From 0784fc7bbab04e5165ef43729f889059e95ad3e0 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Mon, 29 Jun 2026 17:35:59 -0400
Subject: [PATCH 01/15] Update count_type to list with raw, clean, filt, norm
 options (default: filt)

---
 .codeocean/app-panel.json | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 9939872..fdbde25 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -37,9 +37,15 @@
 			"name": "Count type",
 			"param_name": "count_type",
 			"description": "Type of counts to use (e.g., filt, norm)",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "filt"
+			"default_value": "filt",
+			"extra_data": [
+				"raw",
+				"clean",
+				"filt",
+				"norm"
+			]
 		},
 		{
 			"id": "sub_count_type_id",

From 2416cecb594a72d8d5f5183b475929ca6900d7d2 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Mon, 29 Jun 2026 18:00:51 -0400
Subject: [PATCH 02/15] Move count_type to first position in Basic category

---
 .codeocean/app-panel.json | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index fdbde25..0b18072 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -16,24 +16,24 @@
 			"id": "7Rr6IxOMDucKMImp",
 			"name": "Input Data Parameters",
 			"description": "Options for defining input data",
-			"icon": "📁"
+			"icon": "\ud83d\udcc1"
 		},
 		{
 			"id": "EzTg1ivlFDHEy9PI",
 			"name": "Basic",
-			"icon": "📂"
+			"icon": "\ud83d\udcc2"
 		},
 		{
 			"id": "FvI4Z2eb9sjL47Jt",
 			"name": "Visualization",
 			"description": "Visualization and plotting options",
-			"icon": "📊"
+			"icon": "\ud83d\udcca"
 		}
 	],
 	"parameters": [
 		{
 			"id": "count_type_id",
-			"category": "FvI4Z2eb9sjL47Jt",
+			"category": "EzTg1ivlFDHEy9PI",
 			"name": "Count type",
 			"param_name": "count_type",
 			"description": "Type of counts to use (e.g., filt, norm)",
@@ -199,4 +199,4 @@
 			"file_name": "figures/pca/pca_2D.png"
 		}
 	]
-}
\ No newline at end of file
+}

From e8e56c706d063d8417030ecaff7e66278a70644e Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Mon, 29 Jun 2026 18:20:54 -0400
Subject: [PATCH 03/15] Update legend_position parameter(s) to list with top,
 bottom, left, right options

---
 .codeocean/app-panel.json | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 0b18072..32ef49e 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -119,9 +119,15 @@
 			"name": "Legend position",
 			"param_name": "legend_position",
 			"description": "Position of the legend",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "top"
+			"default_value": "top",
+			"extra_data": [
+				"top",
+				"bottom",
+				"left",
+				"right"
+			]
 		},
 		{
 			"id": "point_size_id",

From 26626c22a640b3d1fe8b95b9615692de6f18a31d Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 03:42:45 -0400
Subject: [PATCH 04/15] Convert PCA booleans to lists

---
 .codeocean/app-panel.json | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 32ef49e..c39e8b4 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -145,9 +145,13 @@
 			"name": "Add labels",
 			"param_name": "add_label",
 			"description": "Whether to add labels to points",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "TRUE"
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "label_font_size_id",
@@ -185,9 +189,13 @@
 			"name": "Interactive plots",
 			"param_name": "interactive_plots",
 			"description": "Whether to create interactive plots",
-			"type": "text",
+			"type": "list",
 			"value_type": "string",
-			"default_value": "FALSE"
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		},
 		{
 			"id": "color_values_id",

From 1d01fe308cb1b060f8cc4c930539dc0c7e8f9e61 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 03:49:33 -0400
Subject: [PATCH 05/15] Reorganize PCA panel categories

