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 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 writeTrees(trees, label):
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = False
ts.branch_vertical_margin = 20
ts.scale = 0.05
outtrees = open(lengthdir + label + ".newick", "w")
#round the branch lengths
for index, tree in enumerate(trees):
#print(tree)
for branch in tree.traverse():
branch.dist = round(branch.dist)
line = tree.write(format=1)
outtrees.write(line + "\n")
if (showTrees):
for branch in tree.traverse():
if branch.dist != 0:
text_face = TextFace(str(round(branch.dist, 2)), fsize=30)
branch.add_face(text_face, column=1, position="branch-top")
elif branch.name != "":
name_face = AttrFace("name", fsize=30)
branch.add_face(name_face,
column=0,
position="branch-right")
else:
print("Branch found of length zero but not a tip in tree",
label)
print(branch)
filename = label
if len(trees) > 1:
filename += "_" + str(index)
filename += ".png"
tree.render(lengthdir + filename, tree_style=ts)
#foo()
outtrees.close()
def traitTreeMinimal(traits, mapper):
### Take dict of traits and [R,G,B]-returning function
### Draw a tree with the continuous trait painted on via a colormapping function
def rgb2hex(r, g, b):
hex = "#{:02x}{:02x}{:02x}".format(r, g, b)
return hex
ts = TreeStyle()
ts.show_leaf_name = False
ts.rotation = 270
ts.complete_branch_lines_when_necessary = False
#ts.optimal_scale_level = "full"
ts.scale = 800
# default NodeStyle
nstyle = NodeStyle()
nstyle["size"] = 0
nstyle["hz_line_color"] = "grey"
nstyle["vt_line_color"] = "grey"
nstyle["hz_line_width"] = 3
nstyle["vt_line_width"] = 3
for n in tree.traverse():
chroma = rgb2hex(*[
int(val) for val in mapper(traits[n.ND], gamma=0.8, scaleMax=255)
]) # setup for wl2RGB
nf = CircleFace(radius=10, color='none', style='circle', label=None)
n.set_style(nstyle)
n.add_face(nf, column=0, position='branch-top')
outFile = args.output + "/test_trees/cont_trait.pdf"
tree.render(outFile, tree_style=ts)
print >> sys.stderr, outFile
def get_tree(tree1, abundance):
for n in tree1.iter_leaves():
face1 = CircleFace(abundance[n.name][0],
abundance[n.name][1],
style='sphere')
face2 = TextFace(n.name,
ftype='Verdana',
fsize=10,
fgcolor='black',
penwidth=0,
fstyle='normal',
tight_text=False,
bold=False)
face1.opacity = 0.9
n.add_face(face1, column=0)
n.add_face(
face2, column=0,
position="branch-right") #branch-top branch-bottom branch-right
tree1.ladderize()
ts = TreeStyle()
ts.mode = 'r'
ts.scale = scale1
ts.show_leaf_name = False
return tree1, 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 draw_tree(pstrains, names=False, subset=None):
evol = {x.rstrip() for x in open('input/evolution_experiment.txt')}
tree = get_tree('input/tree.nwk')
strains = {x.name for x in tree.traverse() if x.name != ''}
if subset is None:
subset = strains
evol_tree = {x.name for x in tree.traverse() if x.name in evol}
commensals = {}
for x in strains:
if pstrains[x] == 'Commensal strain':
commensals[x] = colors.cnames['blue']
elif pstrains[x] == 'Pathogenic strain':
commensals[x] = colors.cnames['red']
else:
commensals[x] = colors.cnames['white']
ref = NodeStyle()
ref['fgcolor'] = sns.xkcd_rgb['light red']
inner = NodeStyle()
inner['size'] = 0
for n in tree.traverse():
if not n.is_leaf():
n.set_style(inner)
continue
if n.name not in subset:
continue
if not names:
r = RectFace(10, 3, commensals[n.name], commensals[n.name])
n.add_face(r, 0, position="aligned")
ev = NodeStyle()
ev["fgcolor"] = "black"
ev['size'] = 3
n.set_style(ev)
circular_style = TreeStyle()
circular_style.mode = "c"
if not names:
circular_style.scale = 1300
else:
circular_style.scale = 7300
circular_style.show_leaf_name = names
return tree, circular_style
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 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 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 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 markSpeciesOnTree(self, tree, output_name):
for species in self.species:
nstyle = NodeStyle()
nstyle["bgcolor"] = "purple"
(tree & species).set_style(nstyle)
ts = TreeStyle()
#ts.mode = "c"
ts.scale = 500
#tree.show(tree_style=ts)
tree.render(output_name, dpi=300, units="mm", tree_style=ts)
def draw(self, Ts):
circular_style = TreeStyle()
#circular_style.mode = "c"
circular_style.scale = 20
img_fname = '.'.join([self.tree_bname, self.img_format])
self.tree.render(img_fname, tree_style=Ts, w=400, units="mm")
#, tree_style=circular_style)
try:
subprocess.call(['gpicview', img_fname])
except:
pass
