def make_tree_figure(nw_file):
## build tree ##
nw_format = open(nw_file)
nw_read = nw_format.read()
nw_format.close()
print(nw_read)
t = Tree(nw_read, format=1)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.show_leaf_name = False
ts.show_scale = False
t.render("label_tree.png", my_layout, tree_style=ts, dpi=150, w=600)
def plot_uncorrected_phylogeny(tree, species, latin_names, species_history):
"""
Generates a PDF figure of the input tree with same length for all branches.
:param tree: input tree from configuration file
:param species: the current focal species
:param latin_names: a dictionary-like data structure that associates each informal species name to its latin name
:param species_history: the list of ancestor nodes of the focal species, including the focal species and going up to the root.
"""
label_leaves_with_latin_names(tree, latin_names)
node_and_branch_style(tree)
ts = TreeStyle()
# ts.title.add_face(TextFace(" Input phylogenetic tree", ftype="Arial", fsize=18), column=0)
ts.orientation = 1
ts.branch_vertical_margin = 14
ts.show_leaf_name = False # because there is a Face showing it
ts.show_branch_length = False
ts.margin_left = 25
ts.margin_right = 25
ts.margin_top = 25
ts.margin_bottom = 25
ts.scale = 200
ts.show_scale = False
tree.render(os.path.join("rate_adjustment", f"{species}",
f"{_TREE.format(species)}"),
w=4.5,
units="in",
tree_style=ts)
def make_tree(t):
ts = TreeStyle()
## make the tree in to a cladogram
most_distant_leaf, tree_length = t.get_farthest_leaf()
current_dist = 0
for postorder, node in t.iter_prepostorder():
if postorder:
current_dist -= node.dist
else:
if node.is_leaf():
node.dist += tree_length - (current_dist + node.dist)
elif node.up: # node is internal
current_dist += node.dist
## Rotate and color the lables
def rotation_layout(node):
if node.is_leaf():
if node.name == 'X':
F = TextFace(node.name, tight_text=True, fgcolor='Blue')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
elif node.name == 'Y':
F = TextFace(node.name, tight_text=True, fgcolor='Red')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
elif node.name == 'A':
F = TextFace("")
add_face_to_node(F, node, column=0, position="branch-right")
else:
F = TextFace(node.name, tight_text=True, fgcolor='Green')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
## Format the tree image
nstyle = NodeStyle()
nstyle["hz_line_type"] = 0
nstyle["vt_line_color"] = "#ffffff"
nstyle["hz_line_color"] = "#ffffff"
nstyle["vt_line_width"] = 4
nstyle["hz_line_width"] = 4
nstyle["size"] = 0
for n in t.traverse():
n.set_style(nstyle)
## Set background
t.img_style["bgcolor"] = "#2e3440"
## Tree 'shape'
ts.min_leaf_separation = 20
ts.show_leaf_name = False
ts.layout_fn = rotation_layout
ts.rotation = -90
ts.show_scale = False
#t.show(tree_style=ts)
t.render(f"{t.name}.svg", tree_style=ts, dpi=900)
def render_tree(species_tree, bipart1, num_alt, png_fn, replace_taxon=None):
color1 = "blue"
color2 = "black"
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
nstyle = NodeStyle()
nstyle["size"] = 0
ts.title.add_face(
TextFace("{} bipartition in {} gene trees".format(png_fn, num_alt),
fsize=15,
bold=True), 0)
plot_tree = species_tree
for node in plot_tree.traverse():
node.set_style(nstyle)
if node.name in bipart1:
name_face = TextFace(node.name, fgcolor=color1)
else:
name_face = TextFace(node.name, fgcolor=color2)
node.add_face(name_face, 0, 'branch-right')
if replace_taxon:
for leaf in plot_tree.get_leaves:
try:
leaf.name = taxon_subst[leaf.name]
except KeyError:
continue
plot_tree.convert_to_ultrametric()
plot_tree.render(png_fn, tree_style=ts, w=600)
def draw_raw_tree(filename: str) -> None:
"""Draws a raw tree from ete3 representation
stored in a file
Parameters
----------
filename : str
a name of the file
Returns
-------
None
"""
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = layout_raw
ts.rotation = 90
ts.branch_vertical_margin = 10
ts.show_scale = False
ts.scale = 50
ts.title.add_face(TextFace(" ", fsize=20), column=0)
ete3_desc = read_ete3_from_file(filename)
tree = Tree(ete3_desc, format=1)
# tree.show(tree_style=ts)
return tree.render("%%inline",tree_style=ts)
def generate_type_tree_figure(output_file):
""" Generate type_tree.png image.