---
 .codeocean/app-panel.json | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index c39e8b4..5ae5b18 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -12,12 +12,6 @@
 		}
 	],
 	"categories": [
-		{
-			"id": "7Rr6IxOMDucKMImp",
-			"name": "Input Data Parameters",
-			"description": "Options for defining input data",
-			"icon": "\ud83d\udcc1"
-		},
 		{
 			"id": "EzTg1ivlFDHEy9PI",
 			"name": "Basic",
@@ -28,6 +22,12 @@
 			"name": "Visualization",
 			"description": "Visualization and plotting options",
 			"icon": "\ud83d\udcca"
+		},
+		{
+			"id": "7Rr6IxOMDucKMImp",
+			"name": "Advanced",
+			"description": "Advanced input data options",
+			"icon": "\ud83d\udcc1"
 		}
 	],
 	"parameters": [
@@ -49,7 +49,7 @@
 		},
 		{
 			"id": "sub_count_type_id",
-			"category": "FvI4Z2eb9sjL47Jt",
+			"category": "7Rr6IxOMDucKMImp",
 			"name": "Sub count type",
 			"param_name": "sub_count_type",
 			"description": "Sub count type if count_type is a list",
@@ -58,7 +58,7 @@
 		},
 		{
 			"id": "feature_id_colname_id",
-			"category": "FvI4Z2eb9sjL47Jt",
+			"category": "EzTg1ivlFDHEy9PI",
 			"name": "Feature ID column name",
 			"param_name": "feature_id_colname",
 			"description": "Column name for feature IDs",
@@ -67,7 +67,7 @@
 		},
 		{
 			"id": "sample_id_colname_id",
-			"category": "FvI4Z2eb9sjL47Jt",
+			"category": "EzTg1ivlFDHEy9PI",
 			"name": "Sample ID column name",
 			"param_name": "sample_id_colname",
 			"description": "Column name for sample IDs",
@@ -105,7 +105,7 @@
 		},
 		{
 			"id": "principal_components_id",
-			"category": "EzTg1ivlFDHEy9PI",
+			"category": "7Rr6IxOMDucKMImp",
 			"name": "Principal components",
 			"param_name": "principal_components",
 			"description": "Principal components to plot (comma-separated, e.g., 1,2)",

From 1189bd448426eb62fe81717fb072968041dd2d71 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 03:52:49 -0400
Subject: [PATCH 06/15] Adjust PCA panel parameter order

---
 .codeocean/app-panel.json | 58 +++++++++++++++++++--------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 5ae5b18..acc9601 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -47,6 +47,26 @@
 				"norm"
 			]
 		},
+		{
+			"id": "group_colname_id",
+			"category": "EzTg1ivlFDHEy9PI",
+			"name": "Group column name",
+			"param_name": "group_colname",
+			"description": "Column name for sample groups",
+			"type": "text",
+			"value_type": "string",
+			"default_value": "Group"
+		},
+		{
+			"id": "label_colname_id",
+			"category": "EzTg1ivlFDHEy9PI",
+			"name": "Label column name",
+			"param_name": "label_colname",
+			"description": "Column name for sample labels",
+			"type": "text",
+			"value_type": "string",
+			"default_value": "Label"
+		},
 		{
 			"id": "sub_count_type_id",
 			"category": "7Rr6IxOMDucKMImp",
@@ -56,15 +76,6 @@
 			"type": "text",
 			"value_type": "string"
 		},
-		{
-			"id": "feature_id_colname_id",
-			"category": "EzTg1ivlFDHEy9PI",
-			"name": "Feature ID column name",
-			"param_name": "feature_id_colname",
-			"description": "Column name for feature IDs",
-			"type": "text",
-			"value_type": "string"
-		},
 		{
 			"id": "sample_id_colname_id",
 			"category": "EzTg1ivlFDHEy9PI",
@@ -83,26 +94,6 @@
 			"type": "text",
 			"value_type": "string"
 		},
-		{
-			"id": "group_colname_id",
-			"category": "7Rr6IxOMDucKMImp",
-			"name": "Group column name",
-			"param_name": "group_colname",
-			"description": "Column name for sample groups",
-			"type": "text",
-			"value_type": "string",
-			"default_value": "Group"
-		},
-		{
-			"id": "label_colname_id",
-			"category": "7Rr6IxOMDucKMImp",
-			"name": "Label column name",
-			"param_name": "label_colname",
-			"description": "Column name for sample labels",
-			"type": "text",
-			"value_type": "string",
-			"default_value": "Label"
-		},
 		{
 			"id": "principal_components_id",
 			"category": "7Rr6IxOMDucKMImp",
@@ -113,6 +104,15 @@
 			"value_type": "string",
 			"default_value": "1,2"
 		},
+		{
+			"id": "feature_id_colname_id",
+			"category": "7Rr6IxOMDucKMImp",
+			"name": "Feature ID column name",
+			"param_name": "feature_id_colname",
+			"description": "Column name for feature IDs",
+			"type": "text",
+			"value_type": "string"
+		},
 		{
 			"id": "legend_position_id",
 			"category": "FvI4Z2eb9sjL47Jt",