def drawTree(treeFile, ShowBool):
"""
Draw a tree from a phy file
"""
t = Tree(treeFile)
imgFile = treeFile.replace(".tree", ".tree.png")
# Basic tree style
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_support = True
ts.scale = 160
# Draws nodes as small red spheres of diameter equal to 10 pixels
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 10
nstyle["fgcolor"] = "darkred"
#nstyle["faces_bgcolor"] = "pink"
nstyle2 = NodeStyle()
nstyle2["shape"] = "sphere"
nstyle2["size"] = 10
nstyle2["fgcolor"] = "darkblue"
# Gray dashed branch lines
nstyle["hz_line_type"] = 1
nstyle["hz_line_color"] = "#cccccc"
# Applies the same static style to all nodes in the tree. Note that,
# if "nstyle" is modified, changes will affect to all nodes
for n in t.traverse():
if n.is_leaf():
if n.name.split("|")[-1] == "GI":
n.set_style(nstyle)
if n.name.split("|")[-1] == "plasmid":
n.set_style(nstyle2)
gi = n.name.split("|")[1]
n.name = n.name.split("|")[0] #+ " " + n.name.split("|")[1]
n.name = n.name.replace("_tRNA_modification_GTPase_", "")
n.name = n.name.replace("_DNA", "")
n.name = " " + n.name + " "
if n.name[-1] == "_": n.name.rstrip()
taxon, color = taxonToColour(gi)
n.add_face(TextFace(taxon, fgcolor = color, fsize = 8), column=1, position="branch-right")
#n.img_style["bgcolor"] = color
if ShowBool == True: #permet de flipper les braches pour avoir des topologies similaires
t.show(tree_style=ts)
t.render(imgFile, w=393, units="mm", tree_style=ts)
def drawTree(treeFile, ShowBool):
"""
Draw a tree from a phy file
"""
t = Tree(treeFile)
imgFile = treeFile.replace(".tree", ".tree.pdf")
# Basic tree style
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_support = True
ts.scale = 50
# Draws nodes as small red spheres of diameter equal to 10 pixels
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 10
nstyle["fgcolor"] = "darkred"
#nstyle["faces_bgcolor"] = "pink"
nstyle2 = NodeStyle()
nstyle2["shape"] = "sphere"
nstyle2["size"] = 10
nstyle2["fgcolor"] = "darkblue"
# Gray dashed branch lines
nstyle["hz_line_type"] = 1
nstyle["hz_line_color"] = "#cccccc"
# Applies the same static style to all nodes in the tree. Note that,
# if "nstyle" is modified, changes will affect to all nodes
for n in t.traverse():
if n.is_leaf():
if n.name.split("|")[-1] == "GI":
n.set_style(nstyle)
if n.name.split("|")[-1] == "plasmid":
n.set_style(nstyle2)
gi = n.name.split("|")[1]
n.name = n.name.split("|")[0] #+ " " + n.name.split("|")[1]
n.name = n.name.replace("_tRNA_modification_GTPase_", "")
n.name = n.name.replace("_DNA", "")
n.name = " " + n.name + " "
if n.name[-1] == "_": n.name.rstrip()
taxon, color = taxonToColour(gi)
n.add_face(TextFace(taxon, fgcolor=color, fsize=8),
column=1,
position="branch-right")
#n.img_style["bgcolor"] = color
if ShowBool == True: #permet de flipper les braches pour avoir des topologies similaires
t.show(tree_style=ts)
t.render(imgFile, w=1024, units="mm", tree_style=ts)
def Generate_CircleTree(treeData, output_path):
# Define output file name and its path
file_name = "circle_tree.png"
out_file = output_path + "/" + file_name
# Build tree & incorporate desired parameters for visualization
t = Tree(treeData)
circular_style = TreeStyle()
circular_style.mode = "c"
circular_style.scale = 20
# Produce/draw output figure: phylogeny
t.render(file_name, w=183, units="mm", tree_style=circular_style)
def Generate_NormalTree(treeData, output_path):
file_name = "normal_tree.png"
out_file = output_path + "/" + file_name
# Build tree & incorporate desired parameters for visualization
t = Tree(treeData)
#t.populate(50, random_dist=True)
ts = TreeStyle()
ts.show_leaf_name = True
#ts.show_branch_length = True
#ts.show_branch_support = True
ts.scale = 20 # 120 pixels per branch length unit
t.render(file_name, w=183, units="mm", tree_style=ts)
def show_tree(tree):
ts = TreeStyle()
ts.scale = 1
ts.show_leaf_name = True
'''
ts.rotation = 90
ts.branch_vertical_margin = 10
ts.scale = 50
'''
#ts.mode = "c"
tree.show(tree_style=ts)
def main(file_name): t = read_tree(file_name) nstyle = NodeStyle() nstyle["size"] = 0 ts = TreeStyle() ts.show_leaf_name = False ts.scale = 25000 # pixels per branch length unit ts.layout_fn = layout for n in t.traverse(): n.set_style(nstyle) # t.show(tree_style=ts) t.render(out_stem + "." + out_format, tree_style=ts)
def writeTrees(trees, label):
"""
Now that we have branch lengths, write out new Newick trees with the
branch lengths included. Note that ete3 does not seem to write out
the length of the root automatically, so we add it in by hand.
