spapros.ev.ProbesetEvaluator.plot_coexpression

ProbesetEvaluator.plot_coexpression(set_ids=None, **kwargs)

Plot heatmaps of gene correlation matrices

Parameters:

• set_ids (Optional[List[str]]) – List of probeset IDs. Check out ProbesetEvaluator.summary_results for available sets.

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

Return type:

None

Example

import spapros as sp
adata = sp.ut.get_processed_pbmc_data()
selections = sp.se.select_reference_probesets(adata, methods=["PCA","DE", "HVG", "random"], n=30, verbosity=0)
evaluator = sp.ev.ProbesetEvaluator(adata, verbosity=0, results_dir=None, scheme="custom", metrics=["gene_corr"])
for set_id, df in selections.items():
    gene_set = df[df["selection"]].index.to_list()
    evaluator.evaluate_probeset(gene_set, set_id=set_id)

evaluator.plot_coexpression(n_cols=4)