From df498706eedaf4eb5b8666e244c2a4f680191cd2 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 13:40:48 -0400
Subject: [PATCH 07/15] Update changelog for parameter UI changes

---
 CHANGELOG.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 033542a..67436fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Code Ocean capsule - MOSuite - plot 2D PCA
 
+## Development version
+
+- Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1).
+
 ## v2.0
 
 - Use MOSuite v0.3.0
@@ -9,4 +13,4 @@
 
 Initial release
 
-<https://poc-nci.codeocean.io/capsule/8095429/tree/v1> `bd6ca75`
\ No newline at end of file
+<https://poc-nci.codeocean.io/capsule/8095429/tree/v1> `bd6ca75`

From f24ad6b84cbf01522fd31cf5d98e596a20501be4 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 30 Jun 2026 17:40:55 +0000
Subject: [PATCH 08/15] `air format` (GitHub Actions)

---
 code/main.R | 143 ++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 110 insertions(+), 33 deletions(-)

diff --git a/code/main.R b/code/main.R
index 64d8eb1..1440fac 100644
--- a/code/main.R
+++ b/code/main.R
@@ -13,22 +13,97 @@ setup_capsule_environment()
 # parse CLI arguments
 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$add_argument("--feature_id_colname", type="character", default=NULL, help="Column name for feature IDs")
-parser$add_argument("--sample_id_colname", type="character", default=NULL, help="Column name for sample IDs")
-parser$add_argument("--samples_to_rename", type="character", default="", help="Samples to rename in format old:new,old2:new2")
-parser$add_argument("--group_colname", type="character", default="Group", help="Column name for sample groups")
-parser$add_argument("--label_colname", type="character", default="Label", help="Column name for sample labels")
-parser$add_argument("--principal_components", type="character", default="1,2", help="Principal components to plot (comma-separated)")
-parser$add_argument("--legend_position", type="character", default="top", help="Position of the legend")
-parser$add_argument("--point_size", type="double", default=1, help="Size of points in plot")
-parser$add_argument("--add_label", type="logical", default=TRUE, help="Whether to add labels to points")
-parser$add_argument("--label_font_size", type="double", default=3, help="Font size for labels")
-parser$add_argument("--label_offset_x_", type="double", default=2, help="X-axis offset for labels")
-parser$add_argument("--label_offset_y_", type="double", default=2, help="Y-axis offset for labels")
-parser$add_argument("--interactive_plots", type="logical", default=FALSE, help="Whether to create interactive plots")
-parser$add_argument("--color_values", type="character", default="#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500", help="Comma-separated color values")
+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$add_argument(
+  "--feature_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for feature IDs"
+)
+parser$add_argument(
+  "--sample_id_colname",
+  type = "character",
+  default = NULL,
+  help = "Column name for sample IDs"
+)
+parser$add_argument(
+  "--samples_to_rename",
+  type = "character",
+  default = "",
+  help = "Samples to rename in format old:new,old2:new2"
+)
+parser$add_argument(
+  "--group_colname",
+  type = "character",
+  default = "Group",
+  help = "Column name for sample groups"
+)
+parser$add_argument(
+  "--label_colname",
+  type = "character",
+  default = "Label",
+  help = "Column name for sample labels"
+)
+parser$add_argument(
+  "--principal_components",
+  type = "character",
+  default = "1,2",
+  help = "Principal components to plot (comma-separated)"
+)
+parser$add_argument(
+  "--legend_position",
+  type = "character",
+  default = "top",
+  help = "Position of the legend"
+)
+parser$add_argument(
+  "--point_size",
+  type = "double",
+  default = 1,
+  help = "Size of points in plot"
+)
+parser$add_argument(
+  "--add_label",
+  type = "logical",
+  default = TRUE,
+  help = "Whether to add labels to points"
+)
+parser$add_argument(
+  "--label_font_size",
+  type = "double",
+  default = 3,
+  help = "Font size for labels"
+)
+parser$add_argument(
+  "--label_offset_x_",
+  type = "double",
+  default = 2,
+  help = "X-axis offset for labels"
+)
+parser$add_argument(
+  "--label_offset_y_",
+  type = "double",
+  default = 2,
+  help = "Y-axis offset for labels"
+)
+parser$add_argument(
+  "--interactive_plots",
+  type = "logical",
+  default = FALSE,
+  help = "Whether to create interactive plots"
+)
+parser$add_argument(
+  "--color_values",
+  type = "character",
+  default = "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500",
+  help = "Comma-separated color values"
+)
 
