test: add unit tests for seurat_clustering and cluster_metrics by bianjh-cloud · Pull Request #52 · CCBR/SCOT

bianjh-cloud · 2026-04-21T15:21:39Z

Changes

test-cluster_metrics.R

imports BRCA fixture data, clustered by seurat_clustering
verifies output shape for silhouette parameter
checks numeric results, consistency across metadata variables
expect errors for missing cluster columns, invalid reduction

test-seurat_clustering.R

verifies default parameters
run function on BRCA fixture
checks that low / high resolution cluster(s) numbers are plotted correctly
checks errors for invalid npcs_in, resolution, and algorithm inputs

Issues

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.
R-CMD-check succeeds on the most recent user commit.

- Add test-make_bubble_plot.R and test-make_volcano_plot.R - Update test-split_featurePlot.R - Remove source() calls from test-make_volcano_plot.R - Rename avg_log2FC to avg_log_2_fc in make_volcano_plot.R and tests - Hardcode fixed math expectations (log10 transforms) - Regenerate man/make_volcano_plot.Rd Generated using AI

Add missing test helper that defines selectData(), needed by test-make_bubble_plot.R and test-split_featurePlot.R at load time.

…n, seurat_clustering, and cluster_metrics

kelly-sovacool

Take a look at my review of #49 and apply those concepts here as well

kelly-sovacool · 2026-05-01T16:18:36Z

@wong-nw do you have suggestions for new names to seurat_clustering and cluster_metrics so they are verbs per the style guide? https://style.tidyverse.org/functions.html

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

kelly-sovacool

Looks like you accidentally made a commit on this branch with changes that were supposed to be on the other branch: b6254bd
This PR should only contain changes related to seurat_clustering, cluster_metrics, and the BRCA dataset. Make sure you're aware of which branch you're on when you're making changes so you only work on what is relevant to that particular pull request.

Please revert that commit on this branch and push again:

git revert b6254bd
git push

This reverts commit b6254bd, reversing changes made to 84015e8. revert branch; remove changes that were supposed to be in other feature branches

bianjh-cloud · 2026-05-19T19:46:11Z

Looks like you accidentally made a commit on this branch with changes that were supposed to be on the other branch: b6254bd This PR should only contain changes related to seurat_clustering, cluster_metrics, and the BRCA dataset. Make sure you're aware of which branch you're on when you're making changes so you only work on what is relevant to that particular pull request.

Please revert that commit on this branch and push again:
git revert b6254bd
git push

Reverted, added changes made specifically to clustering functions, along with relevant fixtures and helper scripts.

kelly-sovacool

this is an improvement! see my comments for more details on how to improve this

kelly-sovacool · 2026-05-19T21:39:03Z

+# Load the current fixture
+brca <- readRDS(
+  "tests/testthat/fixtures/BRCA_Combine_and_Renormalize_SO_downsample.rds"
+)


how did you generate the rds file in the first place? it needs to be documented from the very beginning, including where you downloaded it from.

also, use testthat::test_path() to build the path, i.e.

Suggested change

# Load the current fixture

brca <- readRDS(

"tests/testthat/fixtures/BRCA_Combine_and_Renormalize_SO_downsample.rds"

)

# Load the current fixture

brca <- readRDS(

test_path(

"fixtures", "BRCA_Combine_and_Renormalize_SO_downsample.rds"

)

)

still not seeing any documentation or code explaining where the dataset originated from

