stereo.plots.PlotPaga.paga_compare#

PlotPaga.paga_compare(adjacency='connectivities_tree', color=None, size=1, threshold=0.01, layout='fr', random_state=0, cmap='tab20', width=15, height=6, dot_size=30)[source]#

abstract paga plot for the paga result and cell distribute around paga.

Parameters:

  • adjacency (str) – keyword to use for paga or paga tree, available values include ‘connectivities’ and ‘connectivities_tree’. # noqa

  • color (Optional[str]) – the col in cells or a gene name to display in compare plot.

  • size (int) – cell spot size.

  • threshold (float) – prune edges lower than threshold.

  • layout (Literal['fr', 'drl', 'kk', 'grid_fr', 'lgl', 'rt', 'rt_circular', 'fa']) – the method to layout each node.

  • random_state (int) – to control the random initialization.

  • cmap (str) – colormap to use, default with tab20.

  • width (int) – the figure width.

  • height (int) – the figure height.

  • dot_size (int) – The marker size in points**2 (typographic points are 1/72 in.). Default is 30.