It needs ETE dependencies installed
cf http://etetoolkit.org/new_download/ or use anaconda
:param output_file: str
"""
try:
from ete3 import faces, TextFace, TreeStyle
except ImportError as e:
logger.warning(
'ImportError : %s Generation of type_tree figure need ETE dependencies to '
'be installed Use from anaconda, or look at installation procedure on '
'http://etetoolkit.org/new_download/', e)
return
# Define custom tree style
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.orientation = 1
ts.branch_vertical_margin = 20
def my_layout(node):
F = TextFace(node.name, fsize=16, ftype='Courier', bold=True)
faces.add_face_to_node(F, node, column=10, position="branch-right")
ts.layout_fn = my_layout
TYPES_STRING_TREE.render(output_file, tree_style=ts)
def to_diagram(self):
t = self.program.to_tree_node()
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.rotation = 90
t.render(f"./diagrams/{FUNCTION_NAME}_{self.fitness}.png",
tree_style=ts)
def add_labels_n_colors_2_tree(tree_path, refseq_2_entropy, colors, feature, out):
"""
add entropy measurement to a tree and color it's leaves
:param tree_path: a path to a tree
:param refseq_2_entropy: a data base with entropy values for each refseq id
:param out: output directory path to save the results
:return: a tree with colors and entropy labels
"""
print(tree_path)
str_tree = tree_2_string(tree_path)
if str_tree == '':
return
tree = Tree(str_tree)
# get all refseq ids in the tree and all corresponding entropy values
all_leaves = []
for node in tree:
if node.is_leaf():
all_leaves.append(node.name)
#all_values = refseq_2_entropy[refseq_2_entropy['refseq_id'].isin(all_leaves)]['entropy_5'].values
all_values = refseq_2_entropy[feature].values
num_leaves = len(all_leaves)
# create a gradient color bar
#colors = linear_gradient("#DC9221", "#33C193", n=num_leaves)
#mapping = value_2_color(all_values, colors['hex'])
mapping = value_2_color(all_values, colors['hex'])
for node in tree:
if node.is_leaf():
value = refseq_2_entropy[refseq_2_entropy['refseq_id'] == node.name.split('.')[0]][feature].values[0]
virus_name = refseq_2_entropy[refseq_2_entropy['refseq_id'] == node.name.split('.')[0]]['virus_name'].values[0]
# change virus name
node.name = virus_name
c = mapping[str(value)]
node.add_feature("label", value)
label_face = TextFace(node.label, fgcolor=c, fsize=22)
node.add_face(label_face, column=0, position='branch-right')
family = os.path.basename(tree_path).split('.')[0]
ts = TreeStyle()
ts.mode = 'c'
ts.scale = 5
# Disable the default tip names config
ts.show_leaf_name = True
ts.show_scale = True
ts.show_branch_length = True
ts.title.add_face(TextFace("{} values for {}".format(feature, family), fsize=20), column=0)
# Draw Tree
tree.render(os.path.join(out, '{}_{}_tree.pdf'.format(family, feature)), dpi=300, tree_style=ts)
def export_tree(tree, filename, insignif_color, signif_color, i_group, width):
'''
exports the given tree to the given filename
'''
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.layout_fn = generate_layout(insignif_color, signif_color, i_group)
tree.render(filename, w=width, tree_style=ts)
def render_tree(T, out):
ts = TreeStyle()
ts.show_leaf_name = False
ts.mode = "c"
ts.scale = 200
ts.show_scale = False
T.render(out, tree_style=ts, layout=layout_black_circles)
def get_tree_style():
ts = TreeStyle()
ts.show_leaf_name = False # True
ts.layout_fn = layout
ts.rotation = 90
ts.branch_vertical_margin = 10
ts.show_scale = False
# ts.mode = "c"
ts.scale = 50
ts.title.add_face(TextFace(" ", fsize=20), column=0)
# for n in t.traverse():
# nstyle = NodeStyle()
# nstyle["fgcolor"] = "red"
# nstyle["size"] = 15
# n.set_style(nstyle)
# ts.show_leaf_name = True
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, NO_SUPPORT_COLOR, NO_SUPPORT_COLOR),
column=0)
ts.legend.add_face(TextFace(" Topic with no support (u(t)=0)"), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "#90ee90", "#90ee90"), column=0)
ts.legend.add_face(TextFace(" Topic with minor support 0<u(t)<=0.4"),
column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "green", "green"), column=0)
ts.legend.add_face(
TextFace(u" Topic with medium support 0.4<u(t)<=0.6 "), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "#004000", "#004000"), column=0)
ts.legend.add_face(TextFace(" Topic with high support u(t)>0.6"),
column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(CircleFace(10, "red"), column=0)
ts.legend.add_face(TextFace(" Gap"), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(40, 40, "#004000", "#004000"),
column=0) # green
# ts.legend.add_face(CircleFace(15, "green"), column=1)
ts.legend.add_face(TextFace(" Head subject or offshoot"), column=1)
ts.legend_position = 4
# ts.title.add_face(TextFace(" ", fsize=20), column=0)
return ts
def draw(self,
file,
colors,
color_internal_nodes=True,
legend_labels=(),
show_branch_support=True,
show_scale=True,
legend_scale=1,
mode="c",
neighbours=None,
neighbours_block=None):
max_color = len(colors)
used_colors = set()
for node in self.tree.traverse():
if not (color_internal_nodes or node.is_leaf()): continue
color = colors[min(node.color, max_color - 1)]
node.img_style['bgcolor'] = color
used_colors.add(color)
ts = TreeStyle()
ts.mode = mode
ts.scale = self.scale
# Disable the default tip names config
ts.show_leaf_name = False
ts.show_branch_support = show_branch_support
# ts.branch_vertical_margin = 20
ts.show_scale = show_scale
cur_max_color = max(v.color for v in self.tree.traverse())
current_colors = colors[0:cur_max_color + 1]
for i, (label, color_) in enumerate(zip(legend_labels,
current_colors)):
if color_ not in used_colors: continue
rf = RectFace(20 * legend_scale, 16 * legend_scale, color_, color_)
rf.inner_border.width = 1
rf.margin_right = 14
rf.margin_left = 14
tf = TextFace(label, fsize=26 * legend_scale)
tf.margin_right = 14
ts.legend.add_face(rf, column=0)
ts.legend.add_face(tf, column=1)
if neighbours:
old_tree = self.tree.copy()
self.draw_neighbours(neighbours, neighbours_block)
self.tree.render(file, w=1000, tree_style=ts)
if neighbours:
self.tree = old_tree
def ete_draw(t,fname=None,title='',mode='r',outfile='ete_tree.png'):
from ete3 import Tree, TreeStyle, Phyloxml, TextFace
t.children
ts = TreeStyle()
#ts.branch_vertical_margin = 10
ts.show_scale=False
ts.scale = 800
ts.show_leaf_name = False
ts.mode = mode
ts.title.add_face(TextFace(title, fsize=20), column=0)
t.render(outfile,dpi=300,h=800,tree_style=ts)
return ts
def _get_motif_tree(tree, data, circle=True, vmin=None, vmax=None):
try:
from ete3 import Tree, NodeStyle, TreeStyle
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
t = Tree(tree)
# Determine cutoff for color scale
if not(vmin and vmax):
for i in range(90, 101):
minmax = np.percentile(data.values, i)
if minmax > 0:
break
if not vmin:
vmin = -minmax
if not vmax:
vmax = minmax
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap="RdBu_r")
m = 25 / data.values.max()
for node in t.traverse("levelorder"):
val = data[[l.name for l in node.get_leaves()]].values.mean()
style = NodeStyle()
style["size"] = 0
style["hz_line_color"] = to_hex(mapper.to_rgba(val))
style["vt_line_color"] = to_hex(mapper.to_rgba(val))
v = max(np.abs(m * val), 5)
style["vt_line_width"] = v
style["hz_line_width"] = v
node.set_style(style)
ts = TreeStyle()
ts.layout_fn = _tree_layout
ts.show_leaf_name= False
ts.show_scale = False
ts.branch_vertical_margin = 10
if circle:
ts.mode = "c"
ts.arc_start = 180 # 0 degrees = 3 o'clock
ts.arc_span = 180
return t, ts
def plot_clustering_tree(tree, alg_name, cutting=0, tree_format='pdf'):
'''if cutting=True, merge the n nodes at leaf nodes with the same parent.
