Plotting#

Plotting functionality is divided into two broad categories: local and remote (a.k.a. iTOL). Previously, we only supported tree visualization using the rich iTOL framework. However, we are now in the process of deprecating the use of this service for most use cases. We recommend all users to visualize their trees using the local plotting functions, which either use Matplotlib or Plotly, as this option is free and is more reminiscent of plotting in other packages such as Scanpy.

`pl.labels_from_coordinates`(tree[, ...])	Create a (synthetic) labels Numpy array for use with 3D plotting.
`pl.plot_matplotlib`(tree[, depth_key, ...])	Generate a static plot of a tree using Matplotlib.
`pl.plot_plotly`(tree[, depth_key, meta_data, ...])	Generate a static plot of a tree using Plotly.
`pl.Tree3D`(tree[, labels, offset, downscale, ...])	Create a 3D projection of a tree onto a 2D surface.
`pl.upload_and_export_itol`(cassiopeia_tree, ...)	Uploads a tree to iTOL and exports it.