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mod_lefse-plot_cladogram.py
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mod_lefse-plot_cladogram.py
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#!/usr/bin/env python2
#import pdb
import os
import sys
import matplotlib
import argparse
import string
sys.path.append('/home/admin1/miniconda3/envs/lefse/share/lefse-1.0.8.post1-1')
sys.path.append('/home/cheng/softwares/miniconda2/share/lefse-1.0.8.post1-1')
matplotlib.use('Agg')
from pylab import *
# pdb.set_trace()
from lefse import *
import numpy as np
from Bayegy.getColors import get_lefse_colors
dark_colors = [[0.4, 0.0, 0.0], [0.0, 0.2, 0.0], [0.0, 0.0, 0.4], 'm', 'c', [
1.0, 0.5, 0.0], [0.0, 1.0, 0.0], [0.33, 0.125, 0.0], [0.75, 0.75, 0.75], 'k']
class CladeNode:
def __init__(self, name, abundance, viz=True):
self.id = name
self.name = name.split(".")
self.last_name = self.name[-1]
self.abundance = abundance
self.pos = (-1.0, -1.0)
self.children = {}
self.isleaf = True
self.color = 'y'
self.next_leaf = -1
self.prev_leaf = -1
self.viz = viz
def __repr__(self):
return self.last_name
def add_child(self, node):
self.isleaf = False
self.children[node.__repr__()] = node
def get_children(self):
ck = sorted(self.children.keys())
return [self.children[k] for k in ck]
def get_color(self):
return self.color
def set_color(self, c):
self.color = c
def set_pos(self, pos):
self.pos = pos
def read_params(args):
parser = argparse.ArgumentParser(description='Cladoplot')
parser.add_argument('input_file', metavar='INPUT_FILE', type=str, help="tab delimited input file")
parser.add_argument('output_file', metavar='OUTPUT_FILE', type=str, help="the file for the output image")
parser.add_argument('--clade_sep', dest="clade_sep", type=float, default=0.8)
parser.add_argument('--map', dest="map", type=str, default=False)
parser.add_argument('--category', dest="category", type=str, default=False)
parser.add_argument('--colors', dest="colors", type=str, default=False)
parser.add_argument('--max_lev', dest="max_lev", type=int, default=-1)
parser.add_argument('--max_point_size', dest="max_point_size", type=float, default=6.0)
parser.add_argument('--min_point_size', dest="min_point_size", type=float, default=1)
parser.add_argument('--point_edge_width', dest="markeredgewidth", type=float, default=.25)
parser.add_argument('--siblings_connector_width', dest="siblings_connector_width", type=float, default=2)
parser.add_argument('--parents_connector_width', dest="parents_connector_width", type=float, default=0.75)
parser.add_argument('--radial_start_lev', dest="radial_start_lev", type=int, default=1)
parser.add_argument('--labeled_start_lev', dest="labeled_start_lev", type=int, default=2)
parser.add_argument('--labeled_stop_lev', dest="labeled_stop_lev", type=int, default=5)
parser.add_argument('--abrv_start_lev', dest="abrv_start_lev", type=int, default=3)
parser.add_argument('--abrv_stop_lev', dest="abrv_stop_lev", type=int, default=5)
parser.add_argument('--expand_void_lev', dest="expand_void_lev", type=int, default=1)
parser.add_argument('--class_legend_vis', dest="class_legend_vis", type=int, default=1)
parser.add_argument('--colored_connector', dest="colored_connectors", type=int, default=1)
parser.add_argument('--alpha', dest="alpha", type=float, default=0.3)
parser.add_argument('--title', dest="title", type=str, default="Cladogram")
parser.add_argument('--sub_clade', dest="sub_clade", type=str, default="")
parser.add_argument('--title_font_size', dest="title_font_size", type=str, default="14")
parser.add_argument('--right_space_prop', dest="r_prop", type=float, default=0.15)
parser.add_argument('--left_space_prop', dest="l_prop", type=float, default=0.1)
parser.add_argument('--label_font_size', dest="label_font_size", type=str, default="6")
parser.add_argument('--background_color', dest="back_color", type=str,
choices=["k", "w"], default="w", help="set the color of the background")
parser.add_argument('--colored_labels', dest="col_lab", type=int,
choices=[0, 1], default=1, help="draw the label with class color (1) or in black (0)")
parser.add_argument('--class_legend_font_size', dest="class_legend_font_size", type=str, default="10")
parser.add_argument('--dpi', dest="dpi", type=int, default=300)
parser.add_argument('--format', dest="format",
choices=["png", "svg", "pdf"], default="svg", type=str, help="the format for the output file")
parser.add_argument('--all_feats', dest="all_feats", type=str, default="")
args = parser.parse_args()
return vars(args)
def cmp_names(la, lb):
if len(la) != len(lb):
return False
for p in [(a, b) for i, a in enumerate(la) for j, b in enumerate(lb) if i == j]:
if p[0] != p[1]:
return False
return True
def build_tree(father, all_nodes, l, depth, viz):
cc = [n for n in all_nodes if len(n.name) > len(father.name) and cmp_names(father.name, n.name[:len(father.name)])]
children = [n for n in cc if len(n.name) == len(father.name) + 1]
if len(children) == 0 and l < depth - 1: # !!!