 args <- parser$parse_args()
 
@@ -37,21 +112,23 @@ moo <- load_moo_from_data_dir()
 
 # run MOSuite
 plot_pca_2d(
-    moo,
-    count_type = args$count_type,
-    sub_count_type = args$sub_count_type,
-    principal_components = as.integer(parse_optional_vector(args$principal_components)),
-    feature_id_colname = args$feature_id_colname,
-    sample_id_colname = args$sample_id_colname,
-    samples_to_rename = parse_samples_to_rename(args$samples_to_rename),
-    group_colname = args$group_colname,
-    label_colname = args$label_colname,
-    legend_position = args$legend_position,
-    point_size = args$point_size,
-    add_label = args$add_label,
-    label_font_size = args$label_font_size,
-    label_offset_x_ = args$label_offset_x_,
-    label_offset_y_ = args$label_offset_y_,
-    interactive_plots = args$interactive_plots,
-    color_values = parse_optional_vector(args$color_values)
+  moo,
+  count_type = args$count_type,
+  sub_count_type = args$sub_count_type,
+  principal_components = as.integer(parse_optional_vector(
+    args$principal_components
+  )),
+  feature_id_colname = args$feature_id_colname,
+  sample_id_colname = args$sample_id_colname,
+  samples_to_rename = parse_samples_to_rename(args$samples_to_rename),
+  group_colname = args$group_colname,
+  label_colname = args$label_colname,
+  legend_position = args$legend_position,
+  point_size = args$point_size,
+  add_label = args$add_label,
+  label_font_size = args$label_font_size,
+  label_offset_x_ = args$label_offset_x_,
+  label_offset_y_ = args$label_offset_y_,
+  interactive_plots = args$interactive_plots,
+  color_values = parse_optional_vector(args$color_values)
 )

From c38d0cfafb112164545adbfd450e0960bb0dd8a4 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 14:11:00 -0400
Subject: [PATCH 09/15] Add author handle to changelog entry

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 67436fa..08def5d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,7 +2,7 @@
 
 ## Development version
 
-- Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1).
+- Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1, @phoman14).
 
