feat(plots): standardize output figures across MOSuite function calls by phoman14 · Pull Request #223 · CCBR/MOSuite

phoman14 · 2026-07-02T19:51:34Z

Summary

This PR standardizes the appearance of MOSuite output figures across direct plotting calls, workflow calls, and the matching Code Ocean capsules. The intent is that the same data and grouping metadata produce consistent colors, category order, point sizing, and readable legends whether a figure is created by plot_pca_2d(), plot_pca_3d(), plot_histogram(), plot_read_depth(), filter_counts(), normalize_counts(), batch_correct_counts(), or an affected capsule.

Changes

Align MOSuite plot color defaults with Code Ocean capsule defaults while keeping get_mosuite_colors() available for later use.
Preserve random color generation as a fallback only when a selected or provided palette has too few colors.
Respect factor level order for factor grouping columns and metadata first appearance for non-factor grouping columns.
Improve top and bottom legend wrapping and automatic legend text sizing for PCA and histogram plots with many or long labels.
Align filter_counts(), normalize_counts(), and batch_correct_counts() PCA/histogram defaults and forwarded settings.
Add optional group coloring to plot_read_depth() and the clean_raw_counts() read-depth output while preserving the single-color default when no group is selected.
Add package tests for color resolution, PCA legends, histogram legends, filter defaults, normalize defaults, batch correction defaults, and read-depth group coloring/fallback behavior.
Update NEWS.md for the user-facing plotting changes.

Affected capsule repos from these package changes:

NIDAP-Community/MOSuite-clean: feat(app-panel): expose read-depth plot color controls NIDAP-Community/MOSuite-clean#3
NIDAP-Community/MOSuite-filter-counts: fix: Standardize filter output figures across MOSuite function calls NIDAP-Community/MOSuite-filter-counts#3
NIDAP-Community/MOSuite-normalize-counts: fix: Standardize normalize output figures across MOSuite function calls NIDAP-Community/MOSuite-normalize-counts#4
NIDAP-Community/MOSuite-plot-pca-2D: fix: Standardize 2D PCA output figures across MOSuite function calls NIDAP-Community/MOSuite-plot-pca-2D#2
NIDAP-Community/MOSuite-plot-pca-3D: fix: Standardize 3D PCA output figures across MOSuite function calls NIDAP-Community/MOSuite-plot-pca-3D#2
NIDAP-Community/MOSuite-batch-correct-counts: fix: Standardize batch correction figure behavior across function calls NIDAP-Community/MOSuite-batch-correct-counts#4

Validation:

test-plot_pca.R: PASS 21
test-plot_histogram.R: PASS 14
test-filter.R: PASS 27
test-normalize.R: PASS 22
test-batch-correction.R: PASS 22
Focused package validation on FigOutSync@6631ece: devtools::test(filter = plots|plot_read_depth|clean): PASS 25
Clean capsule validation: Rscript tests/testthat.R: PASS 13
Workspace Rmd render succeeded and generated no-group, grouped-color, and one-color fallback read-depth examples in tests/plotting-parameters-test-output/figures/read_depth/.
Rd syntax validations passed for updated PCA/histogram, batch correction, clean, and read-depth docs.
devtools::check(error_on = never) was run locally earlier on FigOutSync@dbf0405: DESeq2 integration and graphics-device-sensitive plot snapshots are skipped during R CMD check; result was 1 error, 0 warnings, 0 notes because two untouched macOS differential-analysis tests still fail. Full check was not rerun after the read-depth follow-up.

Issues

No linked issue.

PR Checklist

(~~Strikethrough~~ any points that are not applicable.)

This comment contains a description of changes with justifications, with any relevant issues linked.
Write unit tests for any new features, bug fixes, or other code changes.
Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
Update NEWS.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
Run devtools::check() locally and fix all notes, warnings, and errors. Local devtools::check(error_on = never) was run on macOS earlier; DESeq2 integration and plot snapshot checks are skipped during R CMD check, leaving 0 warnings and 0 notes, but the check still has 1 test error from untouched differential-analysis expectations in test-differential.R.