nc = CladeNode(father.id + "." + father.id.split(".")[-1], 1.0, viz)
father.add_child(nc)
children.append(nc)
for child in children:
build_tree(child, cc, l + 1, depth, viz)
father.add_child(child)
def get_all_nodes(father):
ret = [father]
children = father.get_children()
for c in children:
ret += get_all_nodes(c)
return ret
def read_data(input_file, params):
with open(input_file, 'r') as inp:
if params['sub_clade'] == "":
rows = [line.strip().split()[:-1] for line in inp.readlines() if params['max_lev']
< 1 or line.split()[0].count(".") < params['max_lev']]
else:
rows = [line.split(params['sub_clade'] + ".")[1].strip().split()[:-1] for line in inp.readlines() if (
params['max_lev'] < 1 or line.split()[0].count(".") < params['max_lev']) and line.startswith(params['sub_clade'] + ".")]
all_names = [lin[0] for lin in rows]
to_add = []
abundances = [float(v) for v in zip(*rows)[1] if v >= 0.0]
tree = {}
tree['classes'] = list(set([v[2] for v in rows if len(v) > 2]))
tree['classes'].sort()
all_nodes = [CladeNode("root." + row[0], float(row[1])) for row in rows]
depth = max([len(n.name) for n in all_nodes])
n2 = ["_".join(nn.name) for nn in all_nodes]
for i, nn in enumerate(all_nodes):
n = nn
while "_".join(n.name[:-1]) not in n2 and len(n.name) > 1:
n = CladeNode(".".join(n.name[:-1]), n.abundance)
all_nodes.append(n)
n2.append("_".join(n.name))
cls2 = []
if params['all_feats'] != "":
cls2 = sorted(params['all_feats'].split(":"))
for i, v in enumerate(rows):
if len(v) > 2:
if len(cls2) > 0:
all_nodes[i].set_color(colors[cls2.index(v[2]) % len(colors)])
else:
if v[2].count('rgbcol') > 0:
ccc = [float(tt) for tt in v[2].split('_')[1:]]
all_nodes[i].set_color(ccc)
else:
all_nodes[i].set_color(colors[sorted(tree['classes']).index(v[2]) % len(colors)])
root = CladeNode("root", -1.0)
root.set_pos((0.0, 0.0))
build_tree(root, all_nodes, 0, depth, params['expand_void_lev'] == 1)
all_nodes = get_all_nodes(root)
tree['root'] = root
tree['max_abs'] = max(abundances)
tree['min_abs'] = min(abundances)
levs = []
for i in range(depth):
depthi = [n for n in all_nodes if len(n.name) == i + 1]
levs.append(len(depthi))
tree['nlev'] = levs
return tree
def add_all_pos(father, n, distn, seps, tsep, mlev, last_leaf=-1, nc=1):
children = father.get_children()
leaves = True if children[0].isleaf else False
for i, child in enumerate(children):
if leaves:
n += 1.0
men = 0.5 if len(children) == 1 else 0.0
child.set_pos((n * distn - men * float(distn) + tsep, (len(father.name)) / float(mlev - 1)))
if last_leaf != -1:
child.prev_leaf = last_leaf
last_leaf.next_leaf = child
last_leaf = child
else:
ln = n
ltsep = tsep
n, tsep, last_leaf = add_all_pos(child, n, distn, seps, tsep, mlev, last_leaf, len(children))
nn = (ln + n) * 0.5 * distn
ssep = (ltsep + tsep) * 0.5
if n - ln == 1:
ssep = ltsep
child.set_pos((nn + ssep, (len(father.name)) / float(mlev - 1)))
tsep += seps[len(father.name) - 1]
return n, tsep, last_leaf
def plot_points(father, params, pt_scale, ax):
children = father.get_children()
children.sort(key=lambda a: -int(a.get_color() == 'y') * a.abundance)
x, r = father.pos[0], father.pos[1]
for i, child in enumerate(children):
xc, rc = plot_points(child, params, pt_scale, ax)
if not father.viz:
return x, r
ps = pt_scale[0] + father.abundance / pt_scale[1] + pt_scale[0]
col = father.get_color()
pw = params['markeredgewidth'] if col == 'y' else params['markeredgewidth'] * 3.0
if x == 0 and r == 0:
ax.plot(x, r, 'o', markersize=ps, color=col, markeredgewidth=0.01, markeredgecolor=params['fore_color'])
else:
ax.plot(x, r, 'o', markersize=ps, color=col, markeredgewidth=pw, markeredgecolor=params['fore_color'])
return x, r
