phlower.pl.nxdraw_holes
- phlower.pl.nxdraw_holes(adata: ~anndata._core.anndata.AnnData, graph_name: str | None = None, layout_name: str | None = None, evector_name: str | None = None, title: str = '', edge_value: ~typing.List[~phlower.plot.plotting.V] = [], vector_dim: int = 0, font_size: int = 0, node_size: float = 1, width: int = 1, edge_cmap=<matplotlib.colors.LinearSegmentedColormap object>, with_labels: bool = False, with_potential='u', flip: bool = False, is_norm: bool = False, is_abs: bool = False, is_arrow: bool = True, ax=None, colorbar=False, **args)
plot holes from eigen decomposition of L1
Parameters
- adata: AnnData
an Annodata object
- graph_name: str
graph_name of the starts ends connected graph
- layout_name: str
layout name show the graph
- evector_name: str
eigen vector of L1
- title: str
title of the plot
- edge_value: list
the value of edges, if not None, use edge_value to plot the edge
- vector_dim: int
the dimension of the eigen vector to plot
- font_size: int
the size of the font
- node_size: int
the size of the node
- width: int
the width of the edge
- edge_cmap: matplotlib colormap
the colormap of the edge
- with_labels: bool
show the label of the node if True
- with_potential: None or length of 2 list,
- use potential u to calculate the direction of an edge,
eigen values * -1 if uend - ustart > 0 else eigen values * 1
- flip: bool
flip the direction of an edge
- is_arrow:bool
show directed graph if True else undirected
- is_norm: bool
normalize the eigen value to [0,1]
- is_abs: bool
take absolute value of eigen value
- ax: matplotlib axis
the axis to plot
- colorbar: bool
show colorbar or not