phlower.pl.plot_traj

phlower.pl.plot_traj(adata: AnnData, graph_name: str | None = None, layout_name: str | None = None, holes: List[List[int]] | None = None, trajectory: List[int] | ndarray | None = None, colorid=None, hole_centers=None, *, ax: Axes | None = None, node_size=5, edge_width=1, plot_node=True, alpha_nodes=0.3, color_palette=[(0.12156862745098039, 0.4666666666666667, 0.7058823529411765), (1.0, 0.4980392156862745, 0.054901960784313725), (0.17254901960784313, 0.6274509803921569, 0.17254901960784313), (0.8392156862745098, 0.15294117647058825, 0.1568627450980392), (0.5803921568627451, 0.403921568627451, 0.7411764705882353), (0.5490196078431373, 0.33725490196078434, 0.29411764705882354), (0.8901960784313725, 0.4666666666666667, 0.7607843137254902), (0.4980392156862745, 0.4980392156862745, 0.4980392156862745), (0.7372549019607844, 0.7411764705882353, 0.13333333333333333), (0.09019607843137255, 0.7450980392156863, 0.8117647058823529)], **args)

plot the trajectory on the graph

Parameters

adata: AnnData

an Annodata object

graph_name: str

key of the graph in adata.uns, default is None

layout_name: str

key of the layout in adata.obsm, default is None

holes: List[List[int]]

holes in the graph, default is None

trajectory: Union[List[int], np.ndarray]

trajectory to plot, default is None

colorid: List[int]

color id for each node, default is None

hole_centers: List[int]

hole centers, default is None

ax: matplotlib axis

axis to plot, default is None

node_size: float

node size, default is 5

edge_width: float

edge width, default is 1

plot_node: bool

whether to plot nodes, default is True

alpha_nodes: float

alpha for nodes, default is 0.3

color_palette: List[str]

color palette, default is sns.color_palette(‘tab10’)