'''
global n, k1
if (cutting):
tree_inner = tree.copy()
cnt = 0
delete_tree_node_list = []
for _n in tree_inner:
try:
_n.category
except AttributeError:
_n.add_features(category=cnt)
for i in _n.get_sisters():
if not (i.is_leaf()):
continue
try:
i.category
except AttributeError:
i.add_features(category=cnt)
delete_tree_node_list.append(i)
cnt += 1
for _n in delete_tree_node_list:
_n.delete()
# rename the tree node
tree_inner = Tree(tree_inner.write(features=[]))
else:
tree_inner = tree
for _n in tree_inner:
try:
_n.macro
break
except AttributeError:
macro_index = int(_n.name) // (n * k1)
micro_index = (int(_n.name) - macro_index * n * k1) // n
_n.macro = macro_index
_n.micro = micro_index
if (len(_n.name) > 3):
_n.name = str(_n.category)
ts = TreeStyle()
ts.rotation = 90
ts.show_scale = False
for _n in tree_inner:
nstyle = NodeStyle()
nstyle['fgcolor'] = color_list[int(_n.macro)]
nstyle['shape'] = shape_list[int(_n.micro)]
_n.set_style(nstyle)
time_str = datetime.now().strftime('%Y-%m-%d-')
file_name = time_str + 'tree_' + alg_name + '.' + tree_format
tree_inner.render(os.path.join('build', file_name), tree_style=ts)
def _get_motif_tree(tree, data, circle=True, vmin=None, vmax=None):
try:
from ete3 import Tree, NodeStyle, TreeStyle
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
t = Tree(tree)
# Determine cutoff for color scale
if not (vmin and vmax):
for i in range(90, 101):
minmax = np.percentile(data.values, i)
if minmax > 0:
break
if not vmin:
vmin = -minmax
if not vmax:
vmax = minmax
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap="RdBu_r")
m = 25 / data.values.max()
for node in t.traverse("levelorder"):
val = data[[l.name for l in node.get_leaves()]].values.mean()
style = NodeStyle()
style["size"] = 0
style["hz_line_color"] = to_hex(mapper.to_rgba(val))
style["vt_line_color"] = to_hex(mapper.to_rgba(val))
v = max(np.abs(m * val), 5)
style["vt_line_width"] = v
style["hz_line_width"] = v
node.set_style(style)
ts = TreeStyle()
ts.layout_fn = _tree_layout
ts.show_leaf_name = False
ts.show_scale = False
ts.branch_vertical_margin = 10
if circle:
ts.mode = "c"
ts.arc_start = 180 # 0 degrees = 3 o'clock
ts.arc_span = 180
return t, ts
def frogTree(startstate):
global frogCount
frogCount = 0
t = Tree()
root = t.add_child(name=startstate)
t.add_face(TextFace(startstate), column=0)
frogalgo(root, root)
messagebox.showinfo("Tree Generation Done",
"number of states:" + str(frogCount))
states.set("Tree Generated! number of states:" + str(frogCount))
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
t.show(tree_style=ts)
def draw_ete3_tree(organism, snplist, tree_file_name, config, c):
'''Draws a phylogenetic tree using ETE3
Keyword arguments:
organism -- the organism of which to make a tree
snplist -- a list of the SNP names, positions and state
file_name -- the name of the out-file _tree.pdf will be added
'''
newick = tree_to_newick(organism, config, c)
tree = Tree(newick, format=1)
tree_depth = int(tree.get_distance(tree.get_farthest_leaf()[0]))
for n in tree.traverse():
# Nodes are set to red colour
nstyle = NodeStyle()
nstyle["fgcolor"] = "#BE0508"
nstyle["size"] = 10
nstyle["vt_line_color"] = "#000000"
nstyle["hz_line_color"] = "#000000"
nstyle["vt_line_type"] = 0
nstyle["hz_line_type"] = 0
nstyle["vt_line_width"] = 2
nstyle["hz_line_width"] = 2
## ['B.3', 'T', 'C', 'A']
for snp in snplist.keys():
if n.name == snp and snplist[snp] == 0:
# If the SNP is missing due to a gap, make it grey
nstyle["fgcolor"] = "#DDDDDD"
nstyle["size"] = 10
nstyle["vt_line_color"] = "#DDDDDD"
nstyle["hz_line_color"] = "#DDDDDD"
nstyle["vt_line_type"] = 1
nstyle["hz_line_type"] = 1
elif n.name == snp and snplist[snp] == 1:
nstyle["fgcolor"] = "#99FF66"
nstyle["size"] = 15
nstyle["vt_line_color"] = "#000000"
nstyle["hz_line_color"] = "#000000"
nstyle["vt_line_type"] = 0
nstyle["hz_line_type"] = 0
n.set_style(nstyle)
ts = TreeStyle()
ts.show_leaf_name = False # Do not print(leaf names, they are added in layout)
ts.show_scale = False # Do not show the scale
ts.layout_fn = self.CanSNPer_tree_layout # Use the custom layout
ts.optimal_scale_level = 'full' # Fully expand the branches of the tree
if config["dev"]:
print("#[DEV] Tree file: %s" % tree_file_name)
tree.render(tree_file_name, tree_style=ts, width=tree_depth * 500)
def get_tree_style():
ts = TreeStyle()
# ts.mode = 'c'
ts.margin_top = 10
ts.margin_bottom = 10
ts.margin_left = 10
ts.margin_right = 10
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
ts.show_scale = False
title = TextFace(" Tax Assignment Tree", fsize=10)
title.hz_align = 2
title.vt_align = 2
ts.title.add_face(TextFace(" "), column=0)
ts.title.add_face(TextFace(" "), column=0)
ts.title.add_face(title, column=0)
return ts
def make_plot():
df = pd.read_csv(f'{args.output}/aa_comp.tsv', sep="\t")
df = df.set_index('Taxon')
z = shc.linkage(df, method='ward')
t = distance_matrix2tree(z, df.index.values)
t.write(outfile=f'{args.output}/distance_matrix.tre')
# Basic tree style
ts = TreeStyle()
ts.show_leaf_name = False
ts.mode = "c"
ts.show_scale = False
ts.layout_fn = mylayout
# PDF rendering
t.render(f'{args.output}/aa_comp_calculator.pdf',
w=183,