"""
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = False
ts.branch_vertical_margin = 20
ts.scale = 0.05
outtrees = open(lengthdir + label + ".newick", "w")
for index, tree in enumerate(trees):
#print(tree)
#If needed: round the branch lengths
# for branch in tree.traverse():
# branch.dist = round(branch.dist)
line = tree.write(format=1)
rootlen = round(tree.get_tree_root().dist)
line = line[:-1] + ":" + str(rootlen) + ";"
outtrees.write(line + "\n")
if (showTrees):
for branch in tree.traverse():
if branch.name != "":
name_face = AttrFace("name", fsize=30)
branch.add_face(name_face,
column=0,
position="branch-right")
if branch.dist != 0:
if branch.name == "":
text_face = TextFace(str(round(branch.dist, 2)),
fsize=30)
branch.add_face(text_face,
column=1,
position="branch-top")
else:
print("Branch found of length zero but not a tip in tree",
label)
print(branch)
filename = label
if len(trees) > 1:
filename += "_" + str(index)
filename += ".png"
tree.render(lengthdir + filename, tree_style=ts)
#foo()
outtrees.close()
def show(tf):
try:
os.environ['DISPLAY']
from ete3 import TreeStyle
flag = 0
except (KeyError, ImportError):
flag = 1
if flag:
tree = dp.Tree.get(path=tf, schema='newick', rooting='force-rooted')
print(tree.as_ascii_plot())
else:
tree = ete.Tree(tf)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.scale = 25
tree.show(tree_style=ts)
return "Done"
def plot_newick(aug_cluster_list, mode='c', db=-1):
circular_style = TreeStyle()
circular_style.mode = mode # draw tree in circular mode
circular_style.scale = 20
circular_style.arc_span = 360
if db > 0:
newick = convert_to_newick_db(aug_cluster_list,
len(aug_cluster_list) - 1, db)
circular_style.mode = mode
else:
newick = convert_to_newick(aug_cluster_list, len(aug_cluster_list) - 1)
newick = newick + ':0;'
t = Tree(newick, format=1)
t.show(tree_style=circular_style)
if False:
t.render('tree3.png', w=100, units='in', tree_style=circular_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 tree_viewer(treefolder):
"""
DESCRIPTION:
A function to create the representation of the tree with ete. Given the folder with the files in the tree folder it
creates the tree representation in the media folder.
:param treefolder: [pathlib] route to the subfolder in the tree folder which contains the data of the inference.
:return: None. It writes the image in the media folder.
