plotly-phylotree 0.0.1

A package to plot phylogenetic trees with Plotly.

Plotly PhyloTree Extension

This package extends Plotly to create interactive plots of phylogenetic trees from Newick strings. It can be used with plotly.py and can also be integrated into Dash Apps.

See also:

• Newick format - https://en.wikipedia.org/wiki/Newick_format
• Plotly - https://github.com/plotly/plotly.py

Installation

pip install plotly-phylotree

Usage

1. Basic Tree

• Labels shown by default
• No distances specified in Newick string

from phylotree import create_phylogenetic_tree

newick_str = "(A,(B,C)D)E;"
fig = create_phylogenetic_tree(newick_str)
fig.show()

2. Basic Tree with specified maximum display level

• Display level specifies level up to which tree is plotted. Defaults to np.inf.

from phylotree import create_phylogenetic_tree

newick_str = "(A,(B,C)D)E;"
fig = create_phylogenetic_tree(newick_str, display_level=1)
fig.show()

3. Tree with specified distances

• Labels shown by default
• Distances specified in Newick string

from phylotree import create_phylogenetic_tree

newick_str = "(Bovine:0.69395,(Gibbon:0.36079,(Orang-Utan:0.33636,(Gorilla:0.17147,(Chimp:0.19268,Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460)"
fig = create_phylogenetic_tree(newick_str)
fig.show()

4. Tree without labels

• Labels deactivated
• Distances specified

from phylotree import create_phylogenetic_tree

newick_str = "(Bovine:0.69395,(Gibbon:0.36079,(Orang-Utan:0.33636,(Gorilla:0.17147,(Chimp:0.19268,Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460)"
fig = create_phylogenetic_tree(newick_str, show_labels=False)
fig.show()

Contributing

Suggestions for improvement are welcome. As this is a small side project, please allow some time for answers and revision.

License

MIT License