scirpy.pl.clonotype_network¶

scirpy.pl.clonotype_network(adata, *, color=None, panel_size=(10, 10), legend_loc=None, palette=None, basis='clonotype_network', edges_color=None, edges_cmap=<matplotlib.colors.LinearSegmentedColormap object>, edges=None, edges_width=0.4, size=None, **kwargs)¶

Plot the Clonotype network.
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Plot the Clonotype network.

Requires running scirpy.tl.clonotype_network() before, to compute the layout.

Parameters

adata : AnnDataAnnData: Annotated data matrix.
color : str, Collection[str], NoneUnion[str, Collection[str], None] (default: None): Keys for annotations of observations/cells or variables/genes, e.g., 'ann1' or ['ann1', 'ann2'].
panel_size : Tuple[float, float]Tuple[float, float] (default: (10, 10)): Size tuple (width, height) of a single panel in inches.
legend_loc : str, NoneOptional[str] (default: None): Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend. When set to None automatically determines the legend position based on the following criteria: (1) 'on data' when coloring by clonotype, (2) 'right margin' if the number of categories < 50, and (3) and 'none' otherwise.
palette : str, Sequence[str], Cycler, NoneUnion[str, Sequence[str], Cycler, None] (default: None): Colors to use for plotting categorical annotation groups. The palette can be a valid ListedColormap name ('Set2', 'tab20', …) or a Cycler object. It is possible to specify a list of the same size as color to choose a different color map for each panel.
basis : strstr (default: 'clonotype_network'): Key under which the graph layout coordinates are stored in adata.obsm
edges_color : str, NoneOptional[str] (default: None): Color of the edges. Set to None to color by connectivity and use the color map provided by edges_cmap.
edges_cmap : Colormap, strUnion[Colormap, str] (default: <matplotlib.colors.LinearSegmentedColormap object at 0x7f0b738df410>): Colors to use for coloring edges by connectivity
edges : bool, NoneOptional[bool] (default: None): Whether to show the edges or not. Defaults to True for < 1000 displayed cells, to False otherwise.
edges_width : floatfloat (default: 0.4): width of the edges
size : float, Sequence[float], NoneUnion[float, Sequence[float], None] (default: None): Point size. If None it is automatically computed as 24000 / n_cells. Can be a sequence containing the size for each cell. The order should be the same as in adata.obs. Other than in the default scanpy implementation this respects that some cells might not be shown in the plot.
**kwargs: Additional arguments which are passed to scirpy.pl.embedding().

Return type

List[Axes]List[Axes]

Returns

A list of axes objects, containing one element for each color, or None if show == True.