"""
filename = os.path.basename(os.path.normpath(treefolder)) + '.txt.treefile'
imagefile = os.path.basename(os.path.normpath(treefolder)) + '.png'
treeroute = treefolder / filename
file = open(treeroute, 'r')
tree = file.read()
file.close()
tree = Tree(tree)
circular_style = TreeStyle()
circular_style.mode = "c"
circular_style.scale = 20
tree.render(str(MEDIA_DIR / imagefile),
w=1024,
units='mm',
tree_style=circular_style)
def showTreeStructure(inputfile):
t = ClusterTree(
"./OUTPUT/%s/NWK/HIER_CLUST_%s.nwk" %
((inputfile.split("_")[0]).upper(), inputfile.split(".")[0]))
def mylayout(node):
global flag
#print node.left
# print "node",len(node )
#if len(node)!=1:# and flag == 1:
# if flag == 1:
# pidlist= getpid(node)
#print pidlist
# dcs=DoCS(pidlist,PRO_pfam)
#print dcs
# if dcs>=0.5:
# flag=0
# print pidlist,len(node),dcs
# print "_____________________"
if node.is_leaf():
node.img_style["shape"] = "sphere"
node.img_style["size"] = 10
node.img_style["fgcolor"] = 'purple'
t.dist = 0
t.convert_to_ultrametric(1, strategy="fixed")
ts = TreeStyle()
ts.scale = 230
ts.root_opening_factor = 5.0
ts.mode = "c"
ts.layout_fn = mylayout
#print mylayout
t.show(tree_style=ts)
print("--------------------------------")
print("completed")
def get_tree_style(**kwargs):
style = TreeStyle()
style.layout_fn = layout
style.allow_face_overlap = True
style.branch_vertical_margin = 5
style.complete_branch_lines_when_necessary = False
style.draw_aligned_faces_as_table = False
style.scale = 1500
style.scale_length = 0.05
style.show_branch_support = False
style.show_leaf_name = False
for key, value in kwargs.items():
if value == "True":
value = True
else:
try:
value = float(value)
except ValueError:
pass
setattr(style, key, value)
return style
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 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)
# remove dodgy sample
big_tree.search_nodes(name="'EBOV|EMLab-RT|IPDPFHGINSP_GUI_2015_5339||GIN|Conakry|?|MinION_LQ05|2015-04-08'")[0].delete(
preserve_branch_length=True
)
# root the same as the MCC tree
ancestor = big_tree.get_common_ancestor(
"'EBOV|EMLab|EM_079422|KR817187|GIN|Macenta|?||2014-03-27'",
"'EBOV|EMLab|Gueckedou-C05|KJ660348|GIN|Gueckedou|?||2014-03-19'",
)
big_tree.set_outgroup(ancestor)
big_tree.ladderize()
ts = TreeStyle()
ts.show_leaf_name = False
# ts.show_branch_support = True
ts.scale = 100000
if mode == "small":
ts.scale = 750000
# add legend
for each in colourDict.keys():
ts.legend.add_face(CircleFace(radius=size[mode] / 2, color=colourDict[each]), column=0)
ts.legend.add_face(TextFace(each, ftype="Helvetica", fsize=size[mode]), column=1)
ts.legend.add_face(CircleFace(radius=size[mode] / 2, color="#F1F1F1"), column=0)
ts.legend.add_face(TextFace("Guinea", ftype="Helvetica", fsize=size[mode]), column=1)
ts.legend.add_face(RectFace(width=size[mode], height=size[mode], bgcolor="#D3D3D3", fgcolor="#FFFFFF"), column=0)
ts.legend.add_face(TextFace("Sierra Leone", ftype="Helvetica", fsize=size[mode]), column=1)
ts.legend.add_face(
RectFace(triangle=True, width=size[mode], height=size[mode], bgcolor="#939393", fgcolor="#FFFFFF"), column=0
)
ts.legend.add_face(TextFace("Liberia", ftype="Helvetica", fsize=size[mode]), column=1)
for key in speciescolors: genusSpecies = key.split() for name in genusSpecies: if name in lineage: nst['bgcolor'] = speciescolors[key] break leaf.img_style = nst nst = NodeStyle() nst["size"] = 0 nst["fgcolor"] = 'black' nst["hz_line_width"] = 2 nst["vt_line_width"]= 2 for n in t.traverse(): if n.is_leaf() == False: n.img_style = nst ts = TreeStyle() for i,ref in enumerate(colormap.keys()): if 'ubi' not in ref and 'HH' not in ref and 'LOMETS' not in ref: ts.title.add_face(TextFace(ref, fsize=12), column=0) ts.title.add_face( RectFace(10 , 10 , colormap[ref] , colormap[ref]), column = 1) #ts.mode = "c" #ts.arc_start = -180 #0 degrees = 3 o'clock ts.scale = 150 ts.show_leaf_name = False ts.show_branch_support = True #t.show(tree_style = ts) outpng = treefile+'outnocolor.png' t.render(outpng , tree_style = ts)
def showTree(delimitation, scale = 500, render = False, fout = "", form = "svg", show_support = False):
"""delimitation: species_setting class"""
tree = delimitation.root
style0 = NodeStyle()
style0["fgcolor"] = "#000000"
style0["vt_line_color"] = "#0000aa"
style0["hz_line_color"] = "#0000aa"
style0["vt_line_width"] = 2
style0["hz_line_width"] = 2
style0["vt_line_type"] = 0
style0["hz_line_type"] = 0
style0["size"] = 0
#tree.clear_face()
tree._faces = _FaceAreas()
for node in tree.get_descendants():
node.set_style(style0)
node.img_style["size"] = 0
node._faces = _FaceAreas()
#node.clear_face()
tree.set_style(style0)
tree.img_style["size"] = 0
style1 = NodeStyle()
