HoloNet.plotting.cell_type_level_network

HoloNet.plotting.cell_type_level_network(sr_network, cell_type_names, edge_thres=0.05, edge_width_times=2.5, linewidths=2.0, edgecolors='black', node_size=600, connectionstyle='arc3, rad = 0.15', arrowstyle='-|>', palette=None, fname=None, display=True, **kwargs)

Plot the relationship network (CEs or FCEs) between cell-types.

Parameters

sr_network ndarray

The sender-receiver network among cell-types (cell_type_num * cell_type_num). The mox edge weight need to be 1.

cell_type_names List[str]

The cell-type name list

edge_thres float (default: 0.05)

The plot threshold of edges. The edge with weight lower than th threshold will not be display in the plot.

edge_width_times float (default: 2.5)

Increase the weight of the edge by a certain factor as the thickness of the arrow。

linewidths float (default: 2.0)

Widths of node borders

edgecolors str (default: 'black')

Colors of node borders

connectionstyle str (default: 'arc3, rad = 0.15')

Pass the connectionstyle parameter to create curved arc of rounding radius rad. See in matplotlib.patches.ConnectionStyle and matplotlib.patches.FancyArrowPatch

arrowstyle str (default: '-|>')

For directed graphs, choose the style of the arrowsheads. See in matplotlib.patches.ArrowStyle

palette dict | NoneOptional[dict] (default: None)

The color dict for each cell-type.

fname str | Path | NoneUnion[str, Path, None] (default: None)

The output file name. If None, not save the figure.

display bool (default: True)

If False, will not display the plot.

kwargs

Other parameters in networkx.draw.