dynamo.vf.rank_velocity_genes
- dynamo.vf.rank_velocity_genes(adata, vkey='velocity_S', prefix_store='rank', **kwargs)[source]
Rank genes based on their raw and absolute velocities for each cell group.
- Parameters:
adata – AnnData object that contains the gene-wise velocities.
vkey – The velocity key.
prefix_store – The prefix added to the key for storing the returned in adata.
kwargs –
additional keys that will be passed to the rank_genes function. It will accept the following arguments: group: str or None (default: None)
The cell group that speed ranking will be grouped-by.
- genes: list or None (default: None)
The gene list that speed will be ranked. If provided, they must overlap the dynamics genes.
- abs: bool (default: False)
When pooling the values in the array (see below), whether to take the absolute values.
- normalize: bool (default: False)
Whether normalize the array across all cells first, if the array is 2d.
- fcn_pool: callable (default: numpy.mean(x, axis=0))
The function used to pool values in the to-be-ranked array if the array is 2d.
- output_values: bool (default: False)
Whether output the values along with the rankings.
- Return type:
- Returns:
AnnData object which has the rank dictionary for velocities in .uns.