def render_tree(tree, context_file):
print('rendering tree...')
print(tree)
ts = TreeStyle()
ts.tree_width = 30
if not args.compressed == True:
tree.render(context_file[0].replace('fna', '_tree_annotated.pdf'),
tree_style=ts)
else:
print(context_file[0].replace('.centroids', '_tree_compressed.pdf'))
tree.render(context_file[0].replace('.centroids',
'_tree_compressed.pdf'),
tree_style=ts)
print('tree rendered!')
(t & item[:item.index(':')]).add_face(seqFace, 0, "aligned")
return t
def get_example_tree_2():
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t= Tree(nwTree)
for item in nwTree.replace('(','').replace(')', '').replace(';', '').replace(',','\t').split('\t'):
seqFace2 = SeqMotifFace(seq, motifs=motifDict_2[item[:item.index(':')]], seq_format="-", gap_format="blank")
(t & item[:item.index(':')]).add_face(seqFace2, 0, "aligned")
return t
if __name__ == '__main__':
t = get_example_tree()
ts = TreeStyle()
ts.tree_width = 300
ts.show_branch_support = True
if args.tree_order:
t.render(args.out_prefix+"_flankgenes_1.svg",tree_style=ts)
else:
t.show(tree_style=ts)
t.render(args.out_prefix+"_flankgenes_1.svg",tree_style=ts)
if __name__ == '__main__':
t = get_example_tree_2()
ts = TreeStyle()
ts.tree_width = 300
ts.show_branch_support = True
if args.tree_order:
t.render(args.out_prefix+"_flankgenes_2.svg", tree_style=ts)
else:
def plot_phylo(nw_tree,
out_name,
parenthesis_classif=True,
show_support=False,
radial_mode=False,
root=False):
from ete3 import Tree, AttrFace, TreeStyle, NodeStyle, TextFace
import orthogroup2phylogeny_best_refseq_uniprot_hity
ete2_tree = Tree(nw_tree, format=0)
if root:
R = ete2_tree.get_midpoint_outgroup()
# and set it as tree outgroup
ete2_tree.set_outgroup(R)
ete2_tree.set_outgroup('Bacillus subtilis')
ete2_tree.ladderize()
if parenthesis_classif:
print('parenthesis_classif!')
name2classif = {}
for lf in ete2_tree.iter_leaves():
print(lf)
try:
classif = lf.name.split('_')[-2][0:-1]
print('classif', classif)
#lf.name = lf.name.split('(')[0]
name2classif[lf.name] = classif
except:
pass
classif_list = list(set(name2classif.values()))
classif2col = dict(
zip(
classif_list,
orthogroup2phylogeny_best_refseq_uniprot_hity.
get_spaced_colors(len(classif_list))))
for lf in ete2_tree.iter_leaves():
#try:
if parenthesis_classif:
try:
col = classif2col[name2classif[lf.name]]
except:
col = 'black'
else:
col = 'black'
#print col
#lf.name = '%s|%s-%s' % (lf.name, accession2name_and_phylum[lf.name][0],accession2name_and_phylum[lf.name][1])
if radial_mode:
ff = AttrFace("name", fsize=12, fstyle='italic')
else:
ff = AttrFace("name", fsize=12, fstyle='italic')
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
if not show_support:
print('support')
for n in ete2_tree.traverse():
print(n.support)
nstyle = NodeStyle()
if float(n.support) < 1:
nstyle["fgcolor"] = "red"
nstyle["size"] = 4
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
else:
for n in ete2_tree.traverse():
nstyle = NodeStyle()
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
#nameFace = AttrFace(lf.name, fsize=30, fgcolor=phylum2col[accession2name_and_phylum[lf.name][1]])
#faces.add_face_to_node(nameFace, lf, 0, position="branch-right")
#
#nameFace.border.width = 1
'''
except:
col = 'red'
print col
lf.name = '%s| %s' % (lf.name, locus2organism[lf.name])
ff = AttrFace("name", fsize=12)
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
'''
#n = TextFace(lf.name, fgcolor = "black", fsize = 12, fstyle = 'italic')
#lf.add_face(n, 0)
'''
for n in ete2_tree.traverse():
nstyle = NodeStyle()
if n.support < 90:
nstyle["fgcolor"] = "black"
nstyle["size"] = 4
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
'''
ts = TreeStyle()