Use the MOSuite palette as the hardcoded filter and normalize plot color default, extend short explicit palettes through the selected palette path, and keep random colors as the get_colors_vctr fallback. Update docs, JSON defaults, and focused color/filter/normalize tests.

for more information, see https://pre-commit.ci

codecov · 2026-07-02T20:03:26Z

Codecov Report

❌ Patch coverage is 87.41722% with 38 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.81%. Comparing base (ce1865a) to head (ee8f925).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
R/batch-correction.R	83.87%	10 Missing ⚠️
R/plot_heatmap.R	57.14%	9 Missing ⚠️
R/filter.R	62.50%	6 Missing ⚠️
R/plot_pca.R	80.64%	6 Missing ⚠️
R/plots.R	90.90%	4 Missing ⚠️
R/plot_read_depth.R	95.12%	2 Missing ⚠️
R/colors.R	97.77%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #223      +/-   ##
==========================================
+ Coverage   79.66%   79.81%   +0.15%     
==========================================
  Files          22       22              
  Lines        3398     3612     +214     
==========================================
+ Hits         2707     2883     +176     
- Misses        691      729      +38

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Copilot

Pull request overview

This PR standardizes MOSuite figure defaults (colors, legend layout, and sizing) so that plots created directly via plotting functions and those produced indirectly by filter_counts(), normalize_counts(), and batch_correct_counts() render consistently (including in downstream capsule workflows).

Changes:

Introduces deterministic color-resolution helpers (including factor-level / first-observed ordering) and applies them across PCA, histogram, and heatmap plots.
Adds automatic legend text sizing and top/bottom legend wrapping for dense legends.
Aligns workflow functions’ plotting defaults/forwarding and expands test coverage + updates docs/JSON defaults.