units="mm",
tree_style=ts)
def plot_spn(spn, context=None, unroll=False, file_name=None, show_ids=False):
assert spn is not None
lin_style = TreeStyle()
def my_layout(node):
style = NodeStyle()
style["size"] = 0
style["vt_line_color"] = "#AAAAAA"
style["hz_line_color"] = "#AAAAAA"
style["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 1
style["vt_line_width"] = 1
style["hz_line_width"] = 1
node.set_style(style)
if node.is_leaf():
name_face = AttrFace("name", fsize=8, ftype="Times")
else:
name_face = TextFace(node.name, fsize=18, ftype="Times")
if node.node_type == Sum:
for child in node.children:
label = TextFace(round(child.support, 3), fsize=6)
child.add_face(label, column=1, position="branch-bottom")
if show_ids:
node.add_face(AttrFace("id", fsize=6),
column=1,
position="branch-top")
faces.add_face_to_node(name_face,
node,
column=1,
position="branch-right")
lin_style.layout_fn = my_layout
lin_style.show_leaf_name = False
lin_style.show_scale = False
tree = spn_to_ete(spn, context, unroll)
if file_name is not None:
return tree.render(file_name, tree_style=lin_style)
def draw(self,
file,
colors,
color_internal_nodes=True,
legend_labels=(),
show_branch_support=True,
show_scale=True,
legend_scale=1,
mode="c"):
max_color = len(colors)
for node in self.tree.traverse():
if not (color_internal_nodes or node.is_leaf()): continue
color = colors[min(node.color, max_color - 1)]
node.img_style['bgcolor'] = color
ts = TreeStyle()
ts.mode = mode
ts.scale = self.scale
# Disable the default tip names config
ts.show_leaf_name = False
ts.show_branch_support = show_branch_support
# ts.branch_vertical_margin = 20
ts.show_scale = show_scale
cur_max_color = max(v.color for v in self.tree.traverse())
current_colors = colors[0:cur_max_color + 1]
for i, (label, color_) in enumerate(zip(legend_labels,
current_colors)):
ts.legend.add_face(CircleFace(24 * legend_scale, color_), column=0)
ts.legend.add_face(CircleFace(13 * legend_scale, 'White'),
column=1)
ts.legend.add_face(TextFace(label, fsize=53 * legend_scale),
column=2)
ts.legend.add_face(CircleFace(13 * legend_scale, 'White'),
column=3)
# self.tree.render("ete_tree.pdf", dpi=300, tree_style=ts)
self.tree.render(file, w=1000, tree_style=ts)
def get_default_tree_style(color_dict):
ts = TreeStyle()
ts.mode = 'c'
# ts.layout_fn = layout
ts.margin_top = 50
ts.margin_bottom = 0
ts.margin_left = 50
ts.margin_right = 50
ts.show_scale = False
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
for p, c in color_dict.iteritems():
ts.legend.add_face(TextFace(" ", fsize=30), column=0)
ts.legend.add_face(CircleFace(10, c), column=1)
ts.legend.add_face(TextFace(" %s" % p, fsize=30), column=2)
legend_margin_line = 5
while legend_margin_line:
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(TextFace(" "), column=2)
legend_margin_line -= 1
ts.legend_position = 3
return ts
def create_plot(self, target_outputfile):
from ete3 import Tree, TreeStyle, NodeStyle, faces, AttrFace, CircleFace, TextFace
t = Tree()
def layout(node):
if node.is_leaf():
N = AttrFace("name", fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature 1/gini index
circle_face = CircleFace(radius=node.weight,
color="RoyalBlue",
style="sphere")
circle_face.hz_align = 2
circle_face.opacity = 0.3
text_face = TextFace(text=node.name)
faces.add_face_to_node(circle_face, node, 0, position="float")
faces.add_face_to_node(text_face, node, 0, position="float")
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
ts.scale = 140
# # Draw a tree
# ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
ts.branch_vertical_margin = 30
ts.show_scale = False
t = self.head_node.create_equivalent_ete_tree()
t.render(target_outputfile, w=183, units="mm", tree_style=ts)
def __init__(self, root_text):
# Inicializa la estructura árbol
tree = Tree()
# Formateamos el árbol indicandole un estilo
style = TreeStyle()
style.show_leaf_name = True
style.show_scale = False
style.scale = 100
style.branch_vertical_margin = 30
style.rotation = 0
style.orientation = 0
self.style = style
self.tree = tree
# Le damos estilo a la raíz del árbol
self.tree.add_face(TextFace(root_text, fsize=10, fgcolor='darkred'),
column=0,
position='branch-right')
self.tree.set_style(NodeStyle(size=20, hz_line_width=2,
fgcolor='blue'))
# Almacenamos la raíz del árbol como nodo actual
self.curr_node = self.tree
def get_default_tree_style(color_dict):
ts = TreeStyle()
ts.mode = "c"
# ts.layout_fn = layout
ts.margin_top = 50
ts.margin_bottom = 0
ts.margin_left = 50
ts.margin_right = 50
ts.show_scale = False
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
for p, c in color_dict.iteritems():
ts.legend.add_face(TextFace(" ", fsize=30), column=0)
ts.legend.add_face(CircleFace(10, c), column=1)
ts.legend.add_face(TextFace(" %s" % p, fsize=30), column=2)
legend_margin_line = 5
while legend_margin_line:
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(TextFace(" "), column=2)
legend_margin_line -= 1
ts.legend_position = 3
return ts
def plot_species_tree(tree_newick, tree_type, gene_name, tree_file_name,
name_list, tree_image_folder):
# set tree parameters
tree = Tree(tree_newick, format=2)
ts = TreeStyle()
