pycallingcards.plotting.plot_matched

pycallingcards.plotting.plot_matched(mdata, peak, gene, name=None, adata_cc='CC', adata='RNA', groupby='cluster', method='logAvginsertions')[source]

Plot matched peak,gene and cluster pair (Designed for mudata object).

Parameters:

  • mdata (MuData) – mdata for both CC and RNA.

  • peak (str) – Peak name.

  • gene (str) – Gene name.

  • name (Optional[str] (default: None)) – The name for peak displyed.

  • adata_cc (str (default: 'CC')) – Name for CC data. Anndata is mdata[adata_cc].

  • adata (str (default: 'RNA')) – Default is ‘RNA’. Name for RNA data. Anndata is mdata[adata].

  • groupby (str (default: 'cluster')) – The name all the cells are grouped by.

  • method (Optional[Literal['avginsertions', 'logAvginsertions', 'suminsertions', 'logSuminsertions']] (default: 'logAvginsertions')) – [“avginsertions”,”logAvginsertions”,”suminsertions”,”logSuminsertions”]. Method to calculate the insertions.

Example:

>>> import pycallingcards as cc
>>> mdata = cc.datasets.mousecortex_data(data="Mudata")
>>> cc.pl.plot_matched(mdata,'chr4_22969921_22973019','Pou3f2')