Reviewed changes

Copilot reviewed 45 out of 47 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/testthat/test-plot_pca.R	Adds PCA tests for color resolution and wrapped legends.
tests/testthat/test-plot_histogram.R	Adds histogram tests for legend wrapping and deterministic color mapping.
tests/testthat/test-plot_heatmap.R	Adds heatmap tests for annotation color resolution order.
tests/testthat/test-normalize.R	Adds tests ensuring normalize forwards plotting args/default colors.
tests/testthat/test-filter.R	Adds tests ensuring filter forwards plotting args/default colors.
tests/testthat/test-colors.R	Updates palette expectations; adds tests for `resolve_plot_colors()`.
tests/testthat/test-batch-correction.R	Adds tests ensuring batch correction forwards plotting args/default colors.
tests/testthat/_snaps/E2E.md	Updates snapshot output reflecting new default `colors_for_plots` type.
R/plots.R	Adds internal legend sizing/wrapping helpers for ggplot color legends.
R/plot_pca.R	Updates PCA defaults; applies deterministic colors + legend layout logic.
R/plot_histogram.R	Applies deterministic colors + legend sizing/wrapping to histograms.
R/plot_heatmap.R	Uses shared color resolver for heatmap annotations; adjusts palette expansion.
R/normalize.R	Aligns normalize defaults and forwards histogram axis/legend settings.
R/filter.R	Aligns filter defaults; improves plot saving sizing and forwards plotting args.
R/colors.R	Adds MOSuite palette + observed-order helper + `resolve_plot_colors()`.
R/batch-correction.R	Aligns batch-correct plotting defaults/forwarding; adds interactive option.
PCA_COLOR_MATCH_NOTES.md	Adds internal design notes for the color-matching changes.
NEWS.md	Documents user-facing plotting default changes.
man/set_color_pal.Rd	Updates default palette function documentation.
man/plot_pca_3d.Rd	Updates color mapping documentation for PCA 3D.
man/plot_pca_2d.Rd	Updates defaults + documents legend font sizing and color mapping rules.
man/plot_histogram.data.frame.Rd	Documents color mapping rules + auto legend font sizing.
man/plot_expr_heatmap.Rd	Documents color mapping rules for heatmap group colors.
man/plot_corr_heatmap-data.frame.Rd	Documents color mapping rules for correlation heatmap annotations.
man/normalize_counts.Rd	Updates defaults and clarifies color/legend behavior.
man/get_colors_vctr.Rd	Updates default palette + ordering behavior documentation.
man/get_colors_lst.Rd	Updates default palette documentation.
man/filter_counts.Rd	Updates defaults and clarifies color/legend behavior.
man/batch_correct_counts.Rd	Updates defaults + documents new forwarded plotting parameters.
inst/extdata/json_args/defaults/plot_pca_2d.json	Updates JSON defaults to match new PCA defaults.
inst/extdata/json_args/defaults/normalize_counts.json	Updates JSON defaults to match new normalize defaults.
inst/extdata/json_args/defaults/filter_counts.json	Updates JSON defaults to match new filter defaults.
inst/extdata/json_args/defaults/batch_correct_counts.json	Updates JSON defaults to match new batch-correct defaults.
inst/extdata/json_args/common/plot_pca_2d.json	Updates shared JSON defaults for PCA point size.
inst/extdata/json_args/common/normalize_counts.json	Updates shared JSON defaults for normalize colors/legend size.
inst/extdata/json_args/common/filter_counts.json	Updates shared JSON defaults for filter colors/legend size.
inst/extdata/galaxy/2_blueprints/plot_pca_3d.json	Updates blueprint descriptions re: deterministic color assignment.
inst/extdata/galaxy/2_blueprints/plot_pca_2d.json	Updates blueprint defaults + descriptions for PCA 2D.
inst/extdata/galaxy/2_blueprints/normalize_counts.json	Updates blueprint defaults + descriptions for normalize.
inst/extdata/galaxy/2_blueprints/filter_counts.json	Updates blueprint defaults + descriptions for filter.
inst/extdata/galaxy/2_blueprints/batch_correct_counts.json	Updates blueprint defaults + descriptions for batch correction.
inst/extdata/galaxy/1_mosuite-templates/normalize_counts.json	Updates template default for histogram grouping.
inst/extdata/galaxy/1_mosuite-templates/filter_counts.json	Updates template default for histogram grouping.
inst/extdata/galaxy/0_nidap-1.0/Normalization_CCBR_.code-template.json	Updates legacy template default for histogram grouping.
inst/extdata/galaxy/0_nidap-1.0/Filter_Low_Counts_CCBR_.code-template.json	Updates legacy template default for histogram grouping.
inst/extdata/galaxy/0_nidap-1.0/Batch_Correction_CCBR_.code-template.json	Updates legacy template default for histogram grouping.
CITATION.cff	Updates a referenced author email.

Files not reviewed (2)

man/batch_correct_counts.Rd: Generated file
man/filter_counts.Rd: Generated file

  return(unname(colorspace::hex(colorspace::LAB(km$centers))))
 }

+get_mosuite_colors <- function(n, ...) {


+  if (!is.null(names(color_values))) {
+    if (all(obs %in% names(color_values))) {
+      return(color_values)
+    }
+  }


        fill = NA,
        linewidth = 1
      ),
      axis.ticks = ggplot2::element_line(linewidth = 1),
-      legend.text = ggplot2::element_text(size = 18)
+      legend.text = ggplot2::element_text(size = legend_font_size),
+      aspect.ratio = 1
    ) +
-    ggplot2::coord_fixed(ratio = 1.5) +
    ggplot2::scale_colour_manual(values = color_values) +


+1. Accept `color_values` and the observed group labels.
+2. Preserve existing names when `color_values` is already a named vector for those labels.
+3. Treat named vectors whose names do not cover the observed groups as palette-label names for compatibility.
+4. When `color_values` is unnamed, assign names deterministically using first-observed group labels, matching `get_colors_vctr()`.
+5. Error when there are more observed groups than colors.


