picea 0.0.13

A lightweight python library for working with trees and biological sequence collections

picea

Lightweight python library for working with trees and sequence collections

pip install picea

The above figure can be generated with the following code

from picea import Tree
import matplotlib.pyplot as plt

newick = '(((a,b),(c,d)),e)'
tree = Tree.from_newick(newick)

fig, (ax1, ax2) = plt.subplots(ncols = 2, figsize = (10, 4))

#left-to-right layout with direct links
tree.layout(ltr = True)
for node1, node2 in tree.links:
    ax1.plot(
        (node1.x, node2.x),
        (node1.y, node2.y),
        c = 'k'
    )
for leaf in tree.leaves:
    ax1.text(
        leaf.x + .1, 
        leaf.y - .1, 
        leaf.name,
        fontsize = 18
    )

#right-to-left layout with square links
tree.layout(ltr = False)
for node1, node2 in tree.links:
    ax2.plot(
        (node1.x, node1.x),
        (node1.y, node2.y)
    )
    ax2.plot(
        (node1.x, node2.x),
        (node2.y, node2.y)
    )

#clean up plots
ax1.set_xlim((-.5, 3.5))
ax2.set_xlim((-3.5, .5))
for ax in (ax1,ax2):
    ax.set_xticks([],[])
    ax.set_yticks([],[])