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) – AnnData object that contains the gene-wise velocities.

  • vkey (str (default: 'velocity_S')) – The velocity key.

  • prefix_store (str (default: 'rank')) – 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.

Returns:

adata: AnnData

AnnData object which has the rank dictionary for velocities in .uns.