scirpy.util.graph.layout_components

scirpy.util.graph.layout_components#

scirpy.util.graph.layout_components(graph, component_layout='fr_size_aware', arrange_boxes='squarify', pad_x=1.0, pad_y=1.0, layout_kwargs=None)#

Compute a graph layout by layouting all connected components individually.

Adapted from https://stackoverflow.com/questions/53120739/lots-of-edges-on-a-graph-plot-in-python

Parameters:

  • graph (Graph) – The igraph object to plot. Requires the vertex attribute “size”, corresponding to the node size.

  • component_layout (str (default: 'fr_size_aware')) – Layout function used to layout individual components. Can be anything that can be passed to igraph.Graph.layout or fr_size_aware for a modified Fruchterman-Rheingold layouting algorithm that respects node sizes. See scirpy.util.graph.layout_fr_size_aware() for more details.

  • arrange_boxes (Literal['size', 'rpack', 'squarify'] (default: 'squarify')) – How to arrange the individual components. Can be “size” to arange them by the component size, or “rpack” to pack them as densly as possible, or “squarify” to arrange them using a treemap algorithm.

  • pad_x (float (default: 1.0)) – Padding between subgraphs in the x dimension.

  • pad_y (float (default: 1.0)) – Padding between subgraphs in the y dimension.

  • layout_kwargs (Optional[dict] (default: None)) – Additional arguments passed to the layouting algorithm used for each component.

Return type:

ndarray

Returns:

pos n_nodes x dim array containing the layout coordinates

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