ts.show_leaf_name = False
#ts.scale=2000
#ts.scale=20000
ts.show_branch_support = show_support
if radial_mode:
ts.mode = "c"
ts.arc_start = -90
ts.arc_span = 360
ts.tree_width = 370
ts.complete_branch_lines_when_necessary = True
ete2_tree.render(out_name, tree_style=ts, w=900)
def get_example_tree(File):
adres=os.getcwd()
file_out_supliment = open(adres+"/out_spliment/"+File, 'w')
node_file = open(adres+"/node/"+File, 'w')
# Create a random tree and add to each leaf a random set of motifs
# from the original set
#t = Tree("( (A, B, C, D, E, F, G), H, I);")
#Считываем все домены
domain_all_legend={}
file_all_domen=os.listdir(adres+"/for_pic/1_tree_nwk/")
file_all_domen.remove(".DS_Store")
file_all_domen.sort()
i=0
for file_domain in file_all_domen:
file_open_domain = open(adres+"/for_pic/3_domain/"+file_domain, 'r')
for line in file_open_domain:
line_=line.split("\t")
try:
if not (line_[2] in domain_all_legend):
domain_all_legend.setdefault(line_[2],dic_domain_pic_pic[i])
i+=1
if i>len(dic_domain_pic_pic):
i=0
except:
a=0
mem=""
file_open = open(adres+"/for_pic/1_tree_nwk/"+File, 'r')
for line in file_open:
mem=mem+line
tt = Tree(mem, format=0)
style = NodeStyle()
style["fgcolor"] = "#000000"
style["size"] = 0
style["vt_line_color"] = "#000000"
style["hz_line_color"] = "#000000"
style["vt_line_width"] = 4
style["hz_line_width"] = 4
style["vt_line_type"] = 8 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 8
for node in tt.traverse("levelorder"):
node.img_style = style
if (len(node.name))>1:
node_file.write(node.name+"\n")
children1=node.children
for element in children1:
element.img_style = style
for node in tt.traverse("preorder"):
node.img_style = style
children1=node.children
for element in children1:
element.img_style = style
node_file.close
#вывести дерево с цветами
#print (tt.get_ascii(attributes=["name", "color"], show_internal=False))
#поиск предка
ancestor1=""
i=0
for element in ancestor_grop:
if i==0:
for node in tt.traverse("postorder"):
if i==0:
node_name=str(node.name)
if (node_name.startswith(element)) and not((node_name.startswith("PPE"))):
ancestor1=str(node.name)
i=1
break
else:
break
else:
break
if not (ancestor1==""):
tt.set_outgroup(ancestor1)
#tt.render(adres+"/out/"+File[:-3]+"_2.png", tree_style=circular_style)
print(str(ancestor1)+" - предок")
file_out_supliment.write(str(ancestor1)+"\t"+" - предполагаемый корень"+"\n")
else:
print("Не нашел предка")
file_out_supliment.write("\n\n\n Выявленные клады\n")
#добавляем цвета к кладам
for leaf in tt:
i=0
node_name=str(leaf.name)
for clad in all_clad:
collor=collor_list[i]
i+=1
for element in clad:
if (node_name.startswith(element)):
leaf.add_features(color=collor)
#print(leaf)
#print(tt)
#забираем монофилитические цвета
#print (tt.get_ascii(attributes=["name", "color"], show_internal=False))
ii=-1
for clad in all_clad:
ii+=1
collor=collor_list[ii]
for monophyletic_tree in tt.get_monophyletic(values=[collor], target_attr="color"):
i=[]
name_node_mono_color=[]
for leaf in monophyletic_tree:
i.append(leaf)
name_node_mono_color.append(leaf.name)
if len(i)>1:
n1 = tt.get_common_ancestor(i)
nst1 = NodeStyle()
nst1["bgcolor"] = collor
nst1["fgcolor"] = "#000000"
nst1["size"] = 0
nst1["vt_line_color"] = "#000000"
nst1["hz_line_color"] = "#000000"
nst1["vt_line_width"] = 4
nst1["hz_line_width"] = 4
nst1["vt_line_type"] = 8 # 0 solid, 1 dashed, 2 dotted
nst1["hz_line_type"] = 8
n1.set_style(nst1)
for element in name_node_mono_color:
file_out_supliment.write(str(element)+"\t"+" - "+collor+"\n")
file_out_supliment.write("\n")
file_out_supliment.write("\n\n\n Легенда доменного состава\n")
#добавляем разметку по доменам
dic_seq={}
dic_domain={}
dic_domain_pic={}
