scdemon.plotting.plot_gene_logfc

scdemon.plotting.plot_gene_logfc(obj, graph_id, basis='graph', attr='celltype', fc_cut=2, p_cut=0.05, cmap=<matplotlib.colors.LinearSegmentedColormap object>, imgdir='./', **kwargs)

Plot logFC for all genes against a specific covariate on a graph or UMAP basis

Parameters:

  • obj (modules) – Object (modules) with graph and 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'

  • fc_cut (float) – Cap for top and bottom of logFC scale

  • p_cut (float) – p-value cutoff for the logFC values

  • cmap – matplotlib colormap to use (default plt.cm.RdYlBu)

  • imgdir (str) – Directory for images

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