fix: Derive norm count subtype internally

.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",

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## development version
 
+- Hide the count subtype parameter and automatically use the `voom` subtype when plotting normalized counts (#11, @phoman14).
 - Sync Code Ocean app panel parameter descriptions with MOSuite package documentation for MOSuite v0.4.1 (#7, @phoman14).
 - Improved the Code Ocean parameter UI for the plot expr heatmap capsule (#4, @phoman14).
 - Use MOSuite v0.3.2. (#1, @kelly-sovacool)

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$group_colname,
@@ -308,5 +303,14 @@ plot_expr_heatmap(
   assign_color_to_sample_groups = parse_optional_vector(
     args$assign_color_to_sample_groups
   ),
-  group_colors = parse_optional_vector(args$group_colors)
+  group_colors = parse_optional_vector(args$group_colors),
+  heatmap_color_scheme = args$heatmap_color_scheme,
+  autoscale_heatmap_color = args$autoscale_heatmap_color,
+  set_min_heatmap_color = args$set_min_heatmap_color,
+  set_max_heatmap_color = args$set_max_heatmap_color,
+  aspect_ratio = args$aspect_ratio,
+  legend_font_size = args$legend_font_size,
+  gene_name_font_size = args$gene_name_font_size,
+  sample_name_font_size = args$sample_name_font_size,
+  display_numbers = args$display_numbers
 )

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)
+}

tests/testthat/test-main.R

@@ -1,3 +1,33 @@
+test_that("every app panel parameter is accepted and used by main.R", {
+  repo_root <- normalizePath(
+    file.path(testthat::test_path(), "..", ".."),
+    mustWork = TRUE
+  )
+  panel <- jsonlite::fromJSON(
+    file.path(repo_root, ".codeocean", "app-panel.json")
+  )
+  main_text <- paste(
+    readLines(file.path(repo_root, "code", "main.R"), warn = FALSE),
+    collapse = "\n"
+  )
+  param_names <- panel$parameters$param_name
+  expect_true(length(param_names) > 0)
+  for (param_name in param_names) {
+    expect_match(
+      main_text,
+      sprintf('"--%s"', param_name),
+      fixed = TRUE,
+      info = sprintf("main.R should define a --%s CLI argument", param_name)
+    )
+    expect_match(
+      main_text,
+      sprintf("args$%s", param_name),
+      fixed = TRUE,
+      info = sprintf("main.R should read args$%s", param_name)
+    )
+  }
+})
+
 test_that("main.R CLI creates expression heatmap plot", {
   setup <- setup_cli_workspace("mosuite_plot_expr_heatmap_test_")
   on.exit(unlink(setup$workspace, recursive = TRUE), add = TRUE)
@@ -12,6 +42,12 @@ test_that("main.R CLI creates expression heatmap plot", {
   expect_plot_created(setup$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)