style1["fgcolor"] = "#000000"
style1["vt_line_color"] = "#ff0000"
style1["hz_line_color"] = "#0000aa"
style1["vt_line_width"] = 2
style1["hz_line_width"] = 2
style1["vt_line_type"] = 0
style1["hz_line_type"] = 0
style1["size"] = 0
style2 = NodeStyle()
style2["fgcolor"] = "#0f0f0f"
style2["vt_line_color"] = "#ff0000"
style2["hz_line_color"] = "#ff0000"
style2["vt_line_width"] = 2
style2["hz_line_width"] = 2
style2["vt_line_type"] = 0
style2["hz_line_type"] = 0
style2["size"] = 0
for node in delimitation.active_nodes:
node.set_style(style1)
node.img_style["size"] = 0
for des in node.get_descendants():
des.set_style(style2)
des.img_style["size"] = 0
for node in delimitation.root.traverse(strategy='preorder'):
if show_support and hasattr(node, "bs"):
if node.bs == 0.0:
node.add_face(TextFace("0", fsize = 8), column=0, position = "branch-top")
else:
node.add_face(TextFace("{0:.2f}".format(node.bs), fsize = 8), column=0, position = "branch-top")
ts = TreeStyle()
"""scale pixels per branch length unit"""
ts.scale = scale
ts.branch_vertical_margin = 7
if render:
tree.render(fout+"."+form, tree_style=ts)
else:
tree.show(tree_style=ts)
def draw_tree(tree, conf, outfile):
try:
from ete3 import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace,
SequenceFace, random_color, SeqMotifFace)
except ImportError as e:
print(e)
return
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=1, position='branch-right')
def ly_supports(node):
if not node.is_leaf() and node.up:
supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly_tax_labels(node):
if node.is_leaf():
c = LABEL_START_COL
largest = 0
for tname in TRACKED_CLADES:
if hasattr(node, "named_lineage") and tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.margin_right = 2
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in range(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_full_alg(node):
pass
def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
last_lt = None
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
TRACKED_CLADES = ["Eukaryota", "Viridiplantae", "Fungi",
"Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta",
"Amoebozoa", "Crypthophyta", "Bacteria",
"Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
"Gammaproteobacteria",]
# ["Opisthokonta", "Apicomplexa"]
colors = random_color(num=len(TRACKED_CLADES), s=0.45)
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])
NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')
LABEL_START_COL = 10
ALG_START_COL = 40
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.scale = 160
ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]
MIXED_RES = set()
MAX_SEQ_LEN = 0
NPR_TREES = []
for n in tree.traverse():
if hasattr(n, "tree_seqtype"):
MIXED_RES.add(n.tree_seqtype)
if hasattr(n, "tree_type"):
NPR_TREES.append(n.tree_type)
seq = getattr(n, "sequence", "")
MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)
if MAX_SEQ_LEN:
ALG_SCALE = min(1, 1000./MAX_SEQ_LEN)
ts.layout_fn.append(ly_block_alg)
if len(NPR_TREES) > 1:
rF = RectFace(4, 4, "steelblue", "steelblue")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" NPR node"), 1)
ts.legend_position = 3
if len(MIXED_RES) > 1:
rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
ts.legend_position = 3
try:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
a = tree.search_nodes(species='Dictyostelium discoideum')[0]
b = tree.search_nodes(species='Chondrus crispus')[0]
#out = tree.get_common_ancestor([a, b])
#out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
tree.set_outgroup(out)
tree.swap_children()
except Exception:
pass
tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
#figure IES loss from __future__ import print_function from ete3 import Tree, NodeStyle, TreeStyle from pyies.userOptions import basePath import os.path import string geneFamily = '4137' analysis = '2' phyldogResultsPath = "analysis/phyldogT" + analysis + "/results" treeF = os.path.join(basePath, 'analysis', 'phyldogT' + analysis, 'results', geneFamily + ".ReconciledTree" ) alnF = os.path.join(basePath, 'analysis', 'msas', 'filtered', 'cluster.' + geneFamily + '.nucl.fa') t = Tree(treeF) ts = TreeStyle() ts.scale = 500 nstyle = NodeStyle() nstyle["size"] = 0 for n in t.traverse(): n.set_style(nstyle) #seqs = SeqGroup(sequences = alnF, format = "fasta") # for leaf in t: # geneId = leaf.name # seq = seqs.get_seq(geneId) # seq = seq.translate(None, string.ascii_lowercase) # keep only CDS # #iesmotif = [[1, len(seq), "line", 2, 5, None, None, None]] # #seqFace = SeqMotifFace(seq = seq, gap_format = "blank", seq_format = "line") # seqFace = SequenceFace(seq, seqtype = 'dna') # leaf.add_face(seqFace, 0, "aligned")
This script plots trees of our wikipedia data.