 ## v2.0
 

From 7f75cbc63e7f4c8824a5d0cacc0df9ad33b84ae1 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 15:47:31 -0400
Subject: [PATCH 10/15] Add PCA 2D capsule tests

---
 tests/test-setup.R            |  7 +++++
 tests/testthat.R              |  3 ++
 tests/testthat/helper-panel.R | 54 ++++++++++++++++++++++++++++++++
 tests/testthat/test-main.R    | 59 +++++++++++++++++++++++++++++++++++
 4 files changed, 123 insertions(+)
 create mode 100644 tests/test-setup.R
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/helper-panel.R
 create mode 100644 tests/testthat/test-main.R

diff --git a/tests/test-setup.R b/tests/test-setup.R
new file mode 100644
index 0000000..c31f6b8
--- /dev/null
+++ b/tests/test-setup.R
@@ -0,0 +1,7 @@
+testthat::test_that("test setup has expected capsule files", {
+  repo_root <- normalizePath(file.path(testthat::test_path(), "..", ".."))
+
+  testthat::expect_true(file.exists(file.path(repo_root, "code", "main.R")))
+  testthat::expect_true(file.exists(file.path(repo_root, "code", "run")))
+  testthat::expect_true(file.exists(file.path(repo_root, ".codeocean", "app-panel.json")))
+})
\ No newline at end of file
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..aca735a
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,3 @@
+library(testthat)
+
+test_dir(file.path("tests", "testthat"))
\ No newline at end of file
diff --git a/tests/testthat/helper-panel.R b/tests/testthat/helper-panel.R
new file mode 100644
index 0000000..2d8d52d
--- /dev/null
+++ b/tests/testthat/helper-panel.R
@@ -0,0 +1,54 @@
+repo_path <- function(...) {
+  file.path(normalizePath(file.path(testthat::test_path(), "..", "..")), ...)
+}
+
+read_repo_file <- function(...) {
+  readLines(repo_path(...), warn = FALSE)
+}
+
+extract_main_arguments <- function(main_lines) {
+  main_text <- paste(main_lines, collapse = "\n")
+  matches <- regmatches(
+    main_text,
+    gregexpr(
+      'parser\\$add_argument\\(\\s*"--([[:alnum:]_]+)"',
+      main_text,
+      perl = TRUE
+    )
+  )[[1]]
+
+  sub('.*"--([[:alnum:]_]+)".*', "\\1", matches)
+}
+
+extract_panel_param_names <- function(panel_lines) {
+  matches <- regmatches(
+    panel_lines,
+    gregexpr('"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)"', panel_lines)
+  )
+  matches <- unlist(matches, use.names = FALSE)
+
+  sub('.*"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)".*', "\\1", matches)
+}
+
+extract_panel_default <- function(panel_lines, param_name) {
+  param_line <- grep(sprintf('"param_name"[[:space:]]*:[[:space:]]*"%s"', param_name), panel_lines)
+  if (length(param_line) != 1) {
+    return(NA_character_)
+  }
+
+  next_param <- grep('"param_name"[[:space:]]*:', panel_lines)
+  next_param <- next_param[next_param > param_line]
+  end_line <- if (length(next_param) > 0) next_param[[1]] - 1 else length(panel_lines)
+  block <- panel_lines[param_line:end_line]
+  default_line <- grep('"default_value"[[:space:]]*:', block, value = TRUE)
+  if (length(default_line) != 1) {
+    return(NA_character_)
+  }
+
+  sub('.*"default_value"[[:space:]]*:[[:space:]]*"([^"]*)".*', "\\1", default_line)
+}
+
+expect_same_values <- function(actual, expected, info = NULL) {
+  testthat::expect_setequal(actual, expected)
+  testthat::expect_equal(length(actual), length(unique(actual)), info = "Values should not be duplicated")
+}
\ No newline at end of file
diff --git a/tests/testthat/test-main.R b/tests/testthat/test-main.R
new file mode 100644
index 0000000..f4998cc
--- /dev/null
+++ b/tests/testthat/test-main.R
@@ -0,0 +1,59 @@
+test_that("Code Ocean panel uses named parameters accepted by main.R", {
+  main_args <- extract_main_arguments(read_repo_file("code", "main.R"))
+  panel_lines <- read_repo_file(".codeocean", "app-panel.json")
+  panel_args <- extract_panel_param_names(panel_lines)
+
+  expect_true(
+    any(grepl('"named_parameters"[[:space:]]*:[[:space:]]*true', panel_lines)),
+    info = "Code Ocean should pass parameters by name to main.R"
+  )
+  expect_same_values(
+    panel_args,
+    main_args,
+    info = "Every app-panel param_name should match a main.R CLI argument"
+  )
+})
+
+test_that("2D PCA capsule keeps expected PCA parameter contract", {
+  main_lines <- read_repo_file("code", "main.R")
+  panel_lines <- read_repo_file(".codeocean", "app-panel.json")
+
+  shared_pca_args <- c(
+    "count_type",
+    "sub_count_type",
+    "feature_id_colname",
+    "sample_id_colname",
+    "samples_to_rename",
+    "group_colname",
+    "label_colname",
+    "principal_components",
+    "point_size",
+    "label_font_size",
+    "color_values"
+  )
+  two_dimensional_args <- c(
+    "legend_position",
+    "add_label",
+    "label_offset_x_",
+    "label_offset_y_",
+    "interactive_plots"
+  )
+
+  expect_same_values(
+    extract_main_arguments(main_lines),
+    c(shared_pca_args, two_dimensional_args),
+    info = "2D PCA main.R should expose shared PCA args plus 2D-specific controls"
+  )
+  expect_match(paste(main_lines, collapse = "\n"), "plot_pca_2d\\(")
+  expect_equal(extract_panel_default(panel_lines, "principal_components"), "1,2")
+  expect_equal(extract_panel_default(panel_lines, "add_label"), "TRUE")
+  expect_equal(extract_panel_default(panel_lines, "interactive_plots"), "FALSE")
+})
+
+test_that("run wrapper prepares result directories and forwards CLI arguments", {
+  run_lines <- read_repo_file("code", "run")
+  run_text <- paste(run_lines, collapse = "\n")
+
+  expect_match(run_text, "mkdir -p \\.\\./results/figures \\.\\./results/moo")
+  expect_match(run_text, 'Rscript main\\.R "\\$@"')
+})
\ No newline at end of file

