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Changelog

Source: NEWS.md

CoPro 1.1.0

Citation

  • The CoPro preprint is now available on bioRxiv: Miao Z, Qu Y, Huang S, Laux L, Peters S, Aristel A, Zhang Z, Niedernhofer L, McMahon A, Kim J, Zhang NR (2026). Dissecting the coordinated progression of cell states in spatial transcriptomics with CoPro. bioRxiv 2026.04.17.719309. doi: 10.64898/2026.04.17.719309. inst/CITATION and the README have been updated accordingly.

New features

  • Added asCoProSingle() and asCoProMulti() S4 generics for one-call coercion from SingleCellExperiment and Seurat objects into CoPro objects. Conversions are gated on their respective packages being installed and delegate to the existing newCoProSingle() / newCoProMulti() constructors so validation stays single-sourced.
  • Exposed normalizeTarget argument on computeDistance() for users who want to control the target value that the low-percentile cell-cell distance is rescaled to. Default preserves existing behavior.

User experience

  • newCoProSingle() / newCoProMulti() now reject NA, NaN, and Inf values in normalizedData at construction time with an informative error instead of producing cryptic downstream failures.
  • newCoProMulti() now validates that when metaData already contains a slideID column, its values match the supplied slideID argument (errors on mismatch instead of silently overwriting).
  • locationData column standardization now emits a message() so silent case-folding of x/y/z headers is visible.
  • subsetData() error on too-few-matched cells now reports the requested cell types and the count that was actually found.
  • computeBidirCorrelation() guards against empty filtered matrices (returns zero correlation with a warning rather than crashing).
  • show() for CoPro objects now reports approximate object size in MB and truncates the metadata field list when there are many columns.
  • runSkrCCA() optimization loop now reports progress via message() that can be silenced with suppressMessages().
  • plotG12Functions() now always returns a stable list(plot, data, summary) shape where plot is always a list with combined and individual elements (one of which may be NULL), regardless of plot_type. Default fallback palette for >8 cell-type pairs now uses the colorblind-friendly viridis palette rather than rainbow().
  • Replaced several cat() progress prints in computeDistance() and plotG12Functions() with message() gated on verbose, so users can suppress output cleanly.

Documentation

  • Added @examples, @family, and @seealso annotations across the main pipeline functions so the pkgdown reference auto-cross-links related steps.
  • New CONTRIBUTING.md covering test runs, vignette render workflow, and roxygen regeneration.

Internal

  • Renamed R/80_get_cs_in_situ.r to R/80_get_cs_in_situ.R for cross-platform portability on case-sensitive filesystems.
  • Bumped actions/checkout to v6 in the lint workflow to match the other CI jobs.

CoPro 1.0.0

Major changes

  • First public release accompanying the CoPro manuscript.
  • Added computeRegressionGeneScores() for regression-based gene weights, which avoids collinearity issues present in PCA back-projection.
  • Added copro_download_data() for easy download of example datasets via piggyback.
  • Corrected PCA back-projection formula in computeGeneAndCellScores(): gene weights now use 1/sdev instead of sdev.
  • Changed transfer_scores() default gs_weight_threshold from 0.005 to 0.
  • Added support for regression-based score transfer via getTransferCellScores(..., gene_score_type = "regression").

New vignettes

  • “Within-cell-type spatial patterns (Organoid)” – single cell type
  • “Cross-cell-type co-progression (Brain MERFISH)” – two cell types
  • “Cross-cell-type co-progression with orthogonal axes (Colon Day 3)”
  • “Multi-slide analysis and score transfer (Colon Day 9)”
  • “Supervised detection of spatial gradients (Kidney)”

Documentation

  • Full pkgdown website with grouped function reference.
  • Cleaned reproducibility scripts in scripts/ directory.
  • Example datasets available via copro_download_data().

CoPro 0.6.1