dynamo.vf.rank_curvature_genes

dynamo.vf.rank_curvature_genes(adata, ckey='curvature', prefix_store='rank', **kwargs)

Rank gene’s absolute, positive, negative curvature by different cell groups.

Parameters:

• adata (AnnData) – AnnData object that contains the reconstructed vector field function in the .uns attribute.

• ckey (str) – The curvature key.

• prefix_store (str) – The prefix of the key that will be used to store the acceleration rank result.

• 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:

AnnData object that is updated with the ‘rank_curvature’ related information in the .uns.