dynamo.pl.arcPlot

dynamo.pl.arcPlot(adata, cluster, cluster_name, edges_list=None, network=None, color=None, cmap='viridis', node_size=100, cbar=True, cbar_title=None, figsize=(6, 6), save_show_or_return='show', save_kwargs={}, **kwargs)[source]

Arc 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.

  • color (str or None (default: None)) – The layer key that will be used to retrieve average expression to color the node of each gene.

  • node_size (float (default: 100)) – The size of the node, a constant.

  • cbar (bool (default: True)) – Whether or not to display colorbar when color is not None.

  • cbar_title (float (default: weight_threshold)) – The title of the color bar when displayed.

  • figsize (None or [float, float] (default: (6, 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 ArcPlot.

Returns:

Nothing but plot an ArcPlot of the input direct network.