cassiopeia/plotting
directory contains modules for visualizing phylogenetic trees and related data using various methods and libraries. It provides functionality for both local plotting using Matplotlib and Plotly, as well as cloud-based visualization using the iTOL (Interactive Tree Of Life) web service. The package also includes utilities for 3D tree visualization and color palette management.
plot_matplotlib
and plot_plotly
functions in local.py
for local tree plotting.upload_and_export_itol
function in itol_utilities.py
for cloud-based visualization using iTOL.Tree3D
class in local_3d.py
for 3D tree visualization.__init__.py
file exports these key functions and classes, making them directly accessible when importing from cassiopeia.plotting
.
local.py
: Contains functions for local tree plotting using Matplotlib and Plotly.itol_utilities.py
: Provides utilities for interacting with the iTOL web service.local_3d.py
: Implements 3D tree visualization using PyVista.utilities.py
: Contains various utility functions for tree placement, color manipulation, and data preparation.palettes.py
: Defines a color palette for use in visualizations.cassiopeia/plotting
package provides a comprehensive set of tools for visualizing phylogenetic trees and associated data, offering flexibility in terms of visualization methods and customization options to suit various research needs.