GSForge.plots.collections package¶

Module contents¶

class GSForge.plots.collections.WithinCollectionOverlapHeatMap(**kwargs)¶

Bases: GSForge.plots.abstract_plot_models.InterfacePlottingBase

Parameters inherited from:

GSForge.plots.abstract_plot_models.AbstractPlottingOperation: apply_default_opts, plot_options

GSForge.models._Interface.Interface: gem, gene_set_collection, selected_gene_sets, selected_genes, gene_set_mode, sample_subset, count_variable, annotation_variables, count_mask, annotation_mask, count_transform

mode = param.ObjectSelector(readonly=False)

mode = 'overlap'¶

static bokeh_opts()¶

static matplotlib_opts()¶

static within_collection_overlap(gene_dict, mode='overlap')¶

name = 'WithinCollectionOverlapHeatMap'¶

class GSForge.plots.collections.UpsetPlotInterface(**kwargs)¶

Bases: GSForge.plots.abstract_plot_models.InterfacePlottingBase

Provides access to set overlap plots using UpsetPlot.

This is needed as passing gene membership dictionaries to UpsetPlot does not always provide the correct counts.

Parameters inherited from:

GSForge.plots.abstract_plot_models.AbstractPlottingOperation: apply_default_opts, plot_options

GSForge.models._Interface.Interface: gem, gene_set_collection, selected_gene_sets, selected_genes, gene_set_mode, sample_subset, count_variable, annotation_variables, count_mask, annotation_mask, count_transform

min_overlap_size = param.Integer(readonly=False)

upset_kwargs = param.Dict(readonly=False)

min_overlap_size = 1¶

upset_kwargs = {}¶

static build_membership_series(gene_dict, min_size: int = 1)¶

name = 'UpsetPlotInterface'¶