def plot_backbone_clades(tree, plot_hull=False, _i=0):
c_noclade = grey(0.6)
if tree.is_leaf():
plt.scatter(*tree.location, c='k')
return
clade, rest = tree.children
# print(clade.tree_size(), rest.tree_size())
if clade.n_leafs() > 5:
plot_tree(clade, color=COLORS[_i]) # , alpha=0.2)
plt.scatter(*clade.get_leaf_locations().T, color=COLORS[_i], s=4.)
if plot_hull:
plot_tree_hull(clade, COLORS[_i])
_i += 1
else:
plot_tree(clade, color=c_noclade)
plt.scatter(*clade.get_leaf_locations().T, color=c_noclade, s=4.)
plot_edge(tree, rest, lw=None, no_arrow=True, zorder=9)
if rest.n_leafs() > 20:
plot_backbone_clades(rest, plot_hull=plot_hull, _i=_i)
else:
# plot_tree(rest, color=c_noclade)
# plt.scatter(*rest.get_leaf_locations().T, color=c_noclade, s=4.)
plot_tree(rest, color=COLORS[_i])
plt.scatter(*rest.get_leaf_locations().T, color=COLORS[_i], s=4.)
def plot_subtree_hulls(tree: Tree):
for i in range(4):
c = COLORS[i]
plot_tree_hull(tree, c=c)
plot_root(tree.location, color=c, edgecolor=grey(1.))
tree = tree.big_child()
tree = tree.big_child()
tree = tree.big_child()
def color_backbone_clades(tree, _i=0):
c_noclade = grey(0.65)
if tree.is_leaf():
tree.color = COLORS[_i]
return
clade, rest = tree.children
if clade.n_leafs() > 5:
color_tree(clade, COLORS[_i])
_i += 1
else:
color_tree(clade, c_noclade)
if rest.n_leafs() > 30:
color_backbone_clades(rest, _i=_i)
else:
# color_tree(rest, c_noclade)
color_tree(rest, COLORS[_i])
rest.color = grey(0.0)
def plot_backbone_splits(tree, plot_edges=True, lw=1., n_clades=10, bb_side=1,
plot_hull=True):
# SUBGROUP_COLOR_IDXS = [0, 1, 1, 1, 2, 3, 3, 4, 5, 6, 7, 8, 9, 10, 11]
# SUBGROUP_COLORS = [COLORS[i] for i in SUBGROUP_COLOR_IDXS]
SUBGROUP_COLORS = COLORS
p = tree
for i in range(n_clades):
if p.is_leaf():
break
c_backbone, c_subgroup = next_split(p)
while c_subgroup.tree_size() < 10:
print('Subgroup Size:', c_subgroup.tree_size(), '--> skipped')
if plot_edges:
plot_tree(c_subgroup, color=grey(0.5), lw=lw)
plot_edge(p, c_backbone, no_arrow=True, lw=2*lw, color='k', zorder=3)
p = c_backbone
if p.is_leaf():
break
c_backbone, c_subgroup = next_split(p)
print('Subgroup Size:', c_subgroup.tree_size())
if plot_edges:
plot_tree(c_subgroup, color=SUBGROUP_COLORS[i], lw=lw)
plot_edge(p, c_backbone, no_arrow=True, lw=2*lw, color='k', zorder=3)
if plot_hull:
plot_tree_hull(c_subgroup, c=SUBGROUP_COLORS[i])
p = c_backbone
# # if mode == 'geo':
if plot_edges:
plot_tree(p, color=SUBGROUP_COLORS[n_clades], lw=lw)
if plot_hull:
plot_tree_hull(p, c=SUBGROUP_COLORS[n_clades])
x = np.dot(node.location, DRIFT_DIRECTION)
return x, t
if __name__ == '__main__':
import matplotlib.pyplot as plt
import geopandas as gpd
from src.beast_interface import run_beast, run_treeannotator, load_tree_from_nexus, \
read_nexus_name_mapping, load_trees
from src.plotting import plot_hpd, plot_tree, plot_posterior_scatter
from src.util import grey
from src.colors import PINK, TURQUOISE
world = gpd.read_file('data/naturalearth_50m_wgs84.geojson')
ax = world.plot(color=grey(.95), edgecolor=grey(0.7), lw=.4, )
CHAIN_LENGTH = 500000
BURNIN = 10000
HPD = 90
MODEL = 'rrw'
USE_OUTGROUP = False
ADAPT_TREE = False
ADAPT_HEIGHT = False
FIX_ROOT = False
# SUFFIX = '_missingClades'
WORKING_DIR = 'data/bantu_{model}_outgroup_{og}_adapttree_{at}_' + \
'adaptheight_{ah}_hpd_{hpd}{fixroot}{suffix}/'
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, \
unicode_literals
import matplotlib.pyplot as plt
from webcolors import hex_to_rgb, rgb_to_hex
import numpy as np
from src.util import grey
# COLORS
PINK = (0.95, 0.15, 0.8)
TURQUOISE = (0, 0.8, 0.9)
COLOR_ROOT_EST = (0.75, 0.2, 0.0)
COLOR_ROOT_TRUE = (0., 0.5, 0.6)
COLOR_PATH = grey(0.5)
COLOR_SCATTER = 'orange'
class Cycler(object):
def __init__(self, data):
self.data = data
def __getitem__(self, i):
n = len(self.data)
return self.data[i % n]
_COLORS = [
'#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b',
'#e377c2', '#7f7f7f', '#bcbd22', '#17becf', '#ffe999', '#802a66', '#058090'