Multi-column grouping
Repeat --column / -c in build or col to group cells by a combination of metadata values:
refmat col sample.rds -c condition -c celltype
refmat build sample.rds -c condition -c celltype -o combined.tsvThis produces group labels such as wt_macrophage and mut_astrocyte. Use --separator ':' to customize the separator. Supported for Seurat, SingleCellExperiment, and AnnData.
- Column argument order determines label order.
- Combined groups contain observed combinations only, in first-appearance order.
- Cells missing any selected grouping value are excluded and reported on stderr.
- Ambiguous joined labels cause an error rather than silently merging distinct groups.
- Single-column syntax and ordering remain supported.
All 17 local tests pass, including combined group means across the three formats. GitHub Actions tests and builds Apple Silicon macOS and AMD64 Linux binaries; SHA256SUMS accompanies the archives.