Changes:
bixverse >= 0.8.0.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.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().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.Internal:
inst/params/params.R. CI checks the generated code does not
drift.Features:
plot_blitzgsea_null() and
plot_blitzgsea_es_null().plot_gse_dotplot() caps the number of terms and wraps long labels.Docs:
Fix:
manifoldsR and bixverse now install from r-universe.dev.Fix:
manifoldsR now installs from r-universe.dev.Fix:
Features:
"spectral" for continuous single cell values.feature_plot_sc() puts every feature on its own colour scale.Fix:
hexbin added properly to dependencies.Fix:
ggExtra added properly to dependencies.Major release:
bixverse suite:
embeddings, dot plots, violin plots, scatter plots and QC plots.label_centroids().