From 61fca7d7ef4b3f8fcf8d518eab70f6f6dd967e4f Mon Sep 17 00:00:00 2001
From: Anagha Shenoy <90294056+anashen@users.noreply.github.com>
Date: Mon, 27 Jul 2026 20:30:35 -0400
Subject: [PATCH 1/3] Add error handling for single-label groups during heatmap
 generation

---
 R/make_qc_heatmaps.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/R/make_qc_heatmaps.R b/R/make_qc_heatmaps.R
index 3a1c2df..1e4acb8 100644
--- a/R/make_qc_heatmaps.R
+++ b/R/make_qc_heatmaps.R
@@ -50,11 +50,22 @@ make_QC_heatmap <- function(
     seurat_obj <- subset(seurat_obj,idents = names(which(table(Idents(seurat_obj))<=max.size)))
   }
   if (!is.null(n_downsample)) seurat_obj <- subset(seurat_obj, downsample=n_downsample)
+
+  ident_groups <- table(Idents(seurat_obj))
+  ident_groups <- ident_groups[ident_groups > 0]
+  if (length(ident_groups) < 2) {
+    stop("QC heatmaps require at least two identity groups with cells after filtering.")
+  }
+
   mark_all <- FindAllMarkers(seurat_obj,only.pos = TRUE,min.pct = min.pct)
   mark_all %>% group_by(.data$cluster) %>%
     dplyr::filter(.data$avg_log2FC > logfc_cutoff) %>%
     slice_head(n = n_markers) %>%
     ungroup() -> top_markers
+
+  if (nrow(top_markers) == 0) {
+    stop("No marker genes were identified for the requested identity groups.")
+  }
   
   if (!is.null(switch_id)) {
     Idents(seurat_obj) <- switch_id
@@ -187,6 +198,12 @@ make_azimuth_QC_heatmaps <- function(
   for (level1 in names(result_list)) {
     lobj <- subset(object,cells = rownames(result_list[[level1]]))
     Idents(lobj) <- final_name
+    ident_groups <- table(Idents(lobj))
+    ident_groups <- ident_groups[ident_groups > 0]
+    if (length(ident_groups) < 2) {
+      cli::cli_warn("Skipping {level1}; QC heatmaps require at least two final annotation groups with cells.")
+      next
+    }
     tryCatch({
       plot_list[[level1]] <- make_QC_heatmap(lobj, min.size = min.final.group, identity = as.character(level1), ...)
     }, error = function(e) {

From 01c1e4472d21462dcf5455ae85ef5e38d1ed85f4 Mon Sep 17 00:00:00 2001
From: Anagha Shenoy <90294056+anashen@users.noreply.github.com>
Date: Mon, 27 Jul 2026 20:30:46 -0400
Subject: [PATCH 2/3] Add tests for QC heatmaps

---
 tests/testthat/test_visualization.R | 84 +++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 tests/testthat/test_visualization.R

diff --git a/tests/testthat/test_visualization.R b/tests/testthat/test_visualization.R
new file mode 100644
index 0000000..25a74f1
--- /dev/null
+++ b/tests/testthat/test_visualization.R
@@ -0,0 +1,84 @@
+
+make_viz_test_object <- function(cells = NULL) {
+  query <- readRDS(test_path("test_obj.rds"))
+  query <- Seurat::NormalizeData(query, verbose = FALSE)
+  if (!is.null(cells)) {
+    query <- subset(query, cells = colnames(query)[seq_len(cells)])
+  }
+  return(query)
+}
+
+set_azimuth_metadata <- function(query, fine, broad, full) {
+  query@meta.data$azimuth_fine <- fine
+  query@meta.data$azimuth_broad <- broad
+  query@meta.data$full_hierarchical_labels <- full
+  query@meta.data$full_consistent_hierarchy <- TRUE
+  return(query)
+}
+
+test_that("make_QC_heatmap rejects single-label inputs before marker detection", {
+  query <- make_viz_test_object()
+  query@meta.data$final_level_labels <- "Unassigned"
+
+  expect_error(
+    make_QC_heatmap(query, group.by = "final_level_labels"),
+    "at least two identity groups",
+    fixed = TRUE
+  )
+})
+
+test_that("make_azimuth_QC_heatmaps skips single-label final annotation groups", {
+  query <- make_viz_test_object()
+  query <- set_azimuth_metadata(
+    query,
+    fine = "Unassigned",
+    broad = "Unassigned",
+    full = "Unassigned"
+  )
+
+  expect_warning(
+    plots <- make_azimuth_QC_heatmaps(query, min.final.group = 10),
+    "Skipping Unassigned_1",
+    fixed = TRUE
+  )
+  expect_false("Unassigned_1" %in% names(plots))
+})
+
+test_that("make_azimuth_QC_heatmaps returns valid plots even when one group errors", {
+  query <- make_viz_test_object(cells = 70)
+  query <- set_azimuth_metadata(
+    query,
+    fine = c(
+      rep("Unassigned", 10),
+      rep("T cell", 10),
+      rep("B cell", 10),
+      rep("Fibroblast", 25),
+      rep("Rare stromal", 15)
+    ),
+    broad = c(
+      rep("Immune cell", 30),
+      rep("Stromal cell", 40)
+    ),
+    full = c(
+      rep("Immune cell|Lymphoid cell", 30),
+      rep("Stromal cell", 40)
+    )
+  )
+
+  # after the filtering, the stromal cell group has only "Rare stromal" left, but this is a single-label group, so it will error out in make_QC_heatmap
+  # the valid plot for "Immune cell" should still be returned, and the error for "Stromal cell" should be caught and reported as a warning
+  expect_warning(
+    plots <- make_azimuth_QC_heatmaps(
+      query,
+      min.final.group = 9,
+      n_markers = 1,
+      max.size = 20
+    ),
+    "Error in processing Stromal cell_1", 
+    fixed = TRUE
+  )
+
+  expect_named(plots, "Immune_Lymphoid cell_1")
+  expect_s3_class(plots[["Immune_Lymphoid cell_1"]], "ggplot")
+  expect_false("Stromal cell_1" %in% names(plots))
+})

From 9c7e3b5f37f61d97a6a2d0ee955558e7e9d7ea83 Mon Sep 17 00:00:00 2001
From: Anagha Shenoy <90294056+anashen@users.noreply.github.com>
Date: Mon, 27 Jul 2026 20:35:50 -0400
Subject: [PATCH 3/3] Bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 96b94f6..d4c5931 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AzimuthAPI
 Title: Pan-Azimuth Web API Interface
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: 
     person("Satija", "Lab", email = "satijalabnygc@gmail.com", role = c("aut", "cre"))
 Description: An R package providing an interface to the Pan-Azimuth Web API for single-cell RNA sequencing analysis.