Drawing Cloud Trees¶

Cloud tree drawings provide a useful way to visualize discordance among sets of trees in a MultiTree object.

In [1]:

import toytree

import toytree

Example dataset¶

In [8]:

# a multi-newick string
NEWICKS = """\
(((a:1,b:1):1,(d:1.5,e:1.5):0.5):1,c:3);
(((a:1,d:1):1,(b:1,e:1):1):1,c:3);
(((a:1.5,b:1.5):1,(d:1,e:1):1.5):1,c:3.5);
(((a:1.25,b:1.25):0.75,(d:1,e:1):1):1,c:3);
(((a:1,b:1):1,(d:1.5,e:1.5):0.5):1,c:3);
(((b:1,a:1):1,(d:1.5,e:1.5):0.5):2,c:4);
(((a:1.5,b:1.5):0.5,(d:1,e:1):1):1,c:3);
(((b:1.5,d:1.5):0.5,(a:1,e:1):1):1,c:3);
"""

# a multi-newick string NEWICKS = """\ (((a:1,b:1):1,(d:1.5,e:1.5):0.5):1,c:3); (((a:1,d:1):1,(b:1,e:1):1):1,c:3); (((a:1.5,b:1.5):1,(d:1,e:1):1.5):1,c:3.5); (((a:1.25,b:1.25):0.75,(d:1,e:1):1):1,c:3); (((a:1,b:1):1,(d:1.5,e:1.5):0.5):1,c:3); (((b:1,a:1):1,(d:1.5,e:1.5):0.5):2,c:4); (((a:1.5,b:1.5):0.5,(d:1,e:1):1):1,c:3); (((b:1.5,d:1.5):0.5,(a:1,e:1):1):1,c:3); """

In [9]:

# create a multitree object
mtree = toytree.mtree(NEWICKS)

# create a multitree object mtree = toytree.mtree(NEWICKS)

Cloud tree drawings¶

The .draw_cloud_tree function takes similar styling arguments as the ToyTree.draw function but accepts a few additional arguments.

In [24]:

# draw a cloud tree
mtree.draw_cloud_tree(
    scale_bar=True,
    edge_style={
        "stroke-opacity": 0.1,
        "stroke-width": 2.5,
    },
);

# draw a cloud tree mtree.draw_cloud_tree( scale_bar=True, edge_style={ "stroke-opacity": 0.1, "stroke-width": 2.5, }, );

Styling individual trees¶

I find it useful to set different styles on different trees in a set to better examine their differences. In this example I set a different color to the edges depending on whether the tree topology matches the most common topology in the set or not.

In [21]:

# make a copy of the multitree on which we will set styles
mtree2 = mtree.copy()

# get unique trees
utrees = mtree2.get_unique_topologies()

# set color to red if most common topology, else green
for tree in mtree2:
    if tree.distance.get_treedist_rf(utrees[0][0]) == 0:
        tree.style.edge_colors = 'red'
    else:
        tree.style.edge_colors = "green"

# draw the cloud tree w/o any overriding args to use individual .style dicts
mtree2.draw_cloud_tree(
    scale_bar=True,
    interior_algorithm=0, 
    edge_style={"stroke-opacity": 0.25},
    tip_labels_style={"font-size": 15},
);

# make a copy of the multitree on which we will set styles mtree2 = mtree.copy() # get unique trees utrees = mtree2.get_unique_topologies() # set color to red if most common topology, else green for tree in mtree2: if tree.distance.get_treedist_rf(utrees[0][0]) == 0: tree.style.edge_colors = 'red' else: tree.style.edge_colors = "green" # draw the cloud tree w/o any overriding args to use individual .style dicts mtree2.draw_cloud_tree( scale_bar=True, interior_algorithm=0, edge_style={"stroke-opacity": 0.25}, tip_labels_style={"font-size": 15}, );