Styling toytree drawings

The number of styling available in toytree is enormous and will continue to grow as development on the project continues. If you have a specific styling option that does not appear to be supported please raise a issue on GitHub and we can discuss adding support for it. Below I try to demonstrate the options and usage of each styling option with at least one example.

import toytree
import toyplot
import numpy as np

# a tree to use for examples
url = "https://eaton-lab.org/data/Cyathophora.tre"
rtre = toytree.tree(url).root(wildcard='prz')

Tip label styling

tip_labels

Type: boolean or list

Allowed: True, False, or list (length of ntips)

Default: True

Description: Shows or hides tip labels (boolean), or replaces tip labels with a user defined list.

# hide tip labels
rtre.draw(tip_labels=False);

# get tip labels from tree
tipnames = rtre.get_tip_labels()

# modify list so that html italic tags surround text
italicnames = ["<i>{}</i>".format(i) for i in tipnames]

# enter the list of names to tip_labels
rtre.draw(tip_labels=italicnames);

tip_labels_align

Type: boolean

Allowed: True, False

Default: False

Description: Add lines connecting tips to tip labels. See edge_align_style for ways to style the extra tip lines (colors, etc.).

rtre.draw(tip_labels_align=True);

tip_labels_colors

Type: (str, tuple, list)

Allowed: Any color values supported in toyplot colors.

Default: "#262626" (near black)

Description: A single value can be applied to color all tip labels, or a list of values can be entered to apply different colors to different tip labels. The order of colors is applied to tip labels in the same order as .get_tip_labels() returns the labels. This order (the plot order) is from the tip located on the zero-axis (e.g., x=0 for right-facing trees) and continuing until the last name. If both tip_labels_colors and tip_labels_style["fill"] are used tip_labels_colors overrides the other. In contrast to the fill style, only this option can be used to apply multiple colors.

# use color from favored toytree color scheme
rtre.draw(
    tip_labels_align=True,
    tip_labels_colors=toytree.colors[1],
);

# enter a list of colors by name
rtre.draw(
    tip_labels_align=True,
    tip_labels_colors=(['goldenrod'] * 11) + (["mediumseagreen"] * 2),
);

# make list of hex color values based on tip labels
colorlist = ["#d6557c" if "rex" in tip else "#5384a3" for tip in rtre.get_tip_labels()]
rtre.draw(
    tip_labels_align=True,
    tip_labels_colors=colorlist
);

tip_labels_style

Type: dictionary of (mostly) CSS styles.

Allowed: CSS styles accepted by toyplot. For example, you could add “stroke”: “red” to draw a stroke around the text. The defaults provide just the most likely styles.

Default: Defaults are shown below.

Description: ‘fill’ is the color of the text; ‘font-size’ should be entered in units of pixels; ‘-toyplot-anchor-shift’ can be used to shift text closer or farther from the tree tips.

rtre.draw(
    tip_labels_style={
        "fill": "#262626",
        "font-size": "11px",
        "-toyplot-anchor-shift": "15px",
    }
);

Node labels styling

node_labels

Type: boolean, str, or list of strings or ints.

Allowed: True, False, string name of features (e.g., “idx”, “support”), or list that is the same length as the number of nodes. Default: False

Description: If True then the node index labels are used.

# shows node idx labels on all nodes
rtre.draw(node_labels=True);

# suppreses nodes
rtre.draw(node_labels=False);

# suppresses node labels, sizes ensures nodes are still shown
rtre.draw(node_labels=False, node_sizes=10);

# shortcut for 'default' features always present in TreeNodes, suppresses tip nodes.
rtre.draw(node_labels="support");

# build a list of values in the correct node plot order
sups = rtre.get_node_values("support", show_root=True, show_tips=True)
rtre.draw(node_labels=sups);

node_labels_style

Type: dictionary.

Allowed: CSS values supported for text by toyplot.

Default: fill: near-black, font-size: ‘11px’.

