spapros.se.ProbesetSelector.plot_coexpression

ProbesetSelector.plot_coexpression(selections=['final', 'pca', 'DE', 'marker', 'pre', 'prior'], **kwargs)

Plot correlation matrix of selected genes

Parameters:

• selections (List[str]) –

  Plot the coexpression of

  • ’final’ : all selected genes (see ProbesetSelector.probeset)

  • ’pca’ : selected genes that also occured in the pca based selection

  • ’DE’ : selected genes that also occured in the 1-vs-all DE based selection

  • ’marker’ : selected genes from the marker list

  • ’pre’ : selected genes that were given as pre selected genes

  • ’prior’ : selected genes that were given as prioritized genes

• kwargs – Any keyword argument from correlation_matrix().

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)
selector.select_probeset()

selector.plot_coexpression()