dynamo.pl.circosPlotDeprecated

dynamo.pl.circosPlotDeprecated(adata, cluster, cluster_name, edges_list, network=None, weight_scale=5000.0, weight_threshold=0.0001, figsize=(12, 6), save_show_or_return='show', save_kwargs={}, **kwargs)[source]

Note: this function is written with nxviz old version (<=0.3.x, or higher) API for the latest nxviz version compatibility, please refer to dyn.pl.circos_plot. Circos plot of gene regulatory network for a particular cell cluster.

Parameters:

  • adata (AnnData.) – AnnData object.

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

  • cluster_name (str (default: None)) – The group whose network and arcplot will be constructed and created.

  • edges_list (dict of pandas.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.

  • network (class:~networkx.classes.digraph.DiGraph) – A direct network for this cluster constructed based on Jacobian analysis.

  • weight_scale (float (default: 1e3)) – Because values in Jacobian matrix is often small, the value will be multiplied by the weight_scale so that the edge will have proper width in display.

  • weight_threshold (float (default: weight_threshold)) – The threshold of weight that will be used to trim the edges for network reconstruction.

  • figsize (None or [float, float] (default: (12, 6)) – The width and height of each panel in the figure.

  • save_show_or_return (str {‘save’, ‘show’, ‘return’} (default: show)) – Whether to save, show or return the figure.

  • save_kwargs (dict (default: {})) – A dictionary that will passed to the save_fig function. By default it is an empty dictionary and the save_fig function will use the {“path”: None, “prefix”: ‘arcplot’, “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.

  • **kwargs – Additional parameters that will eventually pass to CircosPlot.

Returns:

Nothing but plot an CircosPlot of the input direct network.