scanpy.api.tl.sandbag¶
-
scanpy.api.tl.
sandbag
(adata, annotation, gene_names, sample_names, fraction=0.65, filter_genes=None, filter_samples=None)¶ Generate pairs of genes [Scialdone15] [Fechtner18].
Calculates the pairs of genes serving as marker pairs for each phase, based on a matrix of gene counts and an annotation of known phases.
This reproduces the approach of [Scialdone15] in the implementation of [Fechtner18].
More information and bug reports here.
Parameters: - adata :
AnnData
The annotated data matrix.
- categories :
dict
Dictionary of lists, i.e. {phase: [sample, …]}, containing annotation of samples to their phase
- gene_names :
list
List of genes.
- sample_names :
list
List of samples.
- fraction :
float
, optional (default: 0.5) Fraction to be used as threshold.
- filter_genes :
list
orNone
, optional (default:None
) Genes for sampling the reference set. Default is all genes.
- filter_samples :
list
orNone
, optional (default:None
) Cells for sampling the reference set. Default is all samples.
Returns: dict
oflist
oftuple
, i.e.- {phase ([(Gene1, Gene2), …]},)
- containing marker pairs per phase
- adata :