"""
from ete3 import Tree, TreeStyle, NodeStyle
with open('/Users/diyadas/cdips/Topic-Ontology/SimpleWikiTree_u.txt','r') as f:
treestr = f.readlines()[0]
t = Tree( treestr.rstrip(),format=8)
circular_style = TreeStyle()
circular_style.mode = "c" # draw tree in circular mode
circular_style.scale = 120
circular_style.show_leaf_name = True
circular_style.show_branch_length = True
circular_style.show_branch_support = True
t.render("mytree.png", tree_style=circular_style)
nstyle = NodeStyle()
nstyle["hz_line_width"] = 3
nstyle["vt_line_width"] = 3
# Applies the same static style to all nodes in the tree. Note that,
# if "nstyle" is modified, changes will affect to all nodes
for n in t.traverse():
n.set_style(nstyle)
def get_example_tree():
t = Tree()
t.populate(10)
# Margins, alignment, border, background and opacity can now be set for any face
rs1 = faces.TextFace("branch-right\nmargins&borders",
fsize=12, fgcolor="#009000")
rs1.margin_top = 10
rs1.margin_bottom = 50
rs1.margin_left = 40
rs1.margin_right = 40
rs1.border.width = 1
rs1.background.color = "lightgreen"
rs1.inner_border.width = 0
rs1.inner_border.line_style = 1
rs1.inner_border.color= "red"
rs1.opacity = 0.6
rs1.hz_align = 2 # 0 left, 1 center, 2 right
rs1.vt_align = 1 # 0 left, 1 center, 2 right
br1 = faces.TextFace("branch-right1", fsize=12, fgcolor="#009000")
br2 = faces.TextFace("branch-right3", fsize=12, fgcolor="#009000")
# New face positions (branch-top and branch-bottom)
bb = faces.TextFace("branch-bottom 1", fsize=8, fgcolor="#909000")
bb2 = faces.TextFace("branch-bottom 2", fsize=8, fgcolor="#909000")
bt = faces.TextFace("branch-top 1", fsize=6, fgcolor="#099000")
# And faces can also be used as headers or foot notes of aligned
# columns
t1 = faces.TextFace("Header Face", fsize=12, fgcolor="#aa0000")
t2 = faces.TextFace("Footer Face", fsize=12, fgcolor="#0000aa")
# Attribute faces can now contain prefix and suffix fixed text
aligned = faces.AttrFace("name", fsize=12, fgcolor="RoyalBlue",
text_prefix="Aligned (", text_suffix=")")
# horizontal and vertical alignment per face
aligned.hz_align = 1 # 0 left, 1 center, 2 right
aligned.vt_align = 1
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
style = NodeStyle()
style["fgcolor"] = "Gold"
style["shape"] = "square"
style["size"] = 15
style["vt_line_color"] = "#ff0000"
t.set_style(style)
# add a face to the style. This face will be render in any node
# associated to the style.
fixed = faces.TextFace("FIXED branch-right", fsize=11, fgcolor="blue")
t.add_face(fixed, column=1, position="branch-right")
# Bind the precomputed style to the root node
# ETE 2.1 has now support for general image properties
ts = TreeStyle()
# You can add faces to the tree image (without any node
# associated). They will be used as headers and foot notes of the
# aligned columns (aligned faces)
ts.aligned_header.add_face(t1, column = 0)
ts.aligned_header.add_face(t1, 1)
ts.aligned_header.add_face(t1, 2)
ts.aligned_header.add_face(t1, 3)
t1.hz_align = 1 # 0 left, 1 center, 2 right
t1.border.width = 1
ts.aligned_foot.add_face(t2, column = 0)
ts.aligned_foot.add_face(t2, 1)
ts.aligned_foot.add_face(t2, 2)
ts.aligned_foot.add_face(t2, 3)
t2.hz_align = 1
# Set tree image style. Note that aligned header and foot is only
# visible in "rect" mode.
ts.mode = "r"
ts.scale = 10
for node in t.traverse():
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
node.add_face(aligned, column=0, position="aligned")
node.add_face(aligned, column=1, position="aligned")
node.add_face(aligned, column=3, position="aligned")
else:
node.add_face(bt, column=0, position="branch-top")
node.add_face(bb, column=0, position="branch-bottom")
node.add_face(bb2, column=0, position="branch-bottom")
node.add_face(br1, column=0, position="branch-right")
node.add_face(rs1, column=0, position="branch-right")
node.add_face(br2, column=0, position="branch-right")
return t, ts
def format( tree , genedict , detection , includenames , filename , speciescolors = None):
print 'final output...'