From 4bcd41e173d14232e6dfb2a798322dff81a5c7ca Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 30 Jun 2026 19:47:43 +0000
Subject: [PATCH 11/15] `air format` (GitHub Actions)

---
 tests/test-setup.R            |  8 ++++++--
 tests/testthat.R              |  2 +-
 tests/testthat/helper-panel.R | 36 ++++++++++++++++++++++++++++-------
 tests/testthat/test-main.R    |  7 +++++--
 4 files changed, 41 insertions(+), 12 deletions(-)

diff --git a/tests/test-setup.R b/tests/test-setup.R
index c31f6b8..dc1ce41 100644
--- a/tests/test-setup.R
+++ b/tests/test-setup.R
@@ -3,5 +3,9 @@ testthat::test_that("test setup has expected capsule files", {
 
   testthat::expect_true(file.exists(file.path(repo_root, "code", "main.R")))
   testthat::expect_true(file.exists(file.path(repo_root, "code", "run")))
-  testthat::expect_true(file.exists(file.path(repo_root, ".codeocean", "app-panel.json")))
-})
\ No newline at end of file
+  testthat::expect_true(file.exists(file.path(
+    repo_root,
+    ".codeocean",
+    "app-panel.json"
+  )))
+})
diff --git a/tests/testthat.R b/tests/testthat.R
index aca735a..fa13c48 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,3 +1,3 @@
 library(testthat)
 
