scgenome.pl.plot_tree_cn

scgenome.pl.plot_tree_cn(tree, adata, chrom_segments=True, layer_name=None, obs_annotation=None, obs_cmap=None, var_label=None, fig=None, raw=False, max_cn=13)

Plot a tree aligned to a CN values matrix heatmap

Parameters:

• tree (Bio.Phylo.BaseTree.Tree) – phylogenetic tree

• adata (AnnData) – Copy number data, either genes or segments

• chrom_segments (bool, optional) – whether adata is genes or segments, by default True

• layer_name (str, optional) – layer to plot for copy number heatmap, by default None

• obs_annotation (str, optional) – column of adata.obs to annotate cells, by default None

• obs_cmap (matplotlib.colors.ListedColormap, optional) – color map for cell annotations, by default None

• var_label (str, optional) – column of adata.var to use for heatmap var labels, by default None use index

• fig (matplotlib.figure.Figure, optional) – existing figure to plot into, by default None

• raw (bool, optional) – raw plotting, no integer color map, by default False

• max_cn (int, optional) – clip cn at max value, by default 13