ts.mode = "r" # tree model: 'r' for rectangular, 'c' for circular
ts.show_leaf_name = False
tree_title = tree_type + ' (' + gene_name + ')' # define tree title
# set tree title text parameters
ts.title.add_face(TextFace(tree_title,
fsize=8,
fgcolor='black',
ftype='Arial',
tight_text=False),
column=0) # tree title text setting
# set layout parameters
ts.rotation = 0 # from 0 to 360
ts.show_scale = False
ts.margin_top = 10 # top tree image margin
ts.margin_bottom = 10 # bottom tree image margin
ts.margin_left = 10 # left tree image margin
ts.margin_right = 10 # right tree image margin
ts.show_border = False # set tree image border
ts.branch_vertical_margin = 3 # 3 pixels between adjancent branches
# set tree node style
for each_node in tree.traverse():
# leaf node parameters
if each_node.is_leaf():
ns = NodeStyle()
ns['shape'] = 'circle' # dot shape: circle, square or sphere
ns['size'] = 0 # dot size
ns['hz_line_width'] = 0.5 # branch line width
ns['vt_line_width'] = 0.5 # branch line width
ns['hz_line_type'] = 0 # branch line type: 0 for solid, 1 for dashed, 2 for dotted
ns['vt_line_type'] = 0 # branch line type
if each_node.name in name_list:
ns['fgcolor'] = 'red' # the dot setting
each_node.add_face(
TextFace(each_node.name,
fsize=8,
fgcolor='red',
tight_text=False,
bold=False),
column=0,
position='branch-right') # the node name text setting
each_node.set_style(ns)
else:
ns['fgcolor'] = 'blue' # the dot setting
each_node.add_face(
TextFace(each_node.name,
fsize=8,
fgcolor='black',
tight_text=False,
bold=False),
column=0,
position='branch-right') # the node name text setting
each_node.set_style(ns)
# non-leaf node parameters
else:
nlns = NodeStyle()
nlns['size'] = 0 # dot size
each_node.add_face(
TextFace(each_node.name,
fsize=4,
fgcolor='black',
tight_text=False,
bold=False),
column=5,
position='branch-top') # non-leaf node name text setting)
each_node.set_style(nlns)
# set figures size
tree.render('%s/%s.png' % (tree_image_folder, tree_file_name),
w=900,
units='px',
tree_style=ts)
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c0_r1, column=0, position="branch-bottom")
a = t&"a"
a.set_style(NodeStyle())
a.img_style["bgcolor"] = "lightgreen"
b = t&"b"
b.set_style(NodeStyle())
b.img_style["bgcolor"] = "indianred"
c = t&"c"
c.set_style(NodeStyle())
c.img_style["bgcolor"] = "lightblue"
t.set_style(NodeStyle())
t.img_style["bgcolor"] = "lavender"
t.img_style["size"] = 12
for leaf in t.iter_leaves():
leaf.img_style["size"] = 12
leaf.add_face(right_c0_r0, 0, "branch-right")
leaf.add_face(aligned_c0_r1, 0, "aligned")
leaf.add_face(aligned_c0_r0, 0, "aligned")
leaf.add_face(aligned_c1_r1, 1, "aligned")
leaf.add_face(aligned_c1_r0, 1, "aligned")
ts = TreeStyle()
ts.show_scale = False
t.render("/groups/itay_mayrose/udiland/crispys_tomato/families/filtering_scripts/face_positions.png", w=800, tree_style=ts)
def create_tree(tree,
tree_root_key,
filepath,
patient,
phylogeny,
drivers=None):
"""
Takes a networkx tree and creates an ete3 tree and creates a PDF, SVG or PNG according to the given filename at
the given path
:param tree: inferred cancer phylogeny encoded as networkx tree
:param tree_root_key: key of root in networkx tree
:param filepath: path to output file (excluding file extension)
:param patient: data structure around patient
:param phylogeny: inferred cancer phylogeny
:param drivers: defaultdict with mutation IDs and instance of driver class to be highlighted on edges
:return path to the generated ete3 PNG file
"""
# generate ete3 tree
rt = Tree() # generate root
rt.name = 'Germline {}'.format(patient.name)
_generate_ete_tree(tree,
tree_root_key,
rt,
0,
patient,
phylogeny,
gene_names=patient.gene_names,
drivers=drivers)
ts = TreeStyle()
ts.layout_fn = ete_layout
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
ts.show_scale = False
ts.extra_branch_line_color = 'Black'
# ts.complete_branch_lines_when_necessary = False
# Find the maximal number of variants present in a single sample to determine the optimal ETE3 scale level
max_muts = max(no_pres_vars
for no_pres_vars in patient.no_present_vars.values())
def round_to_1(x):
"""
Round to one significant digit
:param x:
:return:
"""
return round(x, -int(math.floor(math.log10(abs(x)))))
# XX pixels per branch length unit
# if max_muts > 20000:
# ts.scale = 0.02
# elif max_muts > 10000:
# ts.scale = 0.05
# elif max_muts > 5000:
# ts.scale = 0.1
# elif max_muts > 2000:
# ts.scale = 0.2
# elif max_muts > 1000:
# ts.scale = 0.5
# elif max_muts > 500:
# ts.scale = 1
# elif max_muts > 200:
# ts.scale = 2
# elif max_muts > 100:
# ts.scale = 5
# elif max_muts > 50:
# ts.scale = 5
# else:
# ts.scale = 10
ts.scale = round_to_1(600 / max_muts)
ts.branch_vertical_margin = 15 # XX pixels between adjacent branches
# rt.show(tree_style=ts)
ete_tree_plot = filepath + '.png'
rt.render(ete_tree_plot, w=183, units="mm", tree_style=ts, dpi=300)
rt.render(filepath + '.pdf', w=183, units="mm", tree_style=ts, dpi=300)
return ete_tree_plot
from ete3 import Tree,TreeStyle,TextFace
t = Tree('tagfrog.phy')
for node in t.traverse():
node.img_style['size'] = 3
if node.is_leaf():
name_face = TextFace(node.name)
ts = TreeStyle()
ts.show_scale = True
