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 or None, optional (default: None): Genes for sampling the reference set. Default is all genes.
filter_samples : list or None, optional (default: None): Cells for sampling the reference set. Default is all samples.

Returns: