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High-level description

This code defines the __init__.py file for the cassiopeia.plotting package, which provides utilities for visualizing phylogenetic trees. It imports and re-exports specific functions and classes from submodules to make them directly accessible at the package level.

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References

This file references symbols from the following files:

  • cassiopeia/plotting/itol_utilities.py
  • cassiopeia/plotting/local.py
  • cassiopeia/plotting/local_3d.py

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Symbols

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Symbol Name

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__all__

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Description

A list of symbols to be exported when using from cassiopeia.plotting import *. This allows users to directly access these functions and classes without needing to know the specific submodules where they are defined.

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Inputs

N/A - This is a variable definition, not a function.

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Outputs

N/A - This is a variable definition, not a function.

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Internal Logic

The list includes the following symbols:

  • upload_and_export_itol: Uploads a tree to the iTOL web service and exports the visualization. (from itol_utilities.py)
  • plot_matplotlib: Generates a static plot of a tree using Matplotlib. (from local.py)
  • plot_plotly: Generates a dynamic plot of a tree using Plotly. (from local.py)
  • labels_from_coordinates: Creates a synthetic labels array from cell coordinates for 3D plotting. (from local_3d.py)
  • Tree3D: A class for creating and manipulating 3D projections of trees onto 2D surfaces. (from local_3d.py)
utilities.pyOverview