i=0
list_legend_domain3=[]
for node in tt.traverse("postorder"):
#длины белков
fasta_sequences=SeqIO.parse(open(adres+"/for_pic/2_MSA/"+File), "fasta")
for element in fasta_sequences:
if str(element.id)==str(node.name):
dic_seq.setdefault(str(node.name),str(element.seq))
#доменный состав
a=[]
file_domain = open(adres+"/for_pic/3_domain/"+File, 'r')
for line in file_domain:
line_=line.split("\t")
if line_[0]==str(node.name):
if not (line_[2] in list_legend_domain3):
list_legend_domain3.append(line_[2])
if not (line_[2] in dic_domain_pic):
dic_domain_pic.setdefault(line_[2],dic_domain_pic_pic[i])
i+=1
#print(dic_domain_pic[line_[2]])
#print(i)
a1=[int(line_[3]),int(line_[4]), "()", None, 15, "black", domain_all_legend[line_[2]], "arial|9|black|"+line_[2]]
a.append(a1)
dic_domain.setdefault(str(node.name),a)
file_out_supliment.write(line_[2]+"\t"+domain_all_legend[line_[2]]+"\n")
else:
a1=[int(line_[3]),int(line_[4]), "()", None, 15, "black", domain_all_legend[line_[2]], "arial|9|black|"+line_[2]]
a.append(a1)
dic_domain.setdefault(str(node.name),a)
for element in dic_domain:
#print(str(element)+" "+ str(dic_domain[element]))
try:
seqFace = SeqMotifFace(seq=dic_seq[element], motifs=dic_domain[element], seq_format="line")
(tt & element).add_face(seqFace, 0, "aligned")
except:
seqFace = SeqMotifFace(seq=dic_seq[element], seq_format="line", gapcolor="red")
(tt & element).add_face(seqFace, 0, "aligned")
print("except")
#Рисуем легенду
circular_style = TreeStyle()
circular_style.show_leaf_name = False
circular_style.show_branch_length = True
circular_style.show_branch_support = True
circular_style.scale = 75
circular_style.tree_width = 50
file_domain.close
file_domain = open(adres+"/for_pic/3_domain/"+File, 'r')
list_legend_domain={}
list_legend_domain2=[]
#считали список доменов
i=0
for line in file_domain:
line_=line.split("\t")
try:
if not(line_[2] in list_legend_domain2):
#print(line_[2])
list_legend_domain2.append(line_[2])
list_legend_domain.setdefault("a"+str(i),line_[2])
i+=1
except:
print("не понял что это за домен")
i=0
#считываем легенду доменов
file_domain_legend2={}
file_domain_legend = open(adres+"/domain_legend.txt", 'r')
for line in file_domain_legend:
line_=line.split("\t")
aaa=line_[1].replace(" ","_")
aaa=aaa.replace("(","_")
aaa=aaa.replace(")","_")
aaa=aaa.replace(",","_")
aaa=aaa.replace(":","_")
aaa=aaa.replace(".","_")
file_domain_legend2.setdefault(line_[0],aaa.replace("\n",""))
#N = AttrFace("name", fsize=12)
#faces.add_face_to_node(N, node, 1, position="branch-right")
#рисуем домены
ww=""
for element in file_domain_legend2:
ww=ww+","+file_domain_legend2[element]
ww="("+ww[1:]+");"
tree_domen_all=Tree(ww)
for element in file_domain_legend2:
try:
element2=domain_all_legend[element]
a1=[10,90, "()", None, 15, "black", domain_all_legend[element], "arial|9|black|"+element]
i+=1
a=[]
a.append(a1)
seqFace = SeqMotifFace(seq=seq_seq, motifs=a, seq_format="line")
#node_node="a"+str(i)
node_node=file_domain_legend2[element]
try:
(tree_domen_all & node_node).add_face(seqFace, 0, "aligned")
except:
q=1
print("не нашел узел")
except:
q=1
circular_style.layout_fn = layout
tree_domen_all.render(adres+"/out_legend_all.png", tree_style=circular_style)
file_domain_out = open(adres+"/123123123.txt", 'w')
w=""
for element in list_legend_domain3:
w=w+","+file_domain_legend2[element]
w="("+w[1:]+");"
tree_domen=Tree(w)
for element in list_legend_domain3:
file_domain_out.write(element+"\n")
a1=[10,90, "()", None, 15, "black", domain_all_legend[element], "arial|9|black|"+element]
i+=1
a=[]
a.append(a1)
try:
seqFace = SeqMotifFace(seq=seq_seq, motifs=a, seq_format="line")
#node_node="a"+str(i)
node_node=file_domain_legend2[element]
