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v1.0.1

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@maggiecam maggiecam released this 13 Jan 17:29
· 9 commits to main since this release
v1.0.1
192bc17

v1.0.1 — Clinical Visualization Enhancements

Released: 2026-01-13

Highlights

  • richer clinical QC/visualization outputs while keeping the CLI interface unchanged
  • linux/amd64 container rebuilt and published as both latest and v1.0.1 (digest sha256:6975c121b6e5c2a7ca068fa4c708bdd555ea297453349af2135515dfabb09734)

Clinical Visualizations

  1. Custom categorical palettes – --clinical_box_colors accepts user-defined color sets (defaults to a 20-color palette) so clinical box plots can align with cohort branding.
  2. Per-level box annotations – signature vs categorical clinical plots now overlay Pearson r and p for each level, matching the one-hot correlations written to tables/clinical_signature_correlations.csv.
  3. Scatter overlays – numeric clinical scatters (both per-gene facets and the signature plot) now show inline r/p text, nudged inside the plotting window for readability.
  4. Opt-in “all” aggregate – combined plots/tables are generated only when the literal lowercase all is included in --categories, reducing unnecessary output by default.

Documentation & Metadata

  • README, CHANGELOG, and session notes describe the new options and annotate the release as v1.0.1.
  • run_parameters.json records whether all was requested (include_all_category) for downstream provenance.

Container / Distribution

  • docker pull ghcr.io/nidap-community/multi-gene-correlations:latest
  • docker pull ghcr.io/nidap-community/multi-gene-correlations:v1.0.1

Both tags reference the same image; use the versioned tag for reproducibility.

Verification

  • Rscript entrypoint.R --counts test_data/counts.tsv --metadata test_data/metadata.csv --gene_column Gene --sample_column SampleID --genes "GATM,GAMT,CKM,SLC6A8,PTEN,SPRY2" --category_column Tissue --categories "Normal,Tumor" --signature_name "Creatine Score" --signature_genes "PTEN,SPRY2,CKM" --clinical_columns "Stage,PSA" --clinical_use_signature true --clinical_use_genes true --output_dir test_output/clinical_demo
  • Rscript entrypoint.R --counts test_data/counts.tsv --metadata test_data/metadata.csv --gene_column Gene --sample_column SampleID --genes "GATM,GAMT,CKM,SLC6A8,PTEN,SPRY2" --category_column Tissue --categories "Normal,Tumor,all" --signature_name "Creatine Score" --signature_genes "PTEN,SPRY2,CKM" --clinical_columns "Stage,PSA" --clinical_use_signature true --clinical_use_genes true --output_dir test_output/clinical_demo_all
  • docker build --platform linux/amd64 -t ghcr.io/nidap-community/multi-gene-correlations:latest -f container/Dockerfile .
  • docker push ghcr.io/nidap-community/multi-gene-correlations:{latest,v1.0.1}

GitHub Release Copy

Use the text above in the GitHub “Releases” tab so users can discover v1.0.1 without cloning the repo. Attach any relevant artifacts (plots, sample outputs) if needed.

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