-test_dir(file.path("tests", "testthat"))
\ No newline at end of file
+test_dir(file.path("tests", "testthat"))
diff --git a/tests/testthat/helper-panel.R b/tests/testthat/helper-panel.R
index 2d8d52d..fbf5a2d 100644
--- a/tests/testthat/helper-panel.R
+++ b/tests/testthat/helper-panel.R
@@ -23,32 +23,54 @@ extract_main_arguments <- function(main_lines) {
 extract_panel_param_names <- function(panel_lines) {
   matches <- regmatches(
     panel_lines,
-    gregexpr('"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)"', panel_lines)
+    gregexpr(
+      '"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)"',
+      panel_lines
+    )
   )
   matches <- unlist(matches, use.names = FALSE)
 
-  sub('.*"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)".*', "\\1", matches)
+  sub(
+    '.*"param_name"[[:space:]]*:[[:space:]]*"([[:alnum:]_]+)".*',
+    "\\1",
+    matches
+  )
 }
 
 extract_panel_default <- function(panel_lines, param_name) {
-  param_line <- grep(sprintf('"param_name"[[:space:]]*:[[:space:]]*"%s"', param_name), panel_lines)
+  param_line <- grep(
+    sprintf('"param_name"[[:space:]]*:[[:space:]]*"%s"', param_name),
+    panel_lines
+  )
   if (length(param_line) != 1) {
     return(NA_character_)
   }
 
   next_param <- grep('"param_name"[[:space:]]*:', panel_lines)
   next_param <- next_param[next_param > param_line]
-  end_line <- if (length(next_param) > 0) next_param[[1]] - 1 else length(panel_lines)
+  end_line <- if (length(next_param) > 0) {
+    next_param[[1]] - 1
+  } else {
+    length(panel_lines)
+  }
   block <- panel_lines[param_line:end_line]
   default_line <- grep('"default_value"[[:space:]]*:', block, value = TRUE)
   if (length(default_line) != 1) {
     return(NA_character_)
   }
 
-  sub('.*"default_value"[[:space:]]*:[[:space:]]*"([^"]*)".*', "\\1", default_line)
+  sub(
+    '.*"default_value"[[:space:]]*:[[:space:]]*"([^"]*)".*',
+    "\\1",
+    default_line
+  )
 }
 
 expect_same_values <- function(actual, expected, info = NULL) {
   testthat::expect_setequal(actual, expected)
-  testthat::expect_equal(length(actual), length(unique(actual)), info = "Values should not be duplicated")
-}
\ No newline at end of file
+  testthat::expect_equal(
+    length(actual),
+    length(unique(actual)),
+    info = "Values should not be duplicated"
+  )
+}
diff --git a/tests/testthat/test-main.R b/tests/testthat/test-main.R
index f4998cc..b0c0746 100644
--- a/tests/testthat/test-main.R
+++ b/tests/testthat/test-main.R
@@ -45,7 +45,10 @@ test_that("2D PCA capsule keeps expected PCA parameter contract", {
     info = "2D PCA main.R should expose shared PCA args plus 2D-specific controls"
   )
   expect_match(paste(main_lines, collapse = "\n"), "plot_pca_2d\\(")
-  expect_equal(extract_panel_default(panel_lines, "principal_components"), "1,2")
+  expect_equal(
+    extract_panel_default(panel_lines, "principal_components"),
+    "1,2"
+  )
   expect_equal(extract_panel_default(panel_lines, "add_label"), "TRUE")
   expect_equal(extract_panel_default(panel_lines, "interactive_plots"), "FALSE")
 })
@@ -56,4 +59,4 @@ test_that("run wrapper prepares result directories and forwards CLI arguments",
 
   expect_match(run_text, "mkdir -p \\.\\./results/figures \\.\\./results/moo")
   expect_match(run_text, 'Rscript main\\.R "\\$@"')
-})
\ No newline at end of file
+})

From 9bf00a7fc7fee66866b91227b8dd665d2e921c66 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Tue, 30 Jun 2026 15:50:21 -0400
Subject: [PATCH 12/15] Update changelog for PCA 2D tests

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08def5d..bd63b2e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## Development version
 
+- Added tests for the plot pca 2D capsule Code Ocean panel and CLI contract (#1, @phoman14).
 - Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1, @phoman14).
 