Description: A dictionary of CSS style options applied to text of node labels.

rtre.draw(
    node_labels='idx',
    node_labels_style={
        "fill": "#262626",
        "font-size": "8px",
    }
);

Node styling

node_sizes

rtre.draw(
    node_labels=False,
    node_sizes=10,
);

# draw random values to use for node sizes
np.random.seed(1234)
sizes = np.random.uniform(5, 15, rtre.nnodes)
rtre.draw(
    node_labels=False,
    node_sizes=sizes,
);

node_colors

# set a single color for all nodes
rtre.draw(
    node_labels=False,
    node_sizes=10,
    node_colors=toytree.colors[1],
);

rtre.get_node_values("support", 1, 0)

array(['100', '100', '100', '100', '100', '100', '100', '100', '99',
       '100', '96', '100', '', '', '', '', '', '', '', '', '', '', '', '',
       ''], dtype='<U21')

# get list of sizes and colors in node plot order with tip nodes suppressed
sizes = [10 if i else 0 for i in rtre.get_node_values('support', 1, 0)]
colors = ['black' if i=='100' else 'red' for i in rtre.get_node_values('support', 1, 0)]

# enter a lists of values
rtre.draw(
    node_labels=None,
    node_sizes=sizes,
    node_colors=colors,
);

node_markers

See toyplot markers for available options.

# enter a lists of values
rtre.draw(
    node_labels="support",
    node_markers="o"
);

# enter a lists of values
rtre.draw(
    height=350,
    node_labels=None,
    node_sizes=[0 if i else 8 for i in rtre.get_node_values(None, 1, 0)],
    node_markers="s",
    node_colors=toytree.colors[1],
);

Rectangular markers can be drawn in many dimensions. Designate “r2x1” for a box that is twice as wide as it is tall.

# rectangles for nodes
rtre.draw(
    width=600,
    height=400,
    node_labels="support",
    node_labels_style={"font-size": "11px"},
    node_markers="r2x1.25",
    node_sizes=12,
);

node_style

# the classic "ape" style tree plot look
rtre.draw(
    width=600,
    height=400,
    node_labels="support",
    node_labels_style={"font-size": "10px"},
    node_markers="r2x1.25",
    node_sizes=12,
    node_style={
        "fill": "lightgrey",
        "stroke": "black",
        "stroke-width": 0.75,
    }
);

node_hover

Enables interactive hover over nodes so that you can see all features associated with each.

rtre.draw(node_hover=True, node_labels=True, node_sizes=15);

Layout

layout

Type: str

Allowed: ‘circular’, ‘c’, ‘right’, ‘r’, ‘down’, ‘d’, (coming: ‘unrooted’, ‘up’, ‘left’)

Default: ‘r’

Description: The layout orients the direction of tip labels. Options include linear trees facing right, left, up, down, as well as circular and unrooted trees.

ttre = toytree.rtree.coaltree(20, seed=123)
ttre.draw(
    layout='d',
    tip_labels_align=True,
    node_sizes=[8 if i else 0 for i in ttre.get_node_values()],
    node_style={"stroke": "black"},
    width=350,
    height=300,
);

ttre = toytree.rtree.unittree(40, seed=123)
ttre.draw(
    layout='c',
    edge_type='c',
    node_sizes=[8 if i else 0 for i in ttre.get_node_values()],
    node_style={"stroke": "black"},
    width=400,
    height=400,
);

ttre = toytree.rtree.unittree(40, seed=123)
ttre.draw(
    layout='c',
    edge_type='p',
    width=400,
    height=400,
);

todo

Type:

Allowed:

Default:

Description:

Aligned Edge Styling

edge_align_style

Type:

Allowed:

Default:

Description:

rtre.draw(
    tip_labels_align=True,
    edge_align_style={
        "stroke": "violet",
        "stroke-width": 1.5,
        "stroke-dasharray": "2,5"    # size of dash, spacing of dashes
    });

Styles

rtre.draw(tree_style='n');

# generate a random coalescent tree and draw in 'coalescent' style
randomtre = toytree.rtree.coaltree(ntips=10, seed=666)
randomtre.draw(tree_style='c');

Scalebar

You can add a scalebar to any tree plot by simply adding scalebar=True. Alternatively, you can add or customize axes by saving the returned variables from the .draw() function and modifying the axes.

rtre.draw(scalebar=True);