Release History
Version 0.1.82
minor bugs in parameter naming conventions for gene trend plotting function
Version 0.1.77
updated for compatibilty with umap-learn >=0.5.0
bugfix of argument
labels
(predetermined cluster labels, overrides via’s clustering): edited the api to clarify that this needs to be of type and sizendarray (nsamples, )
updated function via_umap() to run with simply
via_umap(via_object = v0)
orvia_umap(via_object = v0, init='via')
Version 0.1.73
added lineage pathway visualization to improve the existing edge plotting function
plot_edge_bundle()
for
plot_edge_bundle
, the parameterlineage_pathway:list = []
can be filled with cluster labels from the list of terminal cluster lineages in order to see the fine-grained lineage pathways along edgesexample:
plot_edge_bundle(via_object=v0, lineage_pathway=[7,10,9], linewidth_bundle=0.5, headwidth_bundle=2, cmap='plasma',text_labels=True, show_milestones=True, scale_scatter_size_pop=True)
if you wish to recompute the edge based visualization with different resolution you have two options:
set attribute
via_object.hammerbundle_milestone_dict = None
and then rereunplot_edge_bundle()
Or
via_object.hammerbundle_milestone_dict=make_edgebundle_milestone(via_object=v0, n_milestones=40)
followed byplot_edge_bundle(...)
Examine the single-cell lineage probabilities of each cell towards a particular terminal state using:
see
via_object.single_cell_bp_rownormed
see
via_object.single_cell_bp
is actually lineage normalized so that the probabilities along a very rare lineage are not hidden.
Version 0.1.71
small bugfixes in plotting functions
Version 0.1.70
bugfix
draw_sc_lineage_probability()
to allow plotting multiple and single lineages in same plot
Version 0.1.68
improved
draw_sc_lineage_probability()
to correctly assign subplots whenmarker_lineages = []
is given by user as a subset of the terminal_clusters attribute of via. (corrections to the update in 0.1.57)control fontsize
New Feature! VIA can autocompute via-umap and via-mds by passing
do_compute_embedding = True
andembedding_type = 'via-mds' or 'via-umap'
when initializing a via object. e.g.v0 = via.VIA(X_data....)
or after doingv0.run_via()
Version 0.1.64
Bugfix in
via_mds()
parametersaveto=''
Version 0.1.62
New Feature! Heatmap based gene trends (genes x pseudotime) for each lineage
plot_gene_trend_heatmaps(via_object, df_gene_exp:pd.DataFrame,...)
New Feature! annotate nodes in plot_edge_bundle() by setting text_labels = True uses true_labels as annotations. Optionally provide list of single cell annotations length n_samples to use instead of true_labels. Example figure below
plot_edge_bundle(via_object, text_labels=True)
Version 0.1.61
Bug fix for import module in examples.py
Version 0.1.60
Bug fix for root detection (the initialization for None was over-writing RNA-velocity predicted roots)
Version 0.1.59
corrected the auto-scaling in
draw_sc_lineage_probability()
so that each subplot has the same colorbar scale
Version 0.1.58
fix random_seed so pseudotime and branching probabilities are reproducible
Version 0.1.57
optionally allow user to fix terminal states based on cell index or group label (corresponding to true_label)
optionally allow user to plot only selected lineages (by corresponding terminal cluster number) in get_gene_expression and draw_sc_lineage_probability (marker_lineages = [2,8,10])
Version 0.1.56
support via-guided embeddings. In particular fast via-mds and via-umap which can be adjusted using known time-series data if available