(tree_domen & node_node).add_face(seqFace, 0, "aligned")
except:
#print("Закончились узлы легенды")
k=0
circular_style.layout_fn = layout
tree_domen.render(adres+"/out_legend/"+File[:-4]+".png", tree_style=circular_style)
#удаленние части узлов
for node in tt.traverse("postorder"):
try:
seqFace = SeqMotifFace(seq=dic_seq[str(node.name)], motifs=dic_domain[str(node.name)], seq_format="line")
(tt & node.name).add_face(seqFace, 0, "aligned")
a=0
if len(node.name)<2:
a=1
for element_save in save_node:
if (node.name).startswith(element_save):
a=1
for element_dell in dell_node:
if (node.name).startswith(element_dell):
a=0
if a==0:
node.delete()
except:
if len(node.name)>0:
seqFace = SeqMotifFace(seq=dic_seq[str(node.name)], seq_format="line", gapcolor="red")
(tt & node.name).add_face(seqFace, 0, "aligned")
node.delete()
d0=0
#удаленние части узлов ЗАВЕРШЕНО
#особые точки
node_color=[]
file_node_color = open(adres+"/for_pic/4_color_node/out_list_gene2.txt", 'r')
for line in file_node_color:
node_color.append(line.replace("\n",""))
for node in tt.traverse("postorder"):
if node.name in node_color:
style = NodeStyle()
style["fgcolor"] = "Red"
style["size"] = 9
style["vt_line_color"] = "#000000"
style["hz_line_color"] = "#000000"
style["vt_line_width"] = 4
style["hz_line_width"] = 4
style["vt_line_type"] = 8 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 8
node.set_style(style)
file_out_supliment.close
#забираем монофилитические цвета
#print (tt.get_ascii(attributes=["name", "color"], show_internal=False))
ii=-1
for clad in all_clad:
ii+=1
collor=collor_list[ii]
for monophyletic_tree in tt.get_monophyletic(values=[collor], target_attr="color"):
i=[]
name_node_mono_color=[]
for leaf in monophyletic_tree:
i.append(leaf)
name_node_mono_color.append(leaf.name)
if len(i)>1:
n1 = tt.get_common_ancestor(i)
nst1 = NodeStyle()
nst1["bgcolor"] = collor
nst1["fgcolor"] = "#000000"
nst1["size"] = 0
nst1["vt_line_color"] = "#000000"
nst1["hz_line_color"] = "#000000"
nst1["vt_line_width"] = 4
nst1["hz_line_width"] = 4
nst1["vt_line_type"] = 8 # 0 solid, 1 dashed, 2 dotted
nst1["hz_line_type"] = 8
n1.set_style(nst1)
for element in name_node_mono_color:
file_out_supliment.write(str(element)+"\t"+" - "+collor+"\n")
file_out_supliment.write("\n")
return tt
if __name__ == '__main__':
adres=os.getcwd()
file_all=os.listdir(adres+"/for_pic/1_tree_nwk/")
for File in file_all:
if not(File.startswith(".")):
print(File)
t = get_example_tree(File)
#выбор стиля
circular_style = TreeStyle()
circular_style.show_leaf_name = False
circular_style.show_branch_length = True
circular_style.show_branch_support = True
circular_style.scale = 75
circular_style.tree_width = 50
#circular_style.rotation = 90
#circular_style.extra_branch_line_type=(0)
#circular_style.guiding_lines_type= (0)
#circular_style.title.add_face(TextFace(File, fsize=25), column=0)
circular_style.layout_fn = layout
t.render(adres+"/out/"+File[:-4]+".png", tree_style=circular_style)
circular_style.mode = "r" # draw tree in circular mode
circular_style.extra_branch_line_type=(2)
circular_style.guiding_lines_type= (2)
circular_style.guiding_lines_color =("red")
for n in t.traverse():
nstyle = NodeStyle()
nstyle["fgcolor"] = "red"
nstyle["size"] = 15
n.set_style(nstyle)
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)
t = sys.argv[1]
alg = sys.argv[2]
predic_table = sys.argv[3]
out_img_name = sys.argv[4]
#bilaterian_desc = ncbi.get_descendant_taxa('Bilateria', collapse_subspecies=True)
#print type(bilaterian_desc)
tree_upp = PhyloTree(newick=t, alignment=alg, alg_format="fasta")
R = tree_upp.get_midpoint_outgroup()
tree_upp.set_outgroup(R)
predict_name = {}
