color.by
for both metadata columns and features (other gene sets)summarise.by
argument for geyserEnrichment()
dgCMatrix
heatmapEnrichment()
| 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 |
.colorizer()
, .colorby()
, .orderFunction()
)
removed redundant tidyverse imports..split_*
helpers to cap memory
during parallel scoring/normalization.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.na.omit
, value
, etc.Config/reticulate
for BiocParallel.escape.gene.sets
data object now fully documented with source, usage, and reference.getGeneSets()
gains local caching; supports only Homo sapiens / Mus musculus.groups
parameter handling and data splitting in escape.matrix()
..split_data.matrix()
.performNormalization()
conditional logic and per-gene-set rescaling.heatmapEnrichment()
.densityEnrichment()
GSVA function pulldensityEnrichment()
for new GSVA function nameperformNormalization()
getGeneSets()
to prevent issues with m_df error. performNormalziation()
errors when input.data was a matrix, now requires single-cell object and enrichment datarunEscape()
function.runEscape()
and escape.matrix()
runEscape()
and escape.matrix()
for make.positive.splitEnrichment()
for group.by = NULLrunEscape()
geyserEnrichment()
scatterEnrichment()
heatmapEnrichment()
escape.matrix()
densityEnrichment()
performPCA()
now works with a matrix or single-cell objectpcaEnrichment()
combines biplot-like functionsgetGeneSets()
to output a list of gene set objects with reformatted names following the Seurat "-" convention*Fixed a parenthesis, yeah a parenthesis. (In enrichIt() call I edited for 99.1)
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