dynamo.vf.rank_expression_genes
- dynamo.vf.rank_expression_genes(adata, ekey='M_s', prefix_store='rank', **kwargs)[source]
Rank genes based on their expression values for each cell group.
- Parameters
adata (
AnnData) – AnnData object that contains the normalized or locally smoothed expression.ekey (str (default: 'M_s')) – The expression key, can be any properly normalized layers, e.g. M_s, M_u, M_t, M_n.
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 object which has the rank dictionary for expression in .uns.
- Return type