spe)[, value] * cell_densities[rownames(colData(spe))]
+  absoluteValues <- colData(spe)[, value] * cell_densities
 
   # Add the absolute cell densities as a new column
   colData(spe)[[resName]] <- absoluteValues