for line in open(predic_table):
if line.rstrip() and not line.startswith("#"):
prot_name = line.split("\t")[0]
pred_name = line.split("\t")[5]
predict_name[prot_name] = pred_name
ts = TreeStyle()
ts.show_leaf_name = False
ts.tree_width = 2000
ts.layout_fn = layout
tree_upp.render(out_img_name, tree_style=ts, h=200000, dpi=300, units="px")
def make_tree_figure(tree,
palette,
outfile,
edit_d,
wgd,
outgroups,
usedict=False,
outformat="png",
moved=False,
coutgr=False):
"""
Creates and saves an image for a tree object.
Args:
tree (ete3.Tree): input tree
palette (list): pre-defined list of colors to use
outfile (str): name for the output image
edit_d (dict): dictionary to store/load colors
wgd (str): restrict coloring to specified wgd
usedict (bool, optional): should dictionary be used to load colors
outformat (str, optional): output format for image png (default), svg or pdf
moved (bool, optional): color rearranged non-wgd species leaves
Returns:
dict: colors to leaf names mapping
"""
#create a treestyle that we'll customize
tstyle = TreeStyle()
tstyle.show_leaf_name = True
corrected_wgd_nodes = get_corrected_wgd_nodes(tree, wgd, outgroups)
if not corrected_wgd_nodes and not usedict:
sys.stderr.write(
f"No corrected subtree for wgd {wgd}, no image created.\n")
return edit_d
leaves = {i.name for i in tree.get_leaves()}
if usedict and not leaves.intersection(set(edit_d.keys())):
sys.stderr.write(
f"No corrected subtree for wgd {wgd}, no image created.\n")
return edit_d
for node in tree.traverse():
if not node.is_leaf():
is_corrected_wgd = node in corrected_wgd_nodes
#color duplication, speciation and dubious nodes with convention colors
color_internal_node(node, is_corrected_wgd)
#color edited leaves
else:
ignore = False
if not coutgr and node.S in outgroups:
ignore = True
color_leaves(node,
palette,
edit_d,
wgd,
usedict=usedict,
moved=moved,
ignore=ignore)
#color root node
color_internal_node(tree)
#hide default leaf name since we added custom ones
tstyle.show_leaf_name = False
#set width
tstyle.tree_width = 200
#save image
out = outfile + "." + outformat
tree.render(out, dpi=80, tree_style=tstyle)
sys.stderr.write(f"{out} created !!\n")
return edit_d
def run(args):
if args.text_mode:
from ete3 import Tree
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]",
open(tfile).read())
t = Tree(nw)
else:
t = Tree(tfile)
print(
t.get_ascii(show_internal=args.show_internal_names,
attributes=args.show_attributes))
return
import random
import re
import colorsys
from collections import defaultdict
from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
add_face_to_node, random_color)
global FACES
if args.face:
FACES = parse_faces(args.face)
else:
FACES = []
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = True
ts.tree_width = args.tree_width
for f in FACES:
if f["value"] == "@name":
ts.show_leaf_name = False
break
if args.as_ncbi:
ts.show_leaf_name = False
FACES.extend(
parse_faces([
'value:@sci_name, size:10, fstyle:italic',
'value:@taxid, color:grey, size:6, format:" - %s"',
'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
]))
if args.alg:
FACES.extend(
parse_faces([
'value:@sequence, size:10, pos:aligned, ftype:%s' %
args.alg_type
]))
if args.heatmap:
FACES.extend(
parse_faces(['value:@name, size:10, pos:aligned, ftype:heatmap']))
if args.bubbles:
for bubble in args.bubbles:
FACES.extend(
parse_faces([
'value:@%s, pos:float, ftype:bubble, opacity:0.4' % bubble,
]))
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
ts.layout_fn = lambda x: None
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]",
open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
if args.heatmap:
DEFAULT_COLOR_SATURATION = 0.3
