dynamo.pl.hivePlot

dynamo.pl.hivePlot(adata, edges_list, cluster, cluster_names=None, weight_threshold=0.0001, figsize=(6, 6), save_show_or_return='show', save_kwargs={})[source]

Hive plot of cell cluster specific gene regulatory networks.

Parameters:

  • adata (AnnData) – an AnnData object.

  • edges_list (Dict[str, DataFrame]) – a dictionary of dataframe of interactions between input genes for each group of cells based on ranking information of Jacobian analysis. Each composite dataframe has regulator, target and weight three columns.

  • cluster (str) – the group key that points to the columns of adata.obs.

  • cluster_names (Optional[List[str]] (default: None)) – the group whose network and arcplot will be constructed and created. Defaults to None.

  • weight_threshold (float (default: 0.0001)) – the threshold of weight that will be used to trim the edges for network reconstruction. Defaults to 1e-4.

  • figsize (Tuple[float, float] (default: (6, 6))) – the size of each panel of the figure. Defaults to (6, 6).

  • save_show_or_return (Literal['save', 'show', 'return'] (default: 'show')) – whether to save, show, or return the figure. Could be one of “save”, “show”, or “return”. Defaults to “show”.

  • save_kwargs (Dict[str, Any] (default: {})) – a dictionary that will be passed to the save_fig function. By default, it is an empty dictionary and the save_fig function will use the {“path”: None, “prefix”: ‘hiveplot’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs. Defaults to {}.

Raises:
Return type:

Axes

Returns:

None would be returned by default. If save_show_or_return is set to return, the matplotlib axes of the figure would be returned.