def plot_lines(father, params, depth, ax, xf):
children = father.get_children()
x, r = father.pos[0], father.pos[1]
for i, child in enumerate(children):
xc, rc = plot_lines(child, params, depth, ax, x)
if i == 0:
x_first, r_first = xc, rc
if len(father.name) >= depth - params['radial_start_lev']:
col = params['fore_color']
lw = params['parents_connector_width']
if not child.viz:
continue
if father.get_color() != 'y' and father.get_color() == child.get_color() and params['colored_connectors']:
col = child.get_color()
lw *= 2.5
if col != params['fore_color']:
ax.plot([x, xc], [r, rc], "-", color=params['fore_color'], lw=lw * 1.5)
ax.plot([x, xc], [r, rc], "-", color=col, lw=lw)
if not father.viz or (len(children) == 1 and not children[0].viz):
return x, r
if len(father.name) < depth - params['radial_start_lev']:
col = params['fore_color']
lw = params['parents_connector_width']
if father.get_color() != 'y':
f = True
for child in children:
if child.get_color() != father.get_color() or not params['colored_connectors']:
f = False
break
if f:
col = father.get_color()
lw *= 2.5
if not (x == 0 and r == 0):
xx = xc if len(children) > 0 else x
if len(children) == 0:
rc = r
xt = x if len(children) > 1 else xx
if col != params['fore_color']:
ax.plot([x, xt], [r, rc], "-", color=params['fore_color'], lw=lw * 1.5)
ax.plot([x, xt], [r, rc], "-", color=col, lw=lw)
if len(children) > 0 and 1 < len(father.name) < depth - params['radial_start_lev']:
xs = arange(x_first, xc, 0.01)
ys = [rc for t in xs]
ax.plot(xs, ys, "-", color=col, lw=params['siblings_connector_width'], markeredgecolor=params['fore_color'])
return x, r
def uniqueid():
for l in string.lowercase:
yield l
for l in string.lowercase:
for i in range(10):
yield l + str(i)
i = 0
while True:
yield str(i)
i += 1
def plot_names(father, params, depth, ax, u_i, seps):
children = father.get_children()
l = len(father.name)
if len(children) == 0:
if father.prev_leaf == -1 or father.next_leaf == -1:
fr_0, fr_1 = father.pos[0], father.pos[0]
else:
fr_0, fr_1 = (father.pos[0] + father.prev_leaf.pos[0]) * \
0.5, (father.pos[0] + father.next_leaf.pos[0]) * 0.5
for i, child in enumerate(children):
fr, to = plot_names(child, params, depth, ax, u_i, seps)
if i == 0:
fr_0 = fr
fr_1 = to
if father.get_color() != 'y' and params['labeled_start_lev'] < l <= params['labeled_stop_lev'] + 1:
col = father.get_color()
dd = params['labeled_stop_lev'] - params['labeled_start_lev'] + 1
de = depth - 1
dim = 1.0 / float(de)
perc_ext = 0.65 if dim > 0.1 else 1.0
clto = (de - l + 1) * dim + dim * (dd + 1 - (l - dd - 1)) * perc_ext
clto = (de - l + 1) * dim + dim * (dd - (l - params['labeled_start_lev']) + 1) * perc_ext
des = float(180.0 * (fr_0 + fr_1) / np.pi) * 0.5 - 90
lab = ""
txt = father.last_name
if params['abrv_start_lev'] < l <= params['abrv_stop_lev'] + 1:
ide = u_i.next()
lab = str(ide) + ": " + father.last_name # spi lab(jiang)
txt = str(ide)
# ax.bar(fr_0, clto, width = fr_1-fr_0, bottom = float(l-1)/float(depth-1), alpha = params['alpha'], color=col, edgecolor=col)
ax.bar(fr_0, clto, width=fr_1 - fr_0, bottom=float(l - 1) /
float(de), alpha=params['alpha'], color=col, edgecolor=col)
ax.bar(0.0, 0.0, width=0.0, bottom=0.0, alpha=1.0, color=col, edgecolor=params['fore_color'], label=lab)
if l <= params['abrv_stop_lev'] + 1:
if not params['col_lab']:
col = params['fore_color']
else:
if col not in colors:
col = params['fore_color']
else:
col = dark_colors[colors.index(col) % len(dark_colors)]
ax.text((fr_0 + fr_1) * 0.5, clto + float(l - 1) / float(de) - dim * perc_ext / 2.0, txt,
size=params['label_font_size'], rotation=des, ha="center", va="center", color=col)
