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Post-merge tutorial fixes: heatmap print() + ligand-activity ordering + CI dependencies #4

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Merged
Huangy57 merged 11 commits into from
May 24, 2026
Merged

Post-merge tutorial fixes: heatmap print() + ligand-activity ordering + CI dependencies #4

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bc5435b
notebooks: print() bare make_heatmap_ggplot so ligand-target heatmaps…
Huangy57 May 22, 2026
fbe8455
CI: install only hard deps so checks don't try to clone private ccflowR
Huangy57 May 22, 2026
ae666d1
notebooks: order ligand-activity-score heatmap so the highest score i…
Huangy57 May 22, 2026
6f8497c
DESCRIPTION: drop private ccflowR from Suggests/Remotes so CI can res…
Huangy57 May 22, 2026
3842bea
Revert CI dependencies:'"hard"' workflow change — ccflowR removal is …
Huangy57 May 22, 2026
811926c
CI: keep ccflowR in Suggests, drop only its Remote; install public de…
Huangy57 May 22, 2026
b9e73fe
CI: drop Seurat from check deps (unused in CI, broke macOS/Windows/R4…
Huangy57 May 22, 2026
a9387bf
CI: drop `needs: check`/`coverage` so the solve skips the private ccf…
Huangy57 May 22, 2026
f79c89d
Revert DESCRIPTION + CI workflow to main; keep only the two notebook …
Huangy57 May 22, 2026
b83249f
CI: use SETTYLAB_CI_PAT so pak can resolve the private ccflowR depend…
Huangy57 May 24, 2026
8e2ad16
CI: drop R 4.2 from matrix — package requires R >= 4.4 via SeuratObje…
Huangy57 May 24, 2026
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19 changes: 12 additions & 7 deletions .github/workflows/R-CMD-check.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,17 +9,16 @@ on:
jobs:
R-CMD-check:
runs-on: ${{ matrix.os }}
env:
# Read the private settylab/ccflowR Remote during pak dependency resolution.
GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
strategy:
fail-fast: false
matrix:
# R >= 4.3 only: the package needs SeuratObject (>= 5.0.0), which pulls
# Matrix (>= 1.6.4) requiring R >= 4.4 — R 4.2 cannot solve the graph.
os: [ubuntu-latest, macos-latest, windows-latest]
r-version: ['4.2', '4.3', '4.4']
exclude:
# Reduce matrix size
- os: macos-latest
r-version: '4.2'
- os: windows-latest
r-version: '4.2'
r-version: ['4.3', '4.4']

steps:
- uses: actions/checkout@v4
Expand All @@ -45,6 +44,9 @@ jobs:
test-coverage:
runs-on: ubuntu-latest
needs: R-CMD-check
env:
# Read the private settylab/ccflowR Remote during pak dependency resolution.
GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
steps:
- uses: actions/checkout@v4

Expand All @@ -68,6 +70,9 @@ jobs:

lint:
runs-on: ubuntu-latest
env:
# Read the private settylab/ccflowR Remote during pak dependency resolution.
GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
steps:
- uses: actions/checkout@v4

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4 changes: 2 additions & 2 deletions notebooks/01-getting-started.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -718,14 +718,14 @@
" stop(\"No ligand-target links remain for plotting. Try lowering the filtering threshold or increasing TOP_N_LIGANDS.\")\n",
"}\n",
"\n",
"nichenetr::make_heatmap_ggplot(\n",
"print(nichenetr::make_heatmap_ggplot(\n",
" vis_matrix,\n",
" y_name = \"Predicted target gene\",\n",
" x_name = \"Prioritized ligand\",\n",
" legend_title = \"Regulatory\\npotential\",\n",
" color = \"purple\",\n",
" x_axis_position = \"top\"\n",
")"
"))\n"
],
"id": "cell01-034"
},
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6 changes: 3 additions & 3 deletions notebooks/02-standard-workflow.ipynb
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Expand Up @@ -515,7 +515,7 @@
"activity_matrix <- as.matrix(activity_scores[, \"aupr_corrected\", drop = FALSE])\n",
"rownames(activity_matrix) <- activity_scores$test_ligand\n",
"colnames(activity_matrix) <- \"AUPR_c\"\n",
"activity_matrix <- activity_matrix[best_ligands, , drop = FALSE]\n",
"activity_matrix <- activity_matrix[rev(best_ligands), , drop = FALSE] # rev() so the highest score is the TOP row\n",
"\n",
"nichenetr::make_heatmap_ggplot(\n",
" activity_matrix,\n",
Expand Down Expand Up @@ -555,13 +555,13 @@
"}\n",
"vis_matrix <- vis_matrix[rowSums(vis_matrix) > 0, , drop = FALSE]\n",
"\n",
"nichenetr::make_heatmap_ggplot(\n",
"print(nichenetr::make_heatmap_ggplot(\n",
" vis_matrix,\n",
" y_name = \"Target Gene\",\n",
" x_name = \"Predicted Ligand\",\n",
" legend_title = \"Regulatory\\nPotential\",\n",
" color = \"purple\"\n",
")"
"))\n"
],
"id": "cell02-036"
},
Expand Down
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