Skip to contents

Changelog

Source: NEWS.md

Matisse 0.1.0

Phase 6 (April 2026): unify event input, drop junction_data

  • CreateMatisseObject() now takes a single events parameter that accepts either a SUPPA2 .ioe path (or vector of paths) or a pre-built data.frame. The previous ioe_files and event_data parameters are removed — Matisse auto-dispatches on input class. The IOE-precedence warning that gated the two-parameter form (P14) is gone, since the conflict isn’t possible anymore.
  • junction_data parameter dropped (P7). Per-junction genomic coordinates are auto-parsed from junction IDs at construction and written to seurat[["isoform"]][[]] (the isoform assay’s feature-metadata table). Supported ID formats: chr-start-end-strand, chr:start-end:strand, chr_start_end_strand. Names that don’t match get NA coords with a warning — counts still work, only sashimi plots degrade.
  • Renamed event-annotation columns: inclusion_junctions / exclusion_junctions → inclusion_features / exclusion_features (mode-agnostic — they hold junction IDs in junction mode, transcript IDs in transcript mode).
  • PlotSashimi now reads junction coords from seurat[["isoform"]][[]] instead of obj@misc[["junction_data"]].

Code-review pass (April 2026): API surface tightened, several bug fixes

This release applies a multi-phase code-review pass that simplifies the API surface, fixes four real correctness bugs, and refactors event annotation storage so it lives natively inside the embedded Seurat object.

Architectural changes

  • Per-event annotation now lives in seurat[["psi"]]@meta.data (the Assay5 feature-metadata table), accessed via the [[ ]] API. Previously stored in MatisseObject@misc[["event_data"]]. Single source of truth — annotation rides with the assay through any subset/merge automatically.
  • CreateMatisseObject() now folds the PSI calculation into construction by default. The two-step “construct then CalculatePSI” flow collapses to one. Pass defer_psi = TRUE to skip the PSI step (rare; for power users who want to inspect intermediate state). min_coverage parameter added to the constructor.
  • MatisseObject@misc[["event_data_path"]] records the source path of the event annotation (normalized) for provenance, or NA_character_ when annotation was passed as a data.frame directly.

Breaking API changes

  • Removed accessor wrappers (use the native Seurat API instead):
    • GetJunctionCounts(obj) → Matrix::t(SeuratObject::GetAssayData(GetSeurat(obj)[["isoform"]], "counts"))
    • GetTranscriptCounts(obj) → SeuratObject::GetAssayData(GetSeurat(obj)[["isoform"]], "counts")
    • GetInclusionCounts(obj) → Matrix::t(SeuratObject::GetAssayData(GetSeurat(obj)[["psi"]], "counts"))
    • GetExclusionCounts(obj) → Matrix::t(SeuratObject::GetAssayData(GetSeurat(obj)[["psi"]], "exclusion"))
    • GetEventData(obj) → GetSeurat(obj)[["psi"]][[]] (post-CalculatePSI)
    • GetJunctionData(obj) → obj@misc[["junction_data"]]
    • AddIsoformMetadata(obj, df) → SeuratObject::AddMetaData(matisse_obj, df) (S3 method delegates)
  • Removed BuildSimpleEvents(). Matisse no longer ships a heuristic event caller. Junction-mode users must bring an external event annotation (SUPPA2 IOE, rMATS, or equivalent), as transcript-mode already requires ioe_files.
  • Single-event MatisseObjects are no longer representable. SeuratObject’s Assay5 requires at least 2 features, so the [ operator now errors when an event subset would leave fewer than 2 events. For single-event values, use GetPSI(obj)[, event_id] directly.

Bug fixes

  • MatisseMeta(obj) <- value previously wrote columns by positional index, silently writing the wrong values when value’s rownames disagreed with meta.data’s ordering. Now delegates to SeuratObject::AddMetaData for proper barcode alignment.
  • rlang::abort() was being called with multiple positional string arguments at 8 sites; this silently truncated the message and consumed the second string as the error class. All sites collapsed to a single string so the full message reaches the user.
  • cli::cli_alert_*() had the same multi-arg truncation bug at 5 sites (the second string is id, not message-continuation). Fixed.
  • SCTransform.MatisseObject referenced object@mode == "event", but the slot is input.mode and valid values are "junction" / "transcript". The function crashed on every call; it was untested. The default assay in transcript mode also pointed to a non-existent "transcript" assay (the actual assay name is "isoform"). Both fixed; new tests cover both modes.

Removed dead code

  • .psi_rowmeans_sparse (utils.R) — only caller was its own test.
  • .parse_junction_list (psi.R) — never called; .calculate_psi_matrix inlined the same logic.
  • na_fill parameter — declared on CalculatePSI and threaded through the implementation, but never actually applied. Removed in P5.

Matisse 0.1.0 (initial release)

  • New MatisseObject S4 class wrapping a Seurat object with isoform-resolved layers: junction counts, PSI matrix, inclusion/exclusion counts, event and junction annotation tables, and per-cell isoform metadata.
  • CreateMatisseObject(): primary constructor with input validation and automatic cell-barcode alignment.
  • CalculatePSI(): computes PSI matrices from junction count data and splice event definitions. Supports both MatisseObject and bare matrix input.
  • SummarizePSI(): per-event summary statistics (mean, median, sd, coverage).
  • FilterCells() and FilterEvents(): threshold-based filtering with informative removal summaries.
  • Visualization: PlotUMAP(), PlotViolin(), PlotHeatmap(), PlotSashimi().
  • MergeMatisse(): concatenate two MatisseObjects with cell-prefix deduplication.
  • GitHub Actions workflows for R CMD check (multi-OS), pkgdown website deployment, and test coverage reporting.