fix: Standardize 2D PCA output figures across MOSuite function calls (#2)

* Update count_type to list with raw, clean, filt, norm options (default: filt)

* Move count_type to first position in Basic category

* Update legend_position parameter(s) to list with top, bottom, left, right options

* Convert PCA booleans to lists

* Reorganize PCA panel categories

* Adjust PCA panel parameter order

* Update changelog for parameter UI changes

* `air format` (GitHub Actions)

* Add author handle to changelog entry

* Add PCA 2D capsule tests

* `air format` (GitHub Actions)

* Update changelog for PCA 2D tests

* 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.

* Align PCA color defaults

* docs: update PCA default changelog

* docs: add changelog author attribution

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Author: 3 people

.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",
@@ -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"

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 ## Development version
 
+- Align the PCA color defaults with MOSuite package defaults (#2, @phoman14).
+- Document that color palettes fall back to random colors only when too few colors are provided (#2, @phoman14).
 - Improved the Code Ocean parameter UI for the plot pca 2D capsule (#1, @phoman14).
 
 ## v2.0

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 color values"
+  help = "Comma-separated group colors. Defaults to the MOSuite palette. Extra group colors are generated when needed."
 )
 
 args <- parser$parse_args()