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.