 ## v2.0

From 9143df54cab556bb39fb4bf29a4abee75d409947 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Thu, 2 Jul 2026 13:23:10 -0400
Subject: [PATCH 13/15] Document PCA 2D color fallback behavior

Update color_values help text to describe the MOSuite default palette, supplied-color precedence, generated extra colors, and random fallback behavior.
---
 .codeocean/app-panel.json | 3 ++-
 code/main.R               | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index acc9601..5e28204 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -202,7 +202,8 @@
 			"category": "FvI4Z2eb9sjL47Jt",
 			"name": "Color values",
 			"param_name": "color_values",
-			"description": "Comma-separated color values for groups",
+			"description": "Comma-separated group colors. Defaults to the MOSuite palette.",
+			"help_text": "Use color names or hex codes. Supplied colors are used first; if there are more groups than colors, additional colors are generated from the MOSuite palette, with random colors only if that palette is too short.",
 			"type": "text",
 			"value_type": "string",
 			"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
diff --git a/code/main.R b/code/main.R
index 1440fac..0dc8452 100644
--- a/code/main.R
+++ b/code/main.R
@@ -102,7 +102,7 @@ parser$add_argument(
   "--color_values",
   type = "character",
   default = "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500",
-  help = "Comma-separated color values"
+  help = "Comma-separated group colors. Defaults to the MOSuite palette; supplied colors are used first and extra group colors are generated when needed."
 )
 
 args <- parser$parse_args()

From 54491b4ff5d045b7e4ed9f1023d8442265e38f88 Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Thu, 2 Jul 2026 14:52:12 -0400
Subject: [PATCH 14/15] Align PCA color defaults

---
 .codeocean/app-panel.json | 2 +-
 code/main.R               | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json
index 5e28204..097ca34 100644
--- a/.codeocean/app-panel.json
+++ b/.codeocean/app-panel.json
@@ -137,7 +137,7 @@
 			"description": "Size of points in plot",
 			"type": "text",
 			"value_type": "string",
-			"default_value": "1"
+			"default_value": "3"
 		},
 		{
 			"id": "add_label_id",
diff --git a/code/main.R b/code/main.R
index 0dc8452..89642f2 100644
--- a/code/main.R
+++ b/code/main.R
@@ -65,7 +65,7 @@ parser$add_argument(
 parser$add_argument(
   "--point_size",
   type = "double",
-  default = 1,
+  default = 3,
   help = "Size of points in plot"
 )
 parser$add_argument(
@@ -102,7 +102,7 @@ parser$add_argument(
   "--color_values",
   type = "character",
   default = "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500",
-  help = "Comma-separated group colors. Defaults to the MOSuite palette; supplied colors are used first and extra group colors are generated when needed."
+  help = "Comma-separated group colors. Defaults to the MOSuite palette. Extra group colors are generated when needed."
 )
 
 args <- parser$parse_args()

From 244b7f0d9ffb57025debf886a729f98f0442f6de Mon Sep 17 00:00:00 2001
From: phoman14 <Philip.homan@nih.gov>
Date: Thu, 2 Jul 2026 15:49:31 -0400
Subject: [PATCH 15/15] docs: update PCA default changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bd63b2e..d008cad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## Development version
 
+- Align the PCA color defaults with MOSuite package defaults.
+- Document that color palettes fall back to random colors only when too few colors are provided.
 - Added tests for the plot pca 2D capsule Code Ocean panel and CLI contract (#1, @phoman14).
 - Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1, @phoman14).