Tree annotations¶

The .annotate subpackage offers a clean, readable way to edit an existing tree as an alternative to modifying each argument in the .draw() method. The funcitons provided in this subpackage work by adding marks on top of the most recent canvas created by Toytree. It can be accessed direclty from a tree object (e.g., tree.annotate.{function}()), but some functions require additional arguments to specify axes, styles, etc.

Since this subpackage contains very simple modifications that can be quickly added on top of existing trees, we encourage you to share with us any functions you make that may fit in this subpackage! These can be shared via Github at https://github.com/eaton-lab/toytree/discussions

Current available annotations:¶

Node and edge marks/labels¶

• add_edge_labels
• add_edge_markers
• add_node_markers
• add_node_labels
• add_tip_markers
• add_node_bars

Axes annotations¶

• add_axes_box_outline
• add_axes_scale_bar

Data/graph annotations¶

• add_node_pie_charts
• add_edge_pie_charts

Quick examples¶

In [1]:

import toytree
import numpy as np

import toytree import numpy as np

In [2]:

#add_axes_box_outline

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()


tree.annotate.add_axes_box_outline(axes=axes)

#add_axes_box_outline tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() tree.annotate.add_axes_box_outline(axes=axes)

Out[2]:

<toyplot.coordinates.Cartesian at 0x210a26ad6d0>

In [3]:

#add_edge_labels

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()
m1 = tree.annotate.add_edge_labels(
    axes,
    labels=tree.get_node_data("idx"),
    color='blue',
    style={'font-size': 16, 'baseline-shift': 8}
)

#add_edge_labels tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() m1 = tree.annotate.add_edge_labels( axes, labels=tree.get_node_data("idx"), color='blue', style={'font-size': 16, 'baseline-shift': 8} )

In [4]:

#add_edge_markers

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()
m1 = tree.annotate.add_edge_markers(
     axes,
     marker='s',
     size=9,
     color='red',
     style={'stroke': 'white', 'stroke-width': 2.5}
 )

#add_edge_markers tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() m1 = tree.annotate.add_edge_markers( axes, marker='s', size=9, color='red', style={'stroke': 'white', 'stroke-width': 2.5} )

In [5]:

#add_node_markers

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()
# add markers to all Nodes
m1 = tree.annotate.add_node_markers(
    axes,
    marker='s',
    size=9,
    color='red',
    style={'stroke': 'white', 'stroke-width': 2.5}
)
# add markers to only a few Nodes
m2 = tree.annotate.add_node_markers(
    axes, marker=">", size=20, mask=tree.get_node_mask(9, 10)
)

#add_node_markers tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() # add markers to all Nodes m1 = tree.annotate.add_node_markers( axes, marker='s', size=9, color='red', style={'stroke': 'white', 'stroke-width': 2.5} ) # add markers to only a few Nodes m2 = tree.annotate.add_node_markers( axes, marker=">", size=20, mask=tree.get_node_mask(9, 10) )

In [6]:

#add_node_labels

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()
m1 = tree.annotate.add_node_labels(
    axes,
    labels=tree.get_node_data("idx"),
    color='blue',
    style={'font-size': 16, 'baseline-shift': 8}
)

#add_node_labels tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() m1 = tree.annotate.add_node_labels( axes, labels=tree.get_node_data("idx"), color='blue', style={'font-size': 16, 'baseline-shift': 8} )

In [7]:

#add_node_bars

tree = toytree.rtree.unittree(10, treeheight=1e5)
c, a, m = tree.draw()
node_height = tree.get_node_data("height").values
tree.annotate.add_node_bars(
    axes=a,
    bar_min=node_height * 0.5,
    bar_max=node_height * 1.5,
    size=0.33, z_index=-1, color='purple', opacity=0.4,
)

#add_node_bars tree = toytree.rtree.unittree(10, treeheight=1e5) c, a, m = tree.draw() node_height = tree.get_node_data("height").values tree.annotate.add_node_bars( axes=a, bar_min=node_height * 0.5, bar_max=node_height * 1.5, size=0.33, z_index=-1, color='purple', opacity=0.4, )

Out[7]:

<toytree.drawing.src.mark_annotation.AnnotationRect at 0x210a540f2f0>

In [8]:

#add_tip_markers

tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()
# add markers to all Nodes
m1 = tree.annotate.add_tip_markers(
    axes,
    marker='s',
    size=9,
    color='red',
    style={'stroke': 'white', 'stroke-width': 2.5}
)
# add markers to only a few Nodes
m2 = tree.annotate.add_tip_markers(
    axes, marker=">", size=20, mask=tree.get_node_mask(9)
)

#add_tip_markers tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() # add markers to all Nodes m1 = tree.annotate.add_tip_markers( axes, marker='s', size=9, color='red', style={'stroke': 'white', 'stroke-width': 2.5} ) # add markers to only a few Nodes m2 = tree.annotate.add_tip_markers( axes, marker=">", size=20, mask=tree.get_node_mask(9) )

In [12]:

#add_axes_scale_bar

import toytree

tree = toytree.rtree.unittree(ntips = 10)
canvas, axes, mark = tree.draw()
tree.annotate.add_axes_scale_bar(axes)

#add_axes_scale_bar import toytree tree = toytree.rtree.unittree(ntips = 10) canvas, axes, mark = tree.draw() tree.annotate.add_axes_scale_bar(axes)

Out[12]:

<toyplot.coordinates.Cartesian at 0x210a3067d10>

In [10]:

#add_node_pie_charts
tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()

# generate random pie-like (proportion) data array
ncategories = 3
arr = np.random.random(size=(tree.nnodes, ncategories))
arr = (arr.T / arr.sum(axis=1)).T

# add pie charts to all internal Nodes
tree.annotate.add_node_pie_charts(
    axes=axes, data=arr, size=20, mask=(0, 1, 1),
    istroke_width=0.75, istroke="black", rotate=-45,
)

#add_node_pie_charts tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() # generate random pie-like (proportion) data array ncategories = 3 arr = np.random.random(size=(tree.nnodes, ncategories)) arr = (arr.T / arr.sum(axis=1)).T # add pie charts to all internal Nodes tree.annotate.add_node_pie_charts( axes=axes, data=arr, size=20, mask=(0, 1, 1), istroke_width=0.75, istroke="black", rotate=-45, )

Out[10]:

<toytree.drawing.src.mark_pie.PieChartMark at 0x210a542ad20>

In [11]:

#add_edge_pie_charts
tree = toytree.rtree.unittree(6, seed=123)
canvas, axes, m0 = tree.draw()

# generate random pie-like (proportion) data array
ncategories = 3
arr = np.random.random(size=(tree.nnodes, ncategories))
arr = (arr.T / arr.sum(axis=1)).T

# add pie charts to all internal Nodes
tree.annotate.add_edge_pie_charts(
    axes=axes, data=arr, size=20, mask=(0, 1, 1),
    istroke_width=0.75, istroke="black", rotate=-45,
)

#add_edge_pie_charts tree = toytree.rtree.unittree(6, seed=123) canvas, axes, m0 = tree.draw() # generate random pie-like (proportion) data array ncategories = 3 arr = np.random.random(size=(tree.nnodes, ncategories)) arr = (arr.T / arr.sum(axis=1)).T # add pie charts to all internal Nodes tree.annotate.add_edge_pie_charts( axes=axes, data=arr, size=20, mask=(0, 1, 1), istroke_width=0.75, istroke="black", rotate=-45, )

Out[11]:

<toytree.drawing.src.mark_pie.PieChartMark at 0x210a4e736b0>