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) – an AnnData object.

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

  • cluster_name (str) – the group whose network and arcplot will be constructed and created.

  • edges_list (Optional[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. If None, the network should be provided directly. Defaults to None.

  • network (Optional[DiGraph]) – a direct network for this cluster constructed based on Jacobian analysis. If None, edges_list must be provided to construct the network. Defaults to None.

  • color (Optional[str]) – the layer key that will be used to retrieve average expression to color the node of each gene. If None, the nodes would not be colored. Defaults to None.

  • cmap (str) – the color map used for the ArcPlot. Defaults to “viridis”.

  • node_size (int) – the size of the node, a constant. Defaults to 100.

  • cbar (bool) – whether to display the colorbar when color is not None. Defaults to True.

  • cbar_title (Optional[str]) – the titke of the colorbar when displayed. Defaults to None.

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

  • save_show_or_return (Literal['save', 'show', 'return']) – whether to save, show, or return the plotted ArcPlot. Could be one of ‘save’, ‘show’, or ‘return’. Defaults to “show”.

  • save_kwargs (Dict[str, Any]) – 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”: ‘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. Defaults to {}.

  • **kwargs – any other kwargs that would be passed to ArcPlot.

Raises:

ImportError – networkx not installed.

Return type:

Optional[Any]

Returns:

None would be returned by default. If save_show_or_return is set to ‘return’, the generated ArcPlot object would be return.