t.render('tagfrog.pdf')
## create colors for each genus
for idx, family in enumerate(families):
for cidx, genus_tree in enumerate(genera_trees[idx]):
tf_genera = TreeFace(genus_tree, ts_genera)
tf_genera.border.width = 2
genus = genera[idx][cidx]
color = colors[str(genus)]
tf_genera.border.color = color
(t & family).add_face(tf_genera, column=0, position='aligned')
for n in genus_tree.iter_search_nodes():
if n.dist == 1:
n.img_style = ns_genera
ts_genera.show_leaf_name = False
ts_genera.show_scale = False
ts_genera.layout_fn = my_layout
ts.branch_vertical_margin = 10
ts.show_leaf_name = False
ts.branch_vertical_margin = 15
ts.layout_fn = my_layout
ts.draw_guiding_lines = True
ts.guiding_lines_type = 1
ts.show_scale = False
ts.allow_face_overlap = False
# ts.mode = "c"
# ts.arc_start = 180 # 0 degrees = 3 o'clock
# ts.arc_span = 270
t.show(tree_style=ts)
t.render("mytree.png", w=183, units="mm", tree_style=ts)
def simulate(args):
'''
Simulation subprogram. Can simulate in two modes.
a) Neutral mode. A Galton–Watson process, with mutation probabilities according to a user defined motif model e.g. S5F.
b) Selection mode. Using the same mutation process as in a), but in selection mode the poisson progeny distribution's lambda parameter
is dynamically adjusted accordring to the hamming distance to a list of target sequences. The closer a sequence gets to one of the targets
the higher fitness and the closer lambda will approach 2, vice versa when the sequence is far away lambda approaches 0.
'''
if args.random_seed is not None:
numpy.random.seed(args.random_seed)
random.seed(args.random_seed)
mutation_model = MutationModel(args.mutability, args.substitution)
if args.lambda0 is None:
args.lambda0 = [max([1, int(.01 * len(args.sequence))])]
if args.random_seq is not None:
from Bio import SeqIO
records = list(SeqIO.parse(args.random_seq, "fasta"))
random.shuffle(records)
args.sequence = str(records[0].seq).upper()
else:
args.sequence = args.sequence.upper()
if args.sequence2 is not None:
if len(args.lambda0
) == 1: # Use the same mutation rate on both sequences
args.lambda0 = [args.lambda0[0], args.lambda0[0]]
elif len(args.lambda0) != 2:
raise Exception(
'Only one or two lambda0 can be defined for a two sequence simulation.'
)
# Extract the bounds between sequence 1 and 2:
pair_bounds = ((0, len(args.sequence)),
(len(args.sequence),
len(args.sequence) + len(args.sequence2)))
# Merge the two seqeunces to simplify future dealing with the pair:
args.sequence += args.sequence2.upper()
else:
pair_bounds = None
if args.selection:
assert (
args.B_total >= args.f_full
) # the fully activating fraction on BA must be possible to reach within B_total
# Find the total amount of A necessary for sustaining the inputted carrying capacity:
print((args.carry_cap, args.B_total, args.f_full, args.mature_affy))
A_total = selection_utils.find_A_total(args.carry_cap, args.B_total,
args.f_full, args.mature_affy,
args.U)
# Calculate the parameters for the logistic function:
Lp = selection_utils.find_Lp(args.f_full, args.U)
selection_params = [
args.stop_dist, args.mature_affy, args.naive_affy,
args.target_dist, args.target_count, args.skip_update, A_total,
args.B_total, Lp, args.k, args.outbase
]
else:
selection_params = None
trials = 1000
# This loop makes us resimulate if size too small, or backmutation:
for trial in range(trials):
try:
tree = mutation_model.simulate(args.sequence,
pair_bounds=pair_bounds,
lambda_=args.lambda_,
lambda0=args.lambda0,
n=args.n,
N=args.N,
T=args.T,
verbose=args.verbose,
selection_params=selection_params)
if args.selection:
collapsed_tree = CollapsedTree(tree=tree,
name='GCsim selection',
collapse_syn=False,
allow_repeats=True)
else:
collapsed_tree = CollapsedTree(
tree=tree, name='GCsim neutral'
) # <-- This will fail if backmutations
tree.ladderize()
uniques = sum(node.frequency > 0
for node in collapsed_tree.tree.traverse())
if uniques < 2:
raise RuntimeError(
'collapsed tree contains {} sampled sequences'.format(
uniques))
break
except RuntimeError as e:
print('{}, trying again'.format(e))
else:
raise
if trial == trials - 1:
raise RuntimeError('{} attempts exceeded'.format(trials))
# In the case of a sequence pair print them to separate files:
if args.sequence2 is not None:
fh1 = open(args.outbase + '_seq1.fasta', 'w')
fh2 = open(args.outbase + '_seq2.fasta', 'w')
fh1.write('>naive\n')
fh1.write(args.sequence[pair_bounds[0][0]:pair_bounds[0][1]] + '\n')
fh2.write('>naive\n')
fh2.write(args.sequence[pair_bounds[1][0]:pair_bounds[1][1]] + '\n')
for leaf in tree.iter_leaves():
if leaf.frequency != 0:
fh1.write('>' + leaf.name + '\n')
fh1.write(leaf.sequence[pair_bounds[0][0]:pair_bounds[0][1]] +
'\n')
fh2.write('>' + leaf.name + '\n')
fh2.write(leaf.sequence[pair_bounds[1][0]:pair_bounds[1][1]] +
'\n')
else:
with open(args.outbase + '.fasta', 'w') as f:
f.write('>naive\n')
f.write(args.sequence + '\n')
for leaf in tree.iter_leaves():
if leaf.frequency != 0:
f.write('>' + leaf.name + '\n')
f.write(leaf.sequence + '\n')
# Some observable simulation stats to write:
frequency, distance_from_naive, degree = zip(
*[(node.frequency, hamming_distance(node.sequence, args.sequence),