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex(
tuple([
int(x * 255) for x in colorsys.hls_to_rgb(h, l, s)
]))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
heatmap_data = {}
max_value, min_value = None, None
for line in open(args.heatmap):
if line.startswith('#COLNAMES'):
pass
elif line.startswith('#') or not line.strip():
pass
else:
fields = line.split('\t')
name = fields[0].strip()
values = [float(x) if x else None for x in fields[1:]]
maxv = max(values)
minv = min(values)
if max_value is None or maxv > max_value:
max_value = maxv
if min_value is None or minv < min_value:
min_value = minv
heatmap_data[name] = values
heatmap_center_value = 0
heatmap_color_center = "white"
heatmap_color_up = 0.3
heatmap_color_down = 0.7
heatmap_color_missing = "black"
heatmap_max_value = abs(heatmap_center_value - max_value)
heatmap_min_value = abs(heatmap_center_value - min_value)
if heatmap_center_value <= min_value:
heatmap_max_value = heatmap_min_value + heatmap_max_value
else:
heatmap_max_value = max(heatmap_min_value, heatmap_max_value)
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
f2color = {}
f2last_seed = {}
for node in t.traverse():
node.img_style['size'] = 0
if len(node.children) == 1:
node.img_style['size'] = 2
node.img_style['shape'] = "square"
node.img_style['fgcolor'] = "steelblue"
ftype_pos = defaultdict(int)
for findex, f in enumerate(FACES):
if (f['nodetype'] == 'any'
or (f['nodetype'] == 'leaf' and node.is_leaf()) or
(f['nodetype'] == 'internal' and not node.is_leaf())):
# if node passes face filters
if node_matcher(node, f["filters"]):
if f["value"].startswith("@"):
fvalue = getattr(node, f["value"][1:], None)
else:
fvalue = f["value"]
# if node's attribute has content, generate face
if fvalue is not None:
fsize = f["size"]
fbgcolor = f["bgcolor"]
fcolor = f['color']
if fcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr:
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(
node, color_keyattr, None)
last_seed = f2last_seed.setdefault(
color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(
0.1, 0.2)
f2last_seed[color_keyattr] = seed
fcolor = f2color.setdefault(
color_bin, random_color(h=seed))
if fbgcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr:
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(
node, color_keyattr, None)
last_seed = f2last_seed.setdefault(
color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(
0.1, 0.2)
f2last_seed[color_keyattr] = seed
fbgcolor = f2color.setdefault(
color_bin, random_color(h=seed))
if f["ftype"] == "text":
if f.get("format", None):
fvalue = f["format"] % fvalue
F = TextFace(fvalue,
fsize=fsize,
fgcolor=fcolor or "black",
fstyle=f.get('fstyle', None))
elif f["ftype"] == "fullseq":
F = faces.SeqMotifFace(seq=fvalue,
seq_format="seq",
seqtail_format="seq",
height=fsize)
elif f["ftype"] == "compactseq":
F = faces.SeqMotifFace(
seq=fvalue,
seq_format="compactseq",
seqtail_format="compactseq",
height=fsize)
elif f["ftype"] == "blockseq":
F = faces.SeqMotifFace(
seq=fvalue,
seq_format="blockseq",
seqtail_format="blockseq",
height=fsize,
fgcolor=fcolor or "slategrey",
bgcolor=fbgcolor or "slategrey",
scale_factor=1.0)
fbgcolor = None
elif f["ftype"] == "bubble":
try:
v = float(fvalue)
except ValueError:
rad = fsize
else:
rad = fsize * v
F = faces.CircleFace(radius=rad,
style="sphere",
color=fcolor
or "steelblue")
elif f["ftype"] == "heatmap":
if not f['column']:
col = ftype_pos[f["pos"]]
else:
col = f["column"]
for i, value in enumerate(
heatmap_data.get(node.name, [])):
ftype_pos[f["pos"]] += 1
if value is None:
color = heatmap_color_missing
elif value > heatmap_center_value:
color = gradient_color(
abs(heatmap_center_value - value),
heatmap_max_value,
