scdemon.plotting.plot_genes

scdemon.plotting.plot_genes(obj, graph_id=None, basis='graph', attr=None, color=None, imgdir='./', suffix=None, ext='png', **kwargs)

Plot all genes in a graph on a graph or UMAP basis

Parameters:

  • obj (gene_graph | modules) – Object (gene_graph or modules) with modules to plot

  • graph_id (str) – Name of graph to work with

  • attr (str) – Name of modules in the graph

  • basis (str) – Plotting basis, either 'graph' or 'umap'

  • color (str | list) – Color(s) override

  • imgdir (str) – Directory for images

  • suffix (str) – Suffix for image filenames

  • ext (str) – Extension for image ('png' or 'pdf')

  • **kwargs – Additional arguments for _plot_genes_for_graph, including width, title, and ax