red = Color('red')
blue = Color('blue')
colorvec = list(red.range_to(blue, len(genedict.keys())))
colormap = {}
columnmap = {}
for i,ref in enumerate(genedict):
if ref not in detection:
columnmap[ref] = 3
if 'hybrid' in ref.lower():
columnmap[ref] = 0
if 'eff' in ref.lower():
columnmap[ref] = 1
if 'hap' in ref.lower():
columnmap[ref] = 2
colormap[ref] = colorvec[i].hex
for i,ref in enumerate(detection):
columnmap[ref] = 3 + i
colormap[ref] = colorvec[i].hex
print columnmap
print colormap
circledict = {}
for n in t.traverse():
nst = NodeStyle()
nst["size"] = 0
nst["fgcolor"] = 'black'
nst["hz_line_width"] = 4
nst["vt_line_width"]= 4
nst.show_name = False
if n.is_leaf():
if speciescolors != None and n.name in speciescolors:
nst["bgcolor"] = colors[n.name]
nst.show_name = True
n.add_face( AttrFace(attr = 'name', ftype='Helvetica', fgcolor='black', fsize =18 ,fstyle = 'normal' ), column =0 )
refs = json.loads(n.refs)
for ref in genedict:
if ref in refs and ref in detection:
n.add_face( CircleFace ( 10 , colormap[ref]), column = 2 + columnmap[ref] )
n.img_style = nst
if ref in refs and ref not in detection:
n.add_face( RectFace ( 20 , 20 , colormap[ref], colormap[ref] ), column = 2 + columnmap[ref] )
n.img_style = nst
if ref not in refs and ref not in detection:
n.add_face( RectFace ( 20 , 20 , colormap[ref], 'white' ), column = 2 + columnmap[ref] )
n.img_style = nst
###color by species
if n.name in speciescolors:
nst['bgcolor'] = speciescolors[n.name]
else:
if n.name.strip() in includenames:
n.add_face( AttrFace(attr = 'name', ftype='Helvetica', fgcolor='black', fsize =20 ,fstyle = 'normal' ), column =0 )
nst.size = 2
n.img_style = nst
else:
nst.size = 0
n.img_style = nst
ts = TreeStyle()
for i,ref in enumerate(colormap.keys()):
if 'ubi' not in ref:
ts.title.add_face(TextFace(ref, fsize=12), column=0)
ts.title.add_face( RectFace(10 , 10 , colormap[ref] , colormap[ref]), column = 1)
ts.show_leaf_name=False
"""ts.mode = "c"
ts.arc_start = 270
ts.arc_span = 359
ts.root_opening_factor = 1
"""
ts.scale = 190
t.show(tree_style = ts)
t.render(filename + ".png", tree_style = ts)
t.render( filename +".svg" , tree_style = ts)
F = faces.TextFace(mynode.name,fsize=20)
faces.add_face_to_node(F,mynode,0,position="aligned")
#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
n.set_style(nstyle)
n.img_style["vt_line_width"] = 0
ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
plot_tree.ladderize(direction=1)
my_svg = plot_tree.render(args.svg_name,tree_style=ts,w=595,dpi=300)
if args.show_nodes:
node_style = TreeStyle()
node_style.show_leaf_name=False
node_style.layout_fn = node_text_layout
plot_tree.show(tree_style=node_style)
nstyle["fgcolor"] = "yellow"
nstyle["size"] = 10
n.set_style(nstyle)
my_tree.img_style["size"] = 20
my_tree.img_style["fgcolor"] = "green"
code_name = {
"54263": "Ichthyosaura alpestris",
"8324": "Lissotriton vulgaris",
"8323": "Triturus cristatus",
"8327": "Triturus dobrogicus",
"8325": "Triturus karelinii ",
"57571": "Salamandra salamandra ",
"323754": "Lissotriton montandoni"
}
def mylayout(node):
if node.is_leaf():
longNameFace = faces.TextFace(code_name[node.name],
fsize=15,
fgcolor="green")
faces.add_face_to_node(longNameFace, node, column=0)
ts = TreeStyle()
ts.layout_fn = mylayout
ts.scale = 100
my_tree.show(tree_style=ts)
def testTreesMinimal(scenarios, traits, mapper):
def rgb2hex(r, g, b):
hex = "#{:02x}{:02x}{:02x}".format(r, g, b)
return hex
### Draw test trees. This is a modified version of the test routine in pcoc_num_tree.py, stuffed in a for loop
for cutoff in sorted(scenarios.keys()):
