fix crash filter_data due to cells with zero total counts

FridleyLab · Mar 22, 2024 · 40a6826 · 40a6826
1 parent 8a032e0
commit 40a6826
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/R/filter_data.R b/R/filter_data.R
@@ -167,6 +167,8 @@ filter_data = function(x=NULL,
     col_expr_reads = colSums(df_tmp[grepl(spot_pct_expr, rownames(df_tmp)), ])
     col_expr_percent = col_expr_reads/col_total_reads
     rm(col_expr_reads) # Clean env
+    # Force NaNs tp zero, which result from zero as denominator (i.e., zero counts in the cell)
+    col_expr_percent[is.na(col_expr_percent)] = 0
 
     # If no maximum counts set by user, then make it the max counts of each spot/cell
     if(is.null(spot_maxreads)){