commot.pl.plot_cluster_communication_dotplot

commot.pl.plot_cluster_communication_dotplot(adata, database_name=None, pathway_name=None, clustering=None, lr_pair=None, keys=None, show_pathway_name=False, p_value_cutoff=0.05, p_value_vmin=0.001, size_max=20, size_min=10, vmax_quantile=0.99, vmin_quantile=0.0, cmap='cool', filename=None, font_scale=0.5, top_nclus=- 1, top_ncomm=- 1, cluster_x=False, cluster_y=False, cluster_knn=5, cluster_res=1.0)

Plot cluster-cluster communication through multiple ligand-receptor pairs as dotplot.

../_images/cluster_communication_dotplot.png
Parameters
  • adata (AnnData) – The data matrix of shape n_obs × n_var after running tl.spatial_communication. Rows correspond to cells or positions and columns to genes.

  • pathway_name (Optional[str]) – Name of the signaling pathway.

  • clustering (Optional[str]) – Name of the clustering.

  • lr_pair – A tuple of ligand name and receptor name. If None, the total communication of the pathway will be plotted.

  • keys – A list of keys for the vector field as tuples (pathway_name, ligand, receptor). If given, pathway_name and lr_pair will be ignored. If more than one is given, the average will be plotted.

  • show_pathway_name (bool) – Whether to show pathway_name in yticks.

  • p_value_cutoff (float) – Cutoff for being considered significant.

  • p_value_vmin (float) – The lower bound of p-value corresponding to the biggest dot size.

  • size_max – Size of biggest dot (corresponding to p-value <= p_value_min).

  • size_min – Size of smallest dot (corresponding to p-value = p_value_cutoff).

  • vmax_quantile – The quantile of cluster-cluster communication weights for setting vmax of colormap.

  • vmin_quantile – The quantile of cluster-cluster communication weights for setting vmin of colormap.

  • cmap – The colormap for the nodes.

  • filename – Filename for saving the figure. Set the name to end with ‘.pdf’ or ‘png’ to specify format.

  • font_scale – Font size.

  • top_nclus – If not -1, the top number of cluster-cluster pairs with the highest total communication weight among the signaling pathways are plotted.

  • top_ncomm – If not -1, the top number of ligand-recepter pairs with the highest total communication weight among the cluster-cluster pairs are plotted.

  • cluster_x – Whether to reorder the cluster-cluster pairs according to their patterns among the ligand-receptor pairs.

  • cluster_y – Whether to reorder the ligand-receptor pairs according to their patterns among the cluster-cluster pairs.

  • cluster_knn – The k value of knn graph for clustering if cluster_x or cluster_y is True.

  • cluster_res – The resolution of leiden clustering algorithm if cluster_x or cluster_y is True.