NEWS.md

In ncborcherding/escape: Easy single cell analysis platform for enrichment

2.5.5 (2025-06-11)

Bug fix & enhanced 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

2.5.4 (2025-06-05)

Bug fixes

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

2.5.3 (2025-05-19)

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.

2.4.1 (2025-03-05)

• Version bump to align with Bioconductor release cycle.
• escape.matrix() now silently removes gene-sets with zero detected features.

2.2.4 (2025-01-13)

Underlying changes

• Switched MSigDB dependency from msigdbr ➜ msigdb.
• getGeneSets() gains local caching; supports only Homo sapiens / Mus musculus.

2.2.3 (2024-12-15)

• Fixed groups parameter handling and data splitting in escape.matrix().
• Improved efficiency of internal .split_data.matrix().

2.2.2 (2024-11-30)

• Patched performNormalization() conditional logic and per-gene-set rescaling.

2.2.1 (2024-11-18)

• Version bump for Bioconductor.

2.1.5 (2024-10-23)

• Seurat v5 compatibility; mean/median options for heatmapEnrichment().

2.1.4 (2024-09-13)

• update densityEnrichment() GSVA function pull

2.1.3 (2024-09-13)

UNDERLYING CHANGES

• update densityEnrichment() for new GSVA function name
• Parallelization of performNormalization()
• Refactor of getGeneSets() to prevent issues with m_df error.

2.0.1 (2024-07-26)

UNDERLYING CHANGES

• fixed performNormalziation() errors when input.data was a matrix, now requires single-cell object and enrichment data
• passing parallel processing properly to runEscape() function.

1.99.1 (2024-02-29)

UNDERLYING CHANGES

• 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.

1.99.0 (2024-02-27)

NEW FEATURES

• Added runEscape()
• Added geyserEnrichment()
• Added scatterEnrichment()
• Added heatmapEnrichment()
• Changed enrichIt to escape.matrix()
• Changed enrichmentPlot to densityEnrichment()
• performPCA() now works with a matrix or single-cell object
• pcaEnrichment() combines biplot-like functions

UNDERLYING CHANGES

• Updated interaction with gsva package
• Added support for GSVA calculation
• Added support for AUCell calculation
• Added support of visualizations and calculations for single-cell objects
• Modified getGeneSets() to output a list of gene set objects with reformatted names following the Seurat "-" convention

DEPRECATED AND DEFUNCT

• Deprecate getSignificance()
• Deprecate masterPCAPlot()

CHANGES IN VERSION 1.9.0

• Releveling version for commit to new Bioconductor release
• Removed UCell internal functions to just import the Bioconductor UCell package

CHANGES IN VERSION 1.4.2

• Fixed masterPCAPlot top_n() call to slice_max by top.contributions.

CHANGES IN VERSION 1.4.1

• Version number and small edits for bioconductor compliance
• Removed singscore method
• Added UCell functions internally so they are compatible with Bioconductor
• Fixed performPCA, eliminated merge call.

CHANGES IN VERSION 1.3.4

• Normalization for ssGSEA no longer uses the range of all gene sets, but columns, normalizing it to 0 to 1.
• Added Kruskal-Wallis test for additional support of multi-group comparison

CHANGES IN VERSION 1.3.3

• Added wilcoxon and LR for getSignificance
• median calculated and appended to the getSignificance() function output
• ANOVA in getSignificance() returns p-values for each comparison using TukeyHSD()
• new parameter gene.sets getSignificance() to select only gene sets or subsets.
• enrichmentPlot() beta release
• Added subcategory to getGeneSets to select subsets of libraries.
• Added default coloring to enrichmentPlot()
• enrichmentPlot() now imports calculations partially from GSVA internal functions to facilitate use of C
• Filtering based on min.size now works instead of not working.

CHANGES IN VERSION 1.3.2

• Added removal of gene sets with less than x features parameter in enrichIt - min.size
• Added UCell and singScore support
• new parameter gene.sets in MasterPCAPlot() and performPCA() to allow for selecting specific columns and prevent using other numeric vectors in meta data.

CHANGES IN VERSION 1.3.1

• Aligning versions to the current bioconductor release
• Added DietSeurat() call in vignette to prevent issues
• Adding internal gene sets - escape.gene.sets
• Removed lm.fit using limma from getSignificance

CHANGES IN VERSION 1.0.1

• Removed ggrepel, rlang, and factoextra dependencies.
• Updated Seurat package switch
• Switch the way counts are processed by first eliminating rows with 0 expression in the sparse matrix before converting to a full matrix

CHANGES IN VERSION 0.99.9

• Changing Seurat dependency, updated vignette

CHANGES IN VERSION 0.99.8

• Edited getSignificance ANOVA model call

CHANGES IN VERSION 0.99.7

• Edited getSignificance fit call to match documentation

CHANGES IN VERSION 0.99.6

• Edited match.args() in getSignificance

CHANGES IN VERSION 0.99.5

• Edited match.args() in getSignificance

CHANGES IN VERSION 0.99.4

• Added match.args() to getSignificance
• Changed stop() to message()
• Modified getSignficance to allow for ANOVA and T.test

CHANGES IN VERSION 0.99.3

• Updated link in description of getGeneSets.

CHANGES IN VERSION 0.99.2

*Fixed a parenthesis, yeah a parenthesis. (In enrichIt() call I edited for 99.1)

CHANGES IN VERSION 0.99.1

• Removed parallel call in gsva() and added biocparallel
• Changed cores = 4 to cores = 2 in the vignette

CHANGES IN VERSION 0.99.0

• Preparing for bioconductor submission

ncborcherding/escape documentation built on June 12, 2025, 1 p.m.