fix: Standardize normalize output figures across MOSuite function calls (#4)

* Update boolean parameters to TRUE/FALSE list options

* Move count_type to first position in Basic category

* Update norm_type to list with voom option (default: voom)

* Update voom_normalization_method to list with none, scale, quantile, cyclicloess (default: quantile)

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

* Match PCA point size default to filter capsule

* Split visualization parameters by plot type

* Align normalize capsule color defaults

Use the MOSuite plot color default for normalize-counts and update capsule help text for supplied colors, generated extras, and random fallback behavior.

* Align plot color defaults

* Align histogram legend font default

* docs: update plot default changelog

* build: install FigOutSync package for normalize capsule

* docs: add changelog author attribution

* `air format` (GitHub Actions)

* Delete environment/postInstall

* Update CHANGELOG.md

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

* chore: add MOSuite via syncweaver (#5)

* chore: add MOSuite via syncweaver

* `air format` (GitHub Actions)

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* test: remove capsule environment tests

* `air format` (GitHub Actions)

---------

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Author: phoman14

.codeocean/app-panel.json

@@ -70,6 +70,19 @@
 				"filt"
 			]
 		},
+		{
+			"id": "vA3pMmQwKs8nZx1c",
+			"category": "gn9FXwemlVazWQIo",
+			"name": "Normalization type",
+			"param_name": "norm_type",
+			"description": "Normalization type (default: voom)",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "voom",
+			"extra_data": [
+				"voom"
+			]
+		},
 		{
 			"id": "vB4qNnRxLt9oAy2d",
 			"category": "gn9FXwemlVazWQIo",
@@ -94,19 +107,6 @@
 				"FALSE"
 			]
 		},
-		{
-			"id": "vA3pMmQwKs8nZx1c",
-			"category": "gn9FXwemlVazWQIo",
-			"name": "Normalization type",
-			"param_name": "norm_type",
-			"description": "Normalization type (default: voom)",
-			"type": "list",
-			"value_type": "string",
-			"default_value": "voom",
-			"extra_data": [
-				"voom"
-			]
-		},
 		{
 			"id": "vD6sPpTzNv1qCw4f",
 			"category": "gn9FXwemlVazWQIo",
@@ -178,10 +178,11 @@
 			"category": "VisGeneral",
 			"name": "Colors for plots",
 			"param_name": "colors_for_plots",
-			"description": "Comma-separated list of colors for PCA and histogram",
-			"help_text": "Use color names or hex codes. Leave blank to use defaults",
+			"description": "Comma-separated colors for PCA and histogram. 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"
+			"value_type": "string",
+			"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
 		},
 		{
 			"id": "vK3zWwAgUc8xJd1m",
@@ -271,7 +272,7 @@
 			"description": "Point size for the PCA plot",
 			"type": "text",
 			"value_type": "number",
-			"default_value": "1"
+			"default_value": "3"
 		},
 		{
 			"id": "vS1hEeIoCk6fRl9u",
@@ -326,10 +327,10 @@
 			"category": "VisHistogram",
 			"name": "Legend font size for histogram",
 			"param_name": "legend_font_size_for_histogram",
-			"description": "Legend font size for histogram plot",
+			"description": "Legend font size for histogram plot. Leave blank to scale automatically.",
 			"type": "text",
 			"value_type": "number",
-			"default_value": "10"
+			"default_value": ""
 		},
 		{
 			"id": "vX6mJjNtHp1kWq4z",

.gitattributes

@@ -0,0 +1 @@
+code/MOSuite linguist-vendored

.syncweaver-lock.json

@@ -0,0 +1,12 @@
+{
+  "host": "NIDAP-Community/MOSuite-normalize-counts",
+  "orchestrator": "NIDAP-Community/syncweaver-orchestrator",
+  "syncweaver_version": "0.0.1-dev",
+  "sources": {
+    "code/MOSuite": {
+      "repo_url": "https://github.com/CCBR/MOSuite",
+      "ref": "FigOutSync",
+      "git_sha": "ee8f9259be4cf5c5567e365d31ae452873de46df"
+    }
+  }
+}

CHANGELOG.md

@@ -1,7 +1,9 @@
 # Code Ocean capsule - MOSuite - normalize counts
 
-## development version
+## Development version
 
+- Align plot color defaults with MOSuite package defaults (#4, @phoman14).
+- Leave the histogram legend font size blank by default so MOSuite can scale long or numerous legend labels automatically (#4, @phoman14).
 - Improve the Code Ocean app panel parameter selection and categories. (#3, @phoman14)
 
 ## v3.0

code/MOSuite/.Rbuildignore

@@ -0,0 +1,38 @@
+^renv$
+^renv\.lock$
+^_pkgdown\.yml$
+^\.github$
+^\.lintr$
+^\.pre-commit-config\.yaml$
+^\.prettierignore$
+^\.prettierrc$
+^\.Rproj\.user$
+^CITATION\.cff$
+^codemeta\.json$
+^data-raw$
+^doc$
+^Dockerfile$
+^docker$
+^docs$
+^figures$
+^LICENSE\.md$
+^Meta$
+^MOSuite\.Rproj$
+^pkgdown$
+^README\.Rmd$
+^README\.html$
+^README_files$
+^Rplots\.pdf$
+^moo_input\.rds$
+^plot-volc-enh\.json$
+^volc-sum-params\.json$
+^report_files$
+^inst/quarto/report_files$
+^tests/figures$
+^vignettes/figures/$
+^vignettes/memory\.Rmd$
+^vignettes/cli\.Rmd$
+VennDiagram.*\.log
+^[.]?air[.]toml$
+^\.vscode$
+^SECURITY\.md$

code/MOSuite/.gitattributes

@@ -0,0 +1,4 @@
+CITATION.cff linguist-generated
+codemeta.json linguist-generated
+NAMESPACE linguist-generated
+man/ linguist-generated

code/MOSuite/.github/.Rprofile

@@ -0,0 +1 @@
+rlang::global_entrace()

code/MOSuite/.github/.gitignore

@@ -0,0 +1 @@
+*.html