Changes in version 0.3.0                        

Changes:

  - Requires bixverse >= 0.8.0.
  - Tests follow the 0.8.0 API: full_snn is gone from
    params_sc_neighbours(), the pruning now goes via graph =
    list(pruning = 0). Dropped the removed streaming argument from the
    count loaders.

                        Changes in version 0.2.9                        

Features:

  - milo_nhood_plot_sc(): the Milo neighbourhood graph over an
    embedding. Each neighbourhood sits at its index cell, sized by its
    cell count and connected to the neighbourhoods it shares cells with.
    Coloured by logFC, with the non-significant ones left white
    underneath, or by majority cell type. Needs bixverse >= 0.5.7 for
    extract_milo_plot_data().

                        Changes in version 0.2.8                        

Features:

  - heatmap_plot_sc(): the classic marker genes x cells heatmap to show
    which cluster is what. Cells are grouped and gapped per cluster,
    markers can be grouped per cell type. Every block is drawn as one
    raster, not one tile per cell.
  - plot_binary_heatmap(): on/off matrices in the style of the SCENIC
    paper, e.g. regulon activity per cell. Takes a logical matrix or the
    output of bixverse::extract_binary_heatmap_data(). group_annotation
    adds a second colour strip with a legend on top, e.g. the response
    group of each cell line.

                        Changes in version 0.2.7                        

Internal:

  - Parameter wrappers and their checkmate assertions are now generated
    by devforge from inst/params/params.R. CI checks the generated code
    does not drift.
  - New package logo and favicons.

                        Changes in version 0.2.6                        

Features:

  - Null distribution plots for blitzGSEA, see plot_blitzgsea_null() and
    plot_blitzgsea_es_null().
  - plot_gse_dotplot() caps the number of terms and wraps long labels.

Docs:

  - Vignettes for GSEA (fgsea and blitzGSEA) and over-representation
    results.
  - pkgdown website with a proper style.

Fix:

  - manifoldsR and bixverse now install from r-universe.dev.

                        Changes in version 0.2.5                        

Fix:

  - manifoldsR now installs from r-universe.dev.

                        Changes in version 0.2.4                        

Fix:

  - Dependency graph fixed.

                        Changes in version 0.2.3                        

Features:

  - New palette "spectral" for continuous single cell values.
  - feature_plot_sc() puts every feature on its own colour scale.

                        Changes in version 0.2.2                        

Fix:

  - hexbin added properly to dependencies.

                        Changes in version 0.2.1                        

Fix:

  - ggExtra added properly to dependencies.

                        Changes in version 0.2.0                        

Major release:

  - Single cell plotting helpers for the single cell bixverse suite:
    embeddings, dot plots, violin plots, scatter plots and QC plots.
  - Improved enrichment map.
  - Geom extension to label centroids on scatter plots, see
    label_centroids().

                       Changes in version 0.0.1.0                       

  - Helpers to save plots to disk.
  - Enrichment Map like plots.
  - Dot plots akin to clusterProfiler.
  - Enrichment plots akin to the fgsea plots.