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

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

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

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

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

kelly-sovacool · 2026-06-11T18:55:35Z

+  features = Seurat::VariableFeatures(ifnb)[1:500]
+)
+
+saveRDS(ifnb_sub, file = "tests/testthat/fixtures/ifnb_sub.rds")


use test_path here

kelly-sovacool · 2026-06-11T18:57:25Z

+# Load the current fixture
+brca <- readRDS(
+  "tests/testthat/fixtures/BRCA_Combine_and_Renormalize_SO_downsample.rds"
+)


still not seeing any documentation or code explaining where the dataset originated from

wong-nw · 2026-06-11T19:34:49Z

@wong-nw do you have suggestions for new names to seurat_clustering and cluster_metrics so they are verbs per the style guide? https://style.tidyverse.org/functions.html

seurat_clustering -> cluster_object
cluster_metrics -> calc_cluster_scores

bianjh-cloud and others added 7 commits March 23, 2026 10:05

rewrote calc_sc_gsea

ed645ff

chore: Merge branch 'main' into iss45_rewrite_calc_sc

747e403

test(calc_sc_gsea_score): update snake_case and hardcoded expectations

88bde28

test: add helper-selectData.R with selectData() helper function

f55dab0

Add missing test helper that defines selectData(), needed by test-make_bubble_plot.R and test-split_featurePlot.R at load time.

test: add unit tests for convert_human_gene_list, run_batch_correctio…

50c328b

…n, seurat_clustering, and cluster_metrics

test: add unit tests for seurat_clustering and cluster_metrics

0e7792f

bianjh-cloud linked an issue Apr 21, 2026 that may be closed by this pull request

Seurat Clustering Unit Tests #51

Closed

github-actions Bot added the SCOT RepoName label Apr 21, 2026

bianjh-cloud and others added 8 commits April 21, 2026 15:38

feat: add selectData helper

b5a6cf8

test: add fixture file and selectData helper for split_featurePlot tests

5abb667

feat: set FindClusters() to use function parameters

b7898e7

feat: update seurat_clustering to use parameters, add error catching

b31562a

fix: set replace gns with genes

89bf1c5

ci: 🤖 auto-format

0faf7b8

Merge branch 'main' into 47-unit-tests-for-split_featureplot

1de3773

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kelly-sovacool requested changes May 1, 2026

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Merge branch 'main' into 51-seurat-clustering-unit-tests

84015e8

bianjh-cloud and others added 4 commits May 7, 2026 15:10

feat: downsample data, addressed comments

d6c1fbb

ci: 🤖 auto-format

ca42d15

Update tests/testthat/test-seurat_clustering.R

92d67ba

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

feat: update clustering unit tests according to review 49

b6254bd

kelly-sovacool requested changes May 11, 2026

View reviewed changes

bianjh-cloud added 2 commits May 19, 2026 13:02

Revert "feat: update clustering unit tests according to review 49"

7244fed

This reverts commit b6254bd, reversing changes made to 84015e8. revert branch; remove changes that were supposed to be in other feature branches

feat: update clustering unit tests, fixtures

9a4c39e

Merge branch 'main' into 51-seurat-clustering-unit-tests

958f7d9

kelly-sovacool requested changes May 19, 2026

View reviewed changes

ccbr-bot Bot and others added 17 commits May 19, 2026 22:25

ci: 🤖 auto-format

a9fe37d

ci: 🤖 auto-format

6a8fe66

Merge branch 'main' into 51-seurat-clustering-unit-tests

deedfde

ci: 🤖 auto-format

980cafb

Update R/seurat_clustering.R

12afff2

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

Update tests/testthat/fixtures/downsample_BRCA.R

e1985df

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

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

274a069

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Update tests/testthat/fixtures/downsample_BRCA.R

6f33696

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

Update tests/testthat/test-seurat_clustering.R

7059717

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

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

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Update tests/testthat/fixtures/generate_mtx_fixtures.R

a5fe1b9

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

Update tests/testthat/test-seurat_clustering.R

5fbd352

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

ci: 🤖 auto-format

65e37ee

ci: 🤖 auto-format

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feat: hardcode error messages, regexp when applicable, testpath

1a387a7

Merge branch 'main' into 51-seurat-clustering-unit-tests

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ci: 🤖 auto-format

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kelly-sovacool requested changes Jun 11, 2026

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Merge branch 'main' into 51-seurat-clustering-unit-tests

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wong-nw commented Jun 11, 2026

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bianjh-cloud commented Apr 21, 2026 •

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