v1.19.5 -- fixed a math bug on add_qc_metrics()

LieberInstitute · Dec 16, 2024 · d12e632 · d12e632
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spatialLIBD
 Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved
     transcriptomics data
-Version: 1.19.4
-Date: 2024-12-13
+Version: 1.19.5
+Date: 2024-12-16
 Authors@R:
     c(
     person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# spatialLIBD 1.19.5
+
+BUG FIXES
+
+* Fixed internal errors in `add_qc_metrics()` on the `scuttle::isOutlier()`
+function calls.
+
 # spatialLIBD 1.19.4
 
 NEW FEATURES

diff --git a/R/add_qc_metrics.R b/R/add_qc_metrics.R
@@ -135,8 +135,8 @@ add_qc_metrics <- function(spe, overwrite = FALSE) {
     )
 
     qcfilter <- data.frame(
-        low_lib_size = scater::isOutlier(qc_df$log2sum, type = "lower", log = TRUE, batch = qc_df$sample_id),
-        low_n_features = scater::isOutlier(qc_df$log2detected, type = "lower", log = TRUE, batch = qc_df$sample_id),
+        low_lib_size = scater::isOutlier(qc_df$sum_umi, type = "lower", log = TRUE, batch = qc_df$sample_id),
+        low_n_features = scater::isOutlier(qc_df$sum_gene, type = "lower", log = TRUE, batch = qc_df$sample_id),
         high_subsets_Mito_percent = scater::isOutlier(qc_df$subsets_Mito_percent, type = "higher", batch = qc_df$sample_id)
     ) |>
         dplyr::mutate(discard = (low_lib_size | low_n_features) | high_subsets_Mito_percent)