spapros.se.ProbesetSelector.plot_gene_overlap

ProbesetSelector.plot_gene_overlap(origins=None, **kwargs)

Plot the overlap of origins for the selected genes

Parameters:

• origins (Optional[List[Literal['pre_selected', 'prior_selected', 'pca', 'DE', 'DE_1vsall', 'DE_specific', 'marker_list']]]) –

  Origin groups to investigate. Supported are

  • ”pre_selected” : User defined pre selected genes

  • ”prior_selected” : User defined prior selected genes

  • ”pca” : Genes that originate from the prior pca based selection

  • ”DE” : Genes that occur in the DE test when building the reference DE trees

  • ”DE_1vsall” : Subset of “DE” from tests of single cell types vs background

  • ”DE_specific” : Subset of “DE” from tests of single cell types vs subset of background

  • ”marker_list” : Genes that occur in the user defined marker list

• **kwargs – Any keyword argument from gene_overlap().

Return type:

None

Example

(Takes a few minutes to calculate)

import spapros as sp
adata = sp.ut.get_processed_pbmc_data()
selector = sp.se.ProbesetSelector(adata, "celltype", n=30, verbosity=0, marker_list={"celltypeX": ["PF4"]})
selector.select_probeset()

selector.plot_gene_overlap()