+Implemented helper shape:
+
+```r
+resolve_plot_colors(dat, colname, color_values = NULL, palette_fun = grDevices::palette.colors, ...)


kelly-sovacool

Here's an initial review for changes that definitely need to be made. I'm taking a closer look at the color-picking code locally and will have more suggestions for that soon.

AI notes are removed from file and so not included in .Rbuildignore Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

already skipped on ci (gh actions). this line is redundant. Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Issue should not be skipped locally. If error the issue should be addressed Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

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

phoman14 added 10 commits June 29, 2026 19:58

Make PCA plot outputs square

4c64613

Document and test plotting parameters

ca7b833

Document PCA color matching follow-up

6eea937

Resolve plot colors by category mapping

45d35e6

Align plot color defaults

b24cbfb

Align PCA plot colors with capsule defaults

eea97d9

Improve plot legend wrapping

e81e864

Align histogram legend font defaults

f8a911d

docs: update plot default news

a17dde0

github-actions Bot added the MOSuite RepoName label Jul 2, 2026

[pre-commit.ci] auto fixes from pre-commit.com hooks

d1901ae

for more information, see https://pre-commit.ci

phoman14 requested a review from kelly-sovacool July 2, 2026 19:52

phoman14 changed the title ~~Align plot defaults with capsule behavior~~ Standardize output figures across MOSuite function calls Jul 2, 2026

ccbr-bot Bot added 2 commits July 2, 2026 19:56

ci: 🤖 auto-format

3053b8f

ci: 🤖 auto-format

42c8cb3

phoman14 and others added 3 commits July 6, 2026 11:57

feat: align batch correction plot defaults

9beea50

ci: 🤖 auto-format

c76a9db

Merge branch 'main' into FigOutSync

f254bfb

kelly-sovacool requested a review from Copilot July 6, 2026 16:33

Copilot started reviewing on behalf of kelly-sovacool July 6, 2026 16:33 View session

Copilot AI reviewed Jul 6, 2026

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phoman14 and others added 3 commits July 6, 2026 16:19

test: skip dependency-sensitive checks in R CMD check

dbf0405

feat: color read-depth plots by group

d318630

ci: 🤖 auto-format

6631ece

phoman14 mentioned this pull request Jul 7, 2026

feat(app-panel): expose read-depth plot color controls NIDAP-Community/MOSuite-clean#3

Merged

kelly-sovacool self-assigned this Jul 7, 2026

kelly-sovacool requested changes Jul 7, 2026

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kelly-sovacool changed the title ~~Standardize output figures across MOSuite function calls~~ feat(plots): standardize output figures across MOSuite function calls Jul 7, 2026

phoman14 and others added 6 commits July 7, 2026 11:53

chore: move color match notes out of package

510da94

chore: restore NIDAP 1.0 reference templates

2579ff5

Update .Rbuildignore

328a768

AI notes are removed from file and so not included in .Rbuildignore Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Update tests/testthat/test-plots.R

78cd07f

already skipped on ci (gh actions). this line is redundant. Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Update tests/testthat/test-plots.R

78d3a7a

Issue should not be skipped locally. If error the issue should be addressed Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Merge branch 'main' into FigOutSync

c99d881

phoman14 requested a review from kelly-sovacool July 7, 2026 17:47

Merge branch 'main' into FigOutSync

ee8f925

kelly-sovacool reviewed Jul 7, 2026

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Comment thread tests/testthat/test-deseq2.R Outdated

phoman14 and others added 2 commits July 9, 2026 12:35

Update tests/testthat/test-deseq2.R

4d77b0f

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

chore: ignore .vscode/

f2177f7

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