hue=heatmap_color_up)
elif value < heatmap_center_value:
color = gradient_color(
abs(heatmap_center_value - value),
heatmap_max_value,
hue=heatmap_color_down)
else:
color = heatmap_color_center
node.add_face(RectFace(
20, 20, color, color),
position="aligned",
column=col + i)
# Add header
# for i, name in enumerate(header):
# nameF = TextFace(name, fsize=7)
# nameF.rotation = -90
# tree_style.aligned_header.add_face(nameF, column=i)
F = None
elif f["ftype"] == "profile":
# internal profiles?
F = None
elif f["ftype"] == "barchart":
F = None
elif f["ftype"] == "piechart":
F = None
# Add the Face
if F:
F.opacity = f['opacity'] or 1.0
# Set face general attributes
if fbgcolor:
F.background.color = fbgcolor
if not f['column']:
col = ftype_pos[f["pos"]]
ftype_pos[f["pos"]] += 1
else:
col = f["column"]
node.add_face(F, column=col, position=f["pos"])
if args.image:
t.render("t%d.%s" % (tindex, args.image),
tree_style=ts,
w=args.width,
h=args.height,
units=args.size_units)
else:
t.show(None, tree_style=ts)
def run(args):
if args.text_mode:
from ete3 import Tree
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = Tree(nw)
else:
t = Tree(tfile)
print(t.get_ascii(show_internal=args.show_internal_names,
attributes=args.show_attributes))
return
import random
import re
import colorsys
from collections import defaultdict
from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
add_face_to_node, random_color)
global FACES
if args.face:
FACES = parse_faces(args.face)
else:
FACES = []
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = True
ts.tree_width = args.tree_width
for f in FACES:
if f["value"] == "@name":
ts.show_leaf_name = False
break
if args.as_ncbi:
ts.show_leaf_name = False
FACES.extend(parse_faces(
['value:@sci_name, size:10, fstyle:italic',
'value:@taxid, color:grey, size:6, format:" - %s"',
'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
]))
if args.alg:
FACES.extend(parse_faces(
['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
))
if args.heatmap:
FACES.extend(parse_faces(
['value:@name, size:10, pos:aligned, ftype:heatmap']
))
if args.bubbles:
for bubble in args.bubbles:
FACES.extend(parse_faces(
['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
]))
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
ts.layout_fn = lambda x: None
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
if args.heatmap:
DEFAULT_COLOR_SATURATION = 0.3
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex( tuple([int(x*255) for x in colorsys.hls_to_rgb(h, l, s)]))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
heatmap_data = {}
max_value, min_value = None, None
for line in open(args.heatmap):
if line.startswith('#COLNAMES'):
pass
elif line.startswith('#') or not line.strip():
pass
else:
fields = line.split('\t')
name = fields[0].strip()
values = [float(x) if x else None for x in fields[1:]]
maxv = max(values)
minv = min(values)
if max_value is None or maxv > max_value:
max_value = maxv
if min_value is None or minv < min_value:
min_value = minv
heatmap_data[name] = values
heatmap_center_value = 0
heatmap_color_center = "white"
heatmap_color_up = 0.3
heatmap_color_down = 0.7
heatmap_color_missing = "black"
heatmap_max_value = abs(heatmap_center_value - max_value)
heatmap_min_value = abs(heatmap_center_value - min_value)
if heatmap_center_value <= min_value:
heatmap_max_value = heatmap_min_value + heatmap_max_value
else:
heatmap_max_value = max(heatmap_min_value, heatmap_max_value)
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
f2color = {}
f2last_seed = {}
for node in t.traverse():
node.img_style['size'] = 0
if len(node.children) == 1:
node.img_style['size'] = 2
node.img_style['shape'] = "square"
