Phylogenetic Tree

In [1]:

# %pip install pycirclize

# %pip install pycirclize

1. Simple Tree¶

User can plot the phylogenetic tree with Circos.initialize_from_tree() or track.tree() methods. Both methods return a TreeViz instance, which can be manipulated to set phylogenetic tree annotations such as marker and highlight.

1-1. Default Style¶

In [2]:

from pycirclize import Circos
from pycirclize.utils import load_example_tree_file

tree_file = load_example_tree_file("alphabet.nwk")
circos, tv = Circos.initialize_from_tree(tree_file)
fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_example_tree_file tree_file = load_example_tree_file("alphabet.nwk") circos, tv = Circos.initialize_from_tree(tree_file) fig = circos.plotfig()

1-2. Change Style 1¶

In [3]:

from pycirclize import Circos
from pycirclize.utils import load_example_tree_file

tree_file = load_example_tree_file("alphabet.nwk")
circos, tv = Circos.initialize_from_tree(
    tree_file,
    start=20,                                # Default: 0
    end=340,                                 # Default: 360
    r_lim=(10, 100),                         # Default: (50, 100)
    line_kws=dict(color="red", lw=2),        # Default: {}, Change color & linewidth
    align_line_kws=dict(ls="dashdot", lw=1), # Default: {}, Change linestyle & linewidth
)
fig = circos.plotfig()

from pycirclize import Circos from pycirclize.utils import load_example_tree_file tree_file = load_example_tree_file("alphabet.nwk") circos, tv = Circos.initialize_from_tree( tree_file, start=20, # Default: 0 end=340, # Default: 360 r_lim=(10, 100), # Default: (50, 100) line_kws=dict(color="red", lw=2), # Default: {}, Change color & linewidth align_line_kws=dict(ls="dashdot", lw=1), # Default: {}, Change linestyle & linewidth ) fig = circos.plotfig()

1-3. Change Style 2¶

In [4]:

from pycirclize import Circos
from pycirclize.utils import load_example_tree_file
import matplotlib.pyplot as plt

# Create 2x2 polar subplots
fig = plt.figure(figsize=(16, 16))
fig.subplots_adjust(wspace=0.05, hspace=0.05)
ax_list = fig.subplots(2, 2, subplot_kw=dict(polar=True)).flatten()

# Define 4 types kwargs for `Circos.initialize_from_tree()` method
kwargs_list = [
    dict(outer=True, align_leaf_label=True, ignore_branch_length=False),
    dict(outer=True, align_leaf_label=False, ignore_branch_length=False),
    dict(outer=False, align_leaf_label=True, ignore_branch_length=False),
    dict(outer=True, align_leaf_label=True, ignore_branch_length=True),
]

# Plot trees with different kwargs
tree_file = load_example_tree_file("alphabet.nwk")
for ax, kwargs in zip(ax_list, kwargs_list):
    circos, tv = Circos.initialize_from_tree(tree_file, r_lim=(60, 100), **kwargs)
    kwargs_text = "\n".join([f"{k}: {v}" for k, v in kwargs.items()])
    circos.text(kwargs_text, size=14)
    circos.plotfig(ax=ax)

from pycirclize import Circos from pycirclize.utils import load_example_tree_file import matplotlib.pyplot as plt # Create 2x2 polar subplots fig = plt.figure(figsize=(16, 16)) fig.subplots_adjust(wspace=0.05, hspace=0.05) ax_list = fig.subplots(2, 2, subplot_kw=dict(polar=True)).flatten() # Define 4 types kwargs for `Circos.initialize_from_tree()` method kwargs_list = [ dict(outer=True, align_leaf_label=True, ignore_branch_length=False), dict(outer=True, align_leaf_label=False, ignore_branch_length=False), dict(outer=False, align_leaf_label=True, ignore_branch_length=False), dict(outer=True, align_leaf_label=True, ignore_branch_length=True), ] # Plot trees with different kwargs tree_file = load_example_tree_file("alphabet.nwk") for ax, kwargs in zip(ax_list, kwargs_list): circos, tv = Circos.initialize_from_tree(tree_file, r_lim=(60, 100), **kwargs) kwargs_text = "\n".join([f"{k}: {v}" for k, v in kwargs.items()]) circos.text(kwargs_text, size=14) circos.plotfig(ax=ax)