sum(
hamming_distance(node.sequence, node2.sequence) == 1
for node2 in collapsed_tree.tree.traverse()
if node2.frequency and node2 is not node))
for node in collapsed_tree.tree.traverse() if node.frequency])
stats = pd.DataFrame({
'genotype abundance': frequency,
'Hamming distance to root genotype': distance_from_naive,
'Hamming neighbor genotypes': degree
})
stats.to_csv(args.outbase + '_stats.tsv', sep='\t', index=False)
print('{} simulated observed sequences'.format(
sum(leaf.frequency for leaf in collapsed_tree.tree.traverse())))
# Render the full lineage tree:
ts = TreeStyle()
ts.rotation = 90
ts.show_leaf_name = False
ts.show_scale = False
colors = {}
palette = SVG_COLORS
palette -= set(['black', 'white', 'gray'])
palette = cycle(list(palette)) # <-- Circular iterator
# Either plot by DNA sequence or amino acid sequence:
if args.plotAA and args.selection:
colors[tree.AAseq] = 'gray'
else:
colors[tree.sequence] = 'gray'
for n in tree.traverse():
nstyle = NodeStyle()
nstyle["size"] = 10
if args.plotAA:
if n.AAseq not in colors:
colors[n.AAseq] = next(palette)
nstyle['fgcolor'] = colors[n.AAseq]
else:
if n.sequence not in colors:
colors[n.sequence] = next(palette)
nstyle['fgcolor'] = colors[n.sequence]
n.set_style(nstyle)
# Render and pickle lineage tree:
tree.render(args.outbase + '_lineage_tree.svg', tree_style=ts)
with open(args.outbase + '_lineage_tree.p', 'wb') as f:
pickle.dump(tree, f)
# Render collapsed tree,
# create an id-wise colormap
# NOTE: node.name can be a set
if args.plotAA and args.selection:
colormap = {
node.name: colors[node.AAseq]
for node in collapsed_tree.tree.traverse()
}
else:
colormap = {
node.name: colors[node.sequence]
for node in collapsed_tree.tree.traverse()
}
collapsed_tree.write(args.outbase + '_collapsed_tree.p')
collapsed_tree.render(args.outbase + '_collapsed_tree.svg',
idlabel=args.idlabel,
colormap=colormap)
# Print colormap to file:
with open(args.outbase + '_collapsed_tree_colormap.tsv', 'w') as f:
for name, color in colormap.items():
f.write((name if isinstance(name, str) else ','.join(name)) +
'\t' + color + '\n')
with open(args.outbase + '_collapsed_tree_colormap.p', 'wb') as f:
pickle.dump(colormap, f)
if args.selection:
# Define a list a suitable colors that are easy to distinguish:
palette = [
'crimson', 'purple', 'hotpink', 'limegreen', 'darkorange',
'darkkhaki', 'brown', 'lightsalmon', 'darkgreen', 'darkseagreen',
'darkslateblue', 'teal', 'olive', 'wheat', 'magenta',
'lightsteelblue', 'plum', 'gold'
]
palette = cycle(list(palette)) # <-- circular iterator
colors = {
i: next(palette)
for i in range(int(len(args.sequence) // 3))
}
# The minimum distance to the target is colored:
colormap = {
node.name: colors[node.target_dist]
for node in collapsed_tree.tree.traverse()
}
collapsed_tree.write(args.outbase + '_collapsed_runstat_color_tree.p')
collapsed_tree.render(args.outbase +
'_collapsed_runstat_color_tree.svg',
idlabel=args.idlabel,
colormap=colormap)
# Write a file with the selection run stats. These are also plotted:
with open(args.outbase + '_selection_runstats.p', 'rb') as fh:
runstats = pickle.load(fh)
selection_utils.plot_runstats(runstats, args.outbase, colors)
size = {}
value = {}
node_info = node_fh.readlines()
for info in node_info:
info = info.rstrip('\n')
infos = list(info.split('\t'))
color[infos[0]] = infos[1]
size[infos[0]] = infos[2]
value[infos[0]] = "%.2f %%" % (float(infos[3]) * 100)
tstyle = TreeStyle()
tstyle.complete_branch_lines_when_necessary = False
tstyle.show_leaf_name = False
tstyle.scale = 1
tstyle.branch_vertical_margin = 40
tstyle.show_scale = False
tree_ete.set_style(tstyle)
for node in tree_ete.traverse():
if node.name != "root":
name_face = TextFace(node.name)
abun_face = TextFace(value[node.name])
node.add_face(name_face, column=0, position="branch-top")
node.add_face(abun_face, column=0, position="branch-bottom")
nstyle = NodeStyle()
nstyle["fgcolor"] = color[node.name]
nstyle["size"] = float(size[node.name])
node.set_style(nstyle)
else:
nstyle = NodeStyle()
nstyle["fgcolor"] = "white"
def heatmap_view(tree, orthologous_groups, save_dir):
"""Generates a heatmap of regulation states in all species."""
light_tree = copy.deepcopy(tree) # Tree copy for the light heatmap
# Heat map settings
rect_face_fgcolor = 'black'
locus_tag_len = max(len(gene.locus_tag) + 5
for ortho_grp in orthologous_groups
for gene in ortho_grp.genes)
rect_face_width = locus_tag_len * 8
light_rect_face_width = 20
rect_face_height = 20
rotation = 90
# Sort orthologous groups by the number of regulated genes in each group
orthologous_groups = filter_and_sort_orthologous_grps(orthologous_groups)
# For each species and its gene in each orthologous group, draw a rectangle
for node, light_node in zip(tree.get_leaves(), light_tree.get_leaves()):
for i, orthologous_grp in enumerate(orthologous_groups, start=1):
#get all orthologs in group
matching_genes = [g for g in orthologous_grp.genes \
if g.genome.strain_name == node.name]
#if there is ortholog
if len(matching_genes) > 0:
# Get the first ortholog from the genome in the group
#this is the one with higher probability of regulation.