tree = init_tree(args.tree)
# not mucking with additive trees yet; ultrametrize the tree and normalize to length 1
tree.convert_to_ultrametric(tree_length=1)
# read scenario into a dict
manual_mode_nodes = {"T": [], "C": []}
p_events = scenarios[cutoff].strip().split("/")
for e in p_events:
l_e = map(int, e.split(","))
manual_mode_nodes["T"].append(l_e[0])
manual_mode_nodes["C"].extend(l_e[1:])
ts = TreeStyle()
# ts.allow_face_overlap = True
ts.show_leaf_name = False
ts.rotation = 270
ts.complete_branch_lines_when_necessary = False
# ts.optimal_scale_level = "full"
ts.scale = 800
for n in tree.traverse():
# default NodeStyle
nstyle = NodeStyle()
nstyle["size"] = 0
nstyle["hz_line_color"] = "none"
nstyle["vt_line_color"] = "none"
nstyle["hz_line_width"] = 3
nstyle["vt_line_width"] = 3
# colored faces
chroma = rgb2hex(*[
int(val)
for val in mapper(traits[n.ND], gamma=0.8, scaleMax=255)
]) # setup for wl2RGB
nf = CircleFace(radius=10,
color=chroma,
style='circle',
label=None)
# scenario-dependent features
if manual_mode_nodes:
# if transition node
if n.ND in manual_mode_nodes["T"]:
#nstyle["hz_line_color"] = "orange"
nf.inner_border.width = 4
nf.inner_border.color = 'red'
# if convergent node
elif n.ND in manual_mode_nodes["C"]:
#nstyle["hz_line_color"] = "violet"
nf.inner_border.width = 4
nf.inner_border.color = 'white'
# if ancestral
else:
nstyle["hz_line_color"] = "none"
n.set_style(nstyle)
n.add_face(nf, column=0, position='branch-top')
# limiting number of digits
outFile = args.output + "/test_trees/" + str(cutoff).replace(
'.', '_')[:np.min([5, len(str(cutoff))])] + ".pdf"
tree.render(outFile, tree_style=ts)
print >> sys.stderr, outFile
# for key in prune_count.keys():
# # node_weight = ln(prune_count[key])
# # node_weight = ln(n_children)
# # print(node_weight,n_children)
# # node = lookup[key]
# node.add_features(weight=random.randint(50))
for n in t.traverse():
n.add_face(TextFace(n.name, fsize = 16), column=0, position="branch-bottom")
# n.add_features(weight=random.randint(0,20))
t.prune(prune_list)
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
# ts.mode = "c" # this makes it circular
# False need to add node names manually
ts.show_leaf_name = False
ts.scale = 120
# Show branch data
ts.show_branch_length = False
ts.show_branch_support = True
# print (t.get_ascii(show_internal=True))
t.show(tree_style=ts)
default="pies.svg")
args = parser.parse_args()
plot_tree, subtrees_dict, subtrees_topids = get_phyparts_nodes(
args.species_tree, args.phyparts_root)
concord_dict, conflict_dict = get_concord_and_conflict(args.phyparts_root,
subtrees_dict,
subtrees_topids)
phyparts_dist, phyparts_pies = get_pie_chart_data(args.phyparts_root,
args.num_genes, concord_dict,
conflict_dict)
#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
n.set_style(nstyle)
n.img_style["vt_line_width"] = 0
ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
my_svg = plot_tree.render(args.svg_name, tree_style=ts, w=595)
import random
from ete3 import Tree, TreeStyle, NodeStyle, faces, AttrFace, TreeFace
# Tree Style used to render small trees used as leaf faces
small_ts = TreeStyle()
small_ts.show_leaf_name = True
small_ts.scale = 10
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
t = Tree()
t.populate(10)
T = TreeFace(t, small_ts)
# Let's make the sphere transparent
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def get_example_tree():
# Random tree
t = Tree()
t.populate(20, random_branches=True)
# Some random features in all nodes
for n in t.traverse():
n.add_features(weight=random.randint(0, 50))
