From eefc56e630c915f308dc82b78b97835b195ea5bf Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Mon, 3 Aug 2026 22:10:51 -0400
Subject: [PATCH 1/2] fix: derive norm count subtype internally

---
 .codeocean/app-panel.json | 9 ---------
 code/main.R               | 9 ++-------
 2 files changed, 2 insertions(+), 16 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 22c1eab..06cd004 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -77,15 +77,6 @@
 				"batch"
 			]
 		},
-		{
-			"id": "sub_count_type_id",
-			"category": "FvI4Z2eb9sjL47Jt",
-			"name": "Sub count type",
-			"param_name": "sub_count_type",
-			"description": "Used if count_type is a list in the counts slot. This must be a name in moo@counts[[count_type]].",
-			"type": "text",
-			"value_type": "string"
-		},
 		{
 			"id": "sample_id_colname_id",
 			"category": "FvI4Z2eb9sjL47Jt",
diff --git a/code/main.R b/code/main.R
index a3eee69..c84e82d 100644
--- a/code/main.R
+++ b/code/main.R
@@ -14,12 +14,6 @@ setup_capsule_environment()
 parser <- ArgumentParser()
 
 parser$add_argument("--count_type", type = "character", default = "filt")
-parser$add_argument(
-  "--sub_count_type",
-  type = "character",
-  default = NULL,
-  help = "Sub count type if count_type is a list"
-)
 parser$add_argument(
   "--sample_id_colname",
   type = "character",
@@ -262,6 +256,7 @@ parser$add_argument(
 )
 
 args <- parser$parse_args()
+sub_count_type <- if (identical(args$count_type, "norm")) "voom" else NULL
 
 # load multiOmicDataSet from data directory
 moo <- load_moo_from_data_dir()
@@ -270,7 +265,7 @@ moo <- load_moo_from_data_dir()
 plot_expr_heatmap(
   moo,
   count_type = args$count_type,
-  sub_count_type = args$sub_count_type,
+  sub_count_type = sub_count_type,
   sample_id_colname = args$sample_id_colname,
   feature_id_colname = args$feature_id_colname,
   group_colname = args$group_colname,

From 382f569a056547a54cee6704dd8039cb3da2d6aa Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Mon, 3 Aug 2026 22:21:16 -0400
Subject: [PATCH 2/2] test: cover supported count types

---
 tests/testthat/helper-cli.R | 28 ++++++++++++++++++++++++++++
 tests/testthat/test-main.R  |  6 ++++++
 2 files changed, 34 insertions(+)

diff --git a/tests/testthat/helper-cli.R b/tests/testthat/helper-cli.R
index 658b2b5..259d2ef 100644
--- a/tests/testthat/helper-cli.R
+++ b/tests/testthat/helper-cli.R
@@ -73,3 +73,31 @@ common_cli_args <- c(
   "--display_gene_names=FALSE",
   "--display_sample_names=TRUE"
 )
+
+expect_main_runs_with_count_type <- function(count_type) {
+  setup <- setup_cli_workspace(
+    paste0("mosuite_plot_expr_heatmap_", count_type, "_test_")
+  )
+  on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
+
+  old_wd <- getwd()
+  setwd(setup$code_dir)
+  on.exit(setwd(old_wd), add = TRUE)
+
+  exit_code <- system2(
+    "Rscript",
+    args = c(
+      "main.R",
+      sprintf("--count_type=%s", count_type),
+      "--display_gene_names=FALSE",
+      "--display_sample_names=TRUE"
+    )
+  )
+  expect_equal(
+    exit_code,
+    0,
+    info = paste("main.R should plot", count_type, "counts")
+  )
+
+  expect_plot_created(setup$results_dir)
+}
diff --git a/tests/testthat/test-main.R b/tests/testthat/test-main.R
index 5b25f8d..ba87fc6 100644
--- a/tests/testthat/test-main.R
+++ b/tests/testthat/test-main.R
@@ -12,6 +12,12 @@ test_that("main.R CLI creates expression heatmap plot", {
   expect_plot_created(setup$results_dir)
 })
 
+test_that("main.R CLI plots supported count types", {
+  for (count_type in c("raw", "filt", "norm", "batch")) {
+    expect_main_runs_with_count_type(count_type)
+  }
+})
+
 test_that("run wrapper executes and creates expression heatmap plot", {
   setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_run_test_")
   on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)