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.