node.img_style['fgcolor'] = "steelblue"
ftype_pos = defaultdict(int)
for findex, f in enumerate(FACES):
if (f['nodetype'] == 'any' or
(f['nodetype'] == 'leaf' and node.is_leaf()) or
(f['nodetype'] == 'internal' and not node.is_leaf())):
# if node passes face filters
if node_matcher(node, f["filters"]):
if f["value"].startswith("@"):
fvalue = getattr(node, f["value"][1:], None)
else:
fvalue = f["value"]
# if node's attribute has content, generate face
if fvalue is not None:
fsize = f["size"]
fbgcolor = f["bgcolor"]
fcolor = f['color']
if fcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fcolor = f2color.setdefault(color_bin, random_color(h=seed))
if fbgcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fbgcolor = f2color.setdefault(color_bin, random_color(h=seed))
if f["ftype"] == "text":
if f.get("format", None):
fvalue = f["format"] % fvalue
F = TextFace(fvalue,
fsize = fsize,
fgcolor = fcolor or "black",
fstyle = f.get('fstyle', None))
elif f["ftype"] == "fullseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="seq",
seqtail_format="seq",
height=fsize)
elif f["ftype"] == "compactseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="compactseq",
seqtail_format="compactseq",
height=fsize)
elif f["ftype"] == "blockseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="blockseq",
seqtail_format="blockseq",
height=fsize,
fgcolor=fcolor or "slategrey",
bgcolor=fbgcolor or "slategrey",
scale_factor = 1.0)
fbgcolor = None
elif f["ftype"] == "bubble":
try:
v = float(fvalue)
except ValueError:
rad = fsize
else:
rad = fsize * v
F = faces.CircleFace(radius=rad, style="sphere",
color=fcolor or "steelblue")
elif f["ftype"] == "heatmap":
if not f['column']:
col = ftype_pos[f["pos"]]
else:
col = f["column"]
for i, value in enumerate(heatmap_data.get(node.name, [])):
ftype_pos[f["pos"]] += 1
if value is None:
color = heatmap_color_missing
elif value > heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_up)
elif value < heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_down)
else:
color = heatmap_color_center
node.add_face(RectFace(20, 20, color, color), position="aligned", column=col + i)
# Add header
# for i, name in enumerate(header):
# nameF = TextFace(name, fsize=7)
# nameF.rotation = -90
# tree_style.aligned_header.add_face(nameF, column=i)
F = None
elif f["ftype"] == "profile":
# internal profiles?
F = None
elif f["ftype"] == "barchart":
F = None
elif f["ftype"] == "piechart":
F = None
# Add the Face
if F:
F.opacity = f['opacity'] or 1.0
# Set face general attributes
if fbgcolor:
F.background.color = fbgcolor
if not f['column']:
col = ftype_pos[f["pos"]]
ftype_pos[f["pos"]] += 1
else:
col = f["column"]
node.add_face(F, column=col, position=f["pos"])
if args.image:
t.render("t%d.%s" %(tindex, args.image),
tree_style=ts, w=args.width, h=args.height, units=args.size_units)
else:
t.show(None, tree_style=ts)
(t & "C").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, seq_format="()")
(t & "D").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, motifs=simple_motifs, seq_format="-")
(t & "E").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq=None, motifs=simple_motifs, gap_format="blank")
(t & "F").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, motifs=mixed_motifs, seq_format="-")
(t & "G").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq=None, motifs=box_motifs, gap_format="line")
(t & "H").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq[30:60], seq_format="seq")
(t & "I").add_face(seqFace, 0, "aligned")
return t
if __name__ == '__main__':
t = get_example_tree()
ts = TreeStyle()
ts.tree_width = 50
#t.show(tree_style=ts)
t.render("seq_motif_faces.png", tree_style=ts)
