Colored rectangles to highlight clades

Colored rectangles to highlight clades¶

The easiest way to add colored shapes to a plot is with the Toyplot .rectangle or .fill() functions of cartesian axes objects. For this you simply need to know the coordinates of the area that you wish to fill (See Coordinates). The example below draws two rectangles in the coordinate space and then adds a tree on top of these. You could make more complex polygon shapes using the fill function (see Toyplot docs). Remember you can use axes.show=True to see the axes coordinates if you need a reminder of how to set the x and y coordinates of the rectangles.

In [2]:

import toytree
import toyplot

# generate a random tree
rtre = toytree.rtree.unittree(20, seed=12345)

# make the canvas and axes
canvas = toyplot.Canvas(width=250, height=400)
axes = canvas.cartesian()
axes.show = True

# draw a rectangle (x1, x2, y1, y2)
axes.rectangle(
    -0.75, 0.35, -0.5, 4.5, 
    opacity=0.25,
    color='yellow',
)

# draw a rectangle (x1, x2, y1, y2)
axes.rectangle(
    -0.75, 0.35, 4.5, 8.5, 
    opacity=0.25,
    color='magenta',
)

# add tree to the axes 
rtre.draw(axes=axes);

import toytree import toyplot # generate a random tree rtre = toytree.rtree.unittree(20, seed=12345) # make the canvas and axes canvas = toyplot.Canvas(width=250, height=400) axes = canvas.cartesian() axes.show = True # draw a rectangle (x1, x2, y1, y2) axes.rectangle( -0.75, 0.35, -0.5, 4.5, opacity=0.25, color='yellow', ) # draw a rectangle (x1, x2, y1, y2) axes.rectangle( -0.75, 0.35, 4.5, 8.5, opacity=0.25, color='magenta', ) # add tree to the axes rtre.draw(axes=axes);