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Releases: BorchLab/escape

v2.6.1

31 Oct 14:24
@ncborcherding ncborcherding
v2.6.1
5eae8bd

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v2.6.1

#Version 2.6.1

Bug fix

  • Fix conversion wide-to-long format for heatmapEnrichment()
  • Fix issue with t() call on sparse matrices.
  • Fix issue with GSVA cdf calculation in denistyEnrichment()

New functionality

  • Enable color.by for both metadata columns and features (other gene sets)
  • Introduce summarise.by argument for geyserEnrichment()
  • Enable scaling if color.by is another gene.set.
  • Enable scaling for dgCMatrix
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v2.5.0

20 May 20:00
@ncborcherding ncborcherding
v2.5.0
b9bd5aa

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v2.5.0 Latest
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Highlights

  • Streamlined code-base – major internal refactor for clarity, speed and a ~20 % smaller dependency tree.
  • Consistent, flexible visualisation API across all plotting helpers.
  • Robust unit-test suite (>250 expectations) now ships with the package.

New & enhanced functionality

Area Function(s) What changed
Visualisation ridgeEnrichment() True gradient coloring mode for numeric color.by; optional per-cell rugs; quantile median line; fixed grey-fill bug
densityEnrichment() accepts new rug.height; ~4× faster ranking routine using MatrixGenerics::rowMeans2; cleaner two-panel layout via patchwork
gseaEnrichment() new rug.height; clearer legend showing ES/NES/ p; internal vectorised ES calculation
splitEnrichment() rewritten: split violins when split.by has 2 levels, dodged violins otherwise; inline boxplots; auto Z-scaling; palette helper
scatterEnrichment() density-aware points (via ggpointdensity), hex-bin alternative, optional Pearson/Spearman overlay, continuous or discrete color mapping
Dimensionality reduction performPCA() / pcaEnrichment() uses irlba::prcomp_irlba() automatically for large matrices; stores eigen-values/contribution in misc; add.percent.contribution now always respected
Scoring backend escape.matrix() / .compute_enrichment() lazy loading of heavy back-ends (GSVA, UCell, AUCell); unified .build_gsva_param(); drops empty gene-sets up-front
Normalization performNormalization() chunk-wise expressed-gene scaling (memory-friendly); accepts external scale.factor; optional signed log-transform; returns object with assay <assay>_normalized
Gene-set retrieval getGeneSets() downloads now cached under tools::R_user_dir("escape", "cache"); graceful KEGG append; clearer error for non-human/mouse requests

Performance & dependency reductions

  • Replaced plyr, stringr, rlang usage with base-R helpers; these packages
    are now Suggests only.
  • Common color and label utilities (.colorizer(), .colorby(), .orderFunction())
    removed redundant tidyverse imports.
  • Internal matrices split/chunked with new .split_* helpers to cap memory
    during parallel scoring/normalization.

Bug fixes

  • Gradient mode in ridgeEnrichment() no longer produces grey fills when the
    chosen gene-set is mapped to color.by.
  • pcaEnrichment() axis labels correctly include variance contribution
    when display.factors = FALSE.
  • .grabDimRed() handles both Seurat v5 and <v5 slot structures; fixes missing
    eigen-values for SCE objects.
  • escape.matrix() respects min.size = NULL (no filtering) and handles
    zero-overlap gene-sets gracefully.
  • Global variable declarations consolidated – eliminates R CMD check NOTES
    regarding na.omit, value, etc.

Documentation

  • DESCRIPTION rewritten – heavy packages moved to Suggests; added explicit
    Config/reticulate for BiocParallel.
  • escape.gene.sets data object now fully documented with source, usage, and reference.
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v2.2.3

24 Jan 20:32
@ncborcherding ncborcherding
v2.2.3
5cb4eea
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v2.2.3

UNDERLYING CHANGES

  • fixed handling of groups parameter and data splitting in ````escape.matrix()```
  • improved efficiency of internal .split_data.matrix()
  • fix ```performNormalization()```` conditional statements
  • fix performNormalization() rescaling for per gene set calculations
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v2.2.1

04 Nov 18:52
@ncborcherding ncborcherding
v2.2.1
ae5480b

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v2.2.1

escape VERSION 2.2.1

UNDERLYING CHANGES

  • update handling of v5 Seurat versus <v5 Seurat Objects
  • added mean and median visualization for heatmapEnrichment()
  • update densityEnrichment() GSVA function pull
  • Parallelization of performNormalization()
  • Refactor of getGeneSets() to prevent issues with m_df error.
  • fixed performNormalization() errors when input.data was a matrix, now requires single-cell object and enrichment data
  • passing parallel processing properly to runEscape() function.
  • ordering by mean values no longer changes the color order
  • add explicit BPPARAM argument to runEscape() and escape.matrix()
  • added additional details in runEscape() and escape.matrix() for make.positive.
  • removed plotting of splitEnrichment() for group.by = NULL
  • separated AUC calculation to rankings and AUC, this was only method found to get consistent scores.
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