TrajAtlas.utils.getAttributeBase#

TrajAtlas.utils.getAttributeBase(adata, axis_key, sampleKey='sample', subsetCell=None, subsetGene=None, cell_threshold=40, njobs=-1, bootstrap_iterations=0, **kwargs)[source]#

Get attribute (peak, expression, correlation) base on axis.

See also

Parameters:

  • %(adata)s –

  • featureKey – The specific slot in adata.var that houses the gene-feature relationship information

  • sampleKey (str) – The specific slot in adata.obs that houses the sample information

  • patternKey – Pattern names. If not specific, we use all pattern in adata.obs.featureKey

  • cell_threshold (int) – Minimal cells to keep

  • njobs (int) – number of cores to use

  • bootstrap_iterations (int) – number of bootstrap iterations to perform. If 0, bootstrapping is not performed.

  • adata (AnnData) –

  • subsetCell (List | None) –

  • subsetGene (List | None) –

Returns:

MuData object which contains correlation, expression, peak modal.