return fr_0, fr_1
def draw_tree(out_file, tree, params):
plt_size = 7
nlev = tree['nlev']
pt_scale = (params['min_point_size'], max(1.0, ((tree['max_abs'] - tree['min_abs'])) /
(params['max_point_size'] - params['min_point_size'])))
depth = len(nlev)
sep = (2.0 * np.pi) / float(nlev[-1])
seps = [params['clade_sep'] * sep / float(depth - i + 1) for i in range(1, len(tree['nlev']) + 1)]
totseps = sum([s * nlev[i] for i, s in enumerate(seps[:-1])])
clade_sep_err = True if totseps > np.pi else False
while totseps > np.pi:
params['clade_sep'] *= 0.75
seps = [params['clade_sep'] * sep / (float(depth - i + 1) * 0.25) for i in range(1, len(tree['nlev']) + 1)]
totseps = sum([s * nlev[i] for i, s in enumerate(seps[:-1])])
if clade_sep_err:
print 'clade_sep parameter too large, lowered to', params['clade_sep']
fig = plt.figure(edgecolor=params['back_color'], facecolor=params['back_color'])
ax = fig.add_subplot(111, polar=True, frame_on=False, axis_bgcolor=params['back_color'])
plt.subplots_adjust(right=1.0 - params['r_prop'], left=params['l_prop'], bottom=0.2)
ax.grid(False)
xticks([])
yticks([])
ds = (2.0 * np.pi - totseps) / float(nlev[-1])
add_all_pos(tree['root'], 0.0, ds, seps, 0.0, depth)
plot_lines(tree['root'], params, depth, ax, 0)
plot_points(tree['root'], params, pt_scale, ax)
plot_names(tree['root'], params, depth, ax, uniqueid(), seps)
r = np.arange(0, 3.0, 0.01)
theta = 2 * np.pi * r
def get_col_attr(x):
return hasattr(x, 'set_color') and not hasattr(x, 'set_facecolor')
h, l = ax.get_legend_handles_labels()
if len(l) > 0:
if len(l) > 25:
lab_size_adj = 1
else:
lab_size_adj = 0
# leg = ax.legend(bbox_to_anchor=(1.05, 1), frameon=False, loc=0, borderaxespad=0.,prop={'size':params['label_font_size']})
leg = ax.legend(bbox_to_anchor=(1.05, 1), frameon=False, loc=0, borderaxespad=0., prop={
'size': (int(params['label_font_size']) - lab_size_adj)}) # by jiang
if leg != None:
gca().add_artist(leg)
for o in leg.findobj(get_col_attr):
o.set_color(params['fore_color'])
cll = sorted(tree['classes']) if params['all_feats'] == "" else sorted(params['all_feats'].split(":"))
# print cll
nll = [ax.bar(0.0, 0.0, width=0.0, bottom=0.0, color=colors[i % len(colors)], label=c)
for i, c in enumerate(cll) if c in tree['classes']]
cl = [c for c in cll if c in tree['classes']]
ax.set_title(params['title'], size=params['title_font_size'], color=params['fore_color'])
if len(cl) > 2:
adj = 2.5
else:
adj = 0
if params['class_legend_vis']:
# l2 = legend(nll, cl, loc=2, prop={'size':params['class_legend_font_size']}, frameon=False)
l2 = legend(nll, cl, loc=2, prop={'size': (
int(params['class_legend_font_size']) - adj)}, frameon=False) # by jiang
if l2 != None:
for o in l2.findobj(get_col_attr):
o.set_color(params['fore_color'])
plt.savefig(out_file, format=params['format'], facecolor=params['back_color'],
edgecolor=params['fore_color'], dpi=params['dpi'])
plt.close()
if __name__ == '__main__':
params = read_params(sys.argv)
if params['category'] and params['map']:
category_colors = get_lefse_colors(params['category'], params['map'], params['input_file'])
else:
category_colors = False
# colors = params['colors'].split(',') if params['colors'] else False
colors = get_lefse_colors(params['category'], params['map'], params['input_file'],
colors=params['colors']) if params['colors'] else False
colors = colors or category_colors or ['r', 'g', 'b', 'm', 'c', [
1.0, 0.5, 0.0], [0.0, 1.0, 0.0], [0.33, 0.125, 0.0], [0.75, 0.75, 0.75], 'k']
# print colors
params['fore_color'] = 'w' if params['back_color'] == 'k' else 'k'
clad_tree = read_data(params['input_file'], params)
draw_tree(params['output_file'], clad_tree, params)