# ----------------------------------------------------------------------------
# Copyright (c) 2016--, gneiss development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import pandas as pd
from gneiss.plot._dendrogram import UnrootedDendrogram
try:
from bokeh.models.glyphs import Circle, Segment
from bokeh.models import ColumnDataSource, DataRange1d, Plot
from bokeh.models import HoverTool, BoxZoomTool, ResetTool
except ImportError:
raise ImportWarning('Bokeh not installed. '
'`radialplot` will not be available')
[docs]def radialplot(tree, node_color='node_color', node_size='node_size',
node_alpha='node_alpha', edge_color='edge_color',
edge_alpha='edge_alpha', edge_width='edge_width',
hover_var='hover_var', figsize=(500, 500), **kwargs):
""" Plots unrooted radial tree.
Parameters
----------
tree : instance of skbio.TreeNode
Input tree for plotting.
node_color : str
Name of variable in `tree` to color nodes.
node_size : str
Name of variable in `tree` that specifies the radius of nodes.
node_alpha : str
Name of variable in `tree` to specify node transparency.
edge_color : str
Name of variable in `tree` to color edges.
edge_alpha : str
Name of variable in `tree` to specify edge transparency.
edge_width : str
Name of variable in `tree` to specify edge width.
hover_var : str
Name of variable in `tree` to display in the hover menu.
figsize : tuple, int
Size of resulting figure. default: (500, 500)
**kwargs: dict
Plotting options to pass into bokeh.models.Plot
Returns
-------
bokeh.models.Plot
Interactive plotting instance.
Notes
-----
This assumes that the tree is strictly bifurcating.
See also
--------
bifurcate
"""
# This entire function was motivated by
# http://chuckpr.github.io/blog/trees2.html
t = UnrootedDendrogram.from_tree(tree)
nodes = t.coords(figsize[0], figsize[1])
# fill in all of the node attributes
def _retreive(tree, x, default):
return pd.Series({n.name: getattr(n, x, default)
for n in tree.levelorder()})
# default node color to light grey
nodes[node_color] = _retreive(t, node_color, default='#D3D3D3')
nodes[node_size] = _retreive(t, node_size, default=1)
nodes[node_alpha] = _retreive(t, node_alpha, default=1)
nodes[hover_var] = _retreive(t, hover_var, default=None)
edges = nodes[['child0', 'child1']]
edges = edges.dropna(subset=['child0', 'child1'])
edges = edges.unstack()
edges = pd.DataFrame({'src_node': edges.index.get_level_values(1),
'dest_node': edges.values})
edges['x0'] = [nodes.loc[n].x for n in edges.src_node]
edges['x1'] = [nodes.loc[n].x for n in edges.dest_node]
edges['y0'] = [nodes.loc[n].y for n in edges.src_node]
edges['y1'] = [nodes.loc[n].y for n in edges.dest_node]
ns = [n.name for n in t.levelorder(include_self=True)]
attrs = pd.DataFrame(index=ns)
# default edge color to black
attrs[edge_color] = _retreive(t, edge_color, default='#000000')
attrs[edge_width] = _retreive(t, edge_width, default=1)
attrs[edge_alpha] = _retreive(t, edge_alpha, default=1)
edges = pd.merge(edges, attrs, left_on='dest_node',
right_index=True, how='outer')
edges = edges.dropna(subset=['src_node'])
node_glyph = Circle(x="x", y="y",
radius=node_size,
fill_color=node_color,
fill_alpha=node_alpha)
edge_glyph = Segment(x0="x0", y0="y0",
x1="x1", y1="y1",
line_color=edge_color,
line_alpha=edge_alpha,
line_width=edge_width)
def df2ds(df):
return ColumnDataSource(ColumnDataSource.from_df(df))
ydr = DataRange1d(range_padding=0.05)
xdr = DataRange1d(range_padding=0.05)
plot = Plot(x_range=xdr, y_range=ydr, **kwargs)
plot.add_glyph(df2ds(edges), edge_glyph)
ns = plot.add_glyph(df2ds(nodes), node_glyph)
tooltip = [
("Feature ID", "@index")
]
if hover_var is not None:
tooltip += [(hover_var, "@" + hover_var)]
hover = HoverTool(renderers=[ns], tooltips=tooltip)
plot.add_tools(hover, BoxZoomTool(), ResetTool())
return plot