#so this probability will be displayed for the group
gene = matching_genes[0]
p_regulation = gene.operon.regulation_probability
p_notregulation = 1.0 - p_regulation
p_absence = 0
# No ortholog from this genome
else:
gene = None
p_regulation = 0
p_notregulation = 0
p_absence = 1
# Color of the rectangle is based on probabilities
rect_face_bgcolor = rgb2hex(
p_notregulation, p_regulation, p_absence)
rect_face_text = ('%s [%d]' % (gene.locus_tag, gene.operon.operon_id)
if gene else '')
rect_face_label = {'text': rect_face_text,
'font': 'Courier',
'fontsize': 8,
'color': 'black'}
# Create the rectangle
rect_face = RectFace(rect_face_width, rect_face_height,
rect_face_fgcolor, rect_face_bgcolor,
label=rect_face_label)
light_rect_face = RectFace(light_rect_face_width, rect_face_height,
rect_face_fgcolor, rect_face_bgcolor,
label='')
rect_face.rotation = -rotation
light_rect_face.rotation = -rotation
# Add the rectangle to the corresponding column
node.add_face(rect_face, column=i, position='aligned')
light_node.add_face(light_rect_face, column=i, position='aligned')
ts = TreeStyle()
# Add orthologous group descriptions
descriptions = ['-'.join([grp.description, str(grp.NOGs)]) for grp in orthologous_groups]
max_description_len = max(map(len, descriptions))
descriptions = [
'[%d]' % i + description + ' '*(max_description_len-len(description))
for i, description in enumerate(descriptions, start=1)]
for i, description in enumerate(descriptions, start=1):
text_face = TextFace(description, ftype='Courier')
text_face.hz_align = 1
text_face.vt_align = 1
text_face.rotation = -rotation
ts.aligned_header.add_face(text_face, column=i)
# Rotate the generated heatmap.
ts.margin_left = 10
ts.margin_top = 20
ts.rotation = rotation
ts.show_scale = False
# For some reason, it can't render to PDF in color
tree.render(os.path.join(save_dir, 'heatmap.svg'), tree_style=ts)
light_tree.render(os.path.join(save_dir, 'heatmap_light.svg'), tree_style=ts)
def plot_tree(tree, tree_title, tree_output):
# set tree parameters
ts = TreeStyle()
ts.mode = "r" # tree model: 'r' for rectangular, 'c' for circular
ts.show_leaf_name = 0
# set tree title text parameters
ts.title.add_face(TextFace(tree_title,
fsize=8,
fgcolor='black',
ftype='Arial',
tight_text=False),
column=0) # tree title text setting
# set layout parameters
ts.rotation = 0 # from 0 to 360
ts.show_scale = False
ts.margin_top = 10 # top tree image margin
ts.margin_bottom = 10 # bottom tree image margin
ts.margin_left = 10 # left tree image margin
ts.margin_right = 10 # right tree image margin
ts.show_border = False # set tree image border
ts.branch_vertical_margin = 3 # 3 pixels between adjancent branches
# set tree node style
for each_node in tree.traverse():
# leaf node parameters
if each_node.is_leaf():
ns = NodeStyle()
ns["shape"] = "circle" # dot shape: circle, square or sphere
ns["size"] = 0 # dot size
ns['hz_line_width'] = 0.5 # branch line width
ns['vt_line_width'] = 0.5 # branch line width
ns['hz_line_type'] = 0 # branch line type: 0 for solid, 1 for dashed, 2 for dotted
ns['vt_line_type'] = 0 # branch line type
ns["fgcolor"] = "blue" # the dot setting
each_node.add_face(TextFace(each_node.name,
fsize=5,
fgcolor='black',
tight_text=False,
bold=False),
column=0,
position='branch-right'
) # leaf node the node name text setting
each_node.set_style(ns)
# non-leaf node parameters
else:
nlns = NodeStyle()
nlns["size"] = 0 # dot size
#nlns["rotation"] = 45
each_node.add_face(
TextFace(each_node.name,
fsize=3,
fgcolor='black',
tight_text=False,
bold=False),
column=5,
position='branch-top') # non-leaf node name text setting)
each_node.set_style(nlns)
tree.render(tree_output, w=900, units="px",
tree_style=ts) # set figures size
nw = '(0:0, 1:20);'
fa = """
>0
AA..
>1
CAA.
"""
t = PhyloTree(nw, alignment=fa, alg_format='fasta', format=1)
ts = TreeStyle()
ts.show_branch_length = False
ts.show_leaf_name = False
ts.draw_guiding_lines = True
ts.draw_aligned_faces_as_table = True
ts.show_scale = False
def my_layout(node):
#
# add names to all nodes (not just to leaf nodes)
# ete3/test/test_treeview/face_rotation.py
F = TextFace(node.name, tight_text=True)
add_face_to_node(F, node, column=0, position="branch-right")
#
# add branch lengths
# ete3/treeview/qt4_render.py
if not node.is_root():
bl_face = AttrFace("dist", fsize=8, ftype="Arial",
fgcolor="black", formatter="%0.3g")
#
# This is a failed attempt to center the branch length text on the branch.