def my_layout(node):
if node.is_leaf():
# If terminal node, draws its name
name_face = ete3.AttrFace("name")
else:
# If internal node, draws label with smaller font size
name_face = ete3.AttrFace("name", fsize=10)
# Adds the name face to the image at the preferred position
ete3.faces.add_face_to_node(name_face,
node,
column=0,
position="branch-right")
def tree_profile_layout(node):
if node.is_leaf(
): # the aligned leaf is "column 0", thus traits go to column+1
node.set_style(
ns1) ## may be postponed to when we have ancestral states
ete3.add_face_to_node(ete3.AttrFace("name",
fsize=label_font_size,
text_suffix=" "),
node,
0,
position="aligned")
for column, (rgb_val, lab) in enumerate(
zip(d_seq[node.name], d_seq_lab[
node.name])): ## colour of csv.loc[node.name, "adm2"]
label = {
"text": lab[:10],
"color": "Black",
"fontsize": label_font_size - 1
}
ete3.add_face_to_node(ete3.RectFace(50,
10,
fgcolor=rgb_val,
bgcolor=rgb_val,
label=label),
node,
column + 1,
position="aligned")
else:
node.set_style(ns2)
def mylayout(n):
if not n.is_leaf():
#print("\n\n\nintnode_lossdict", intnode_lossdict.keys())
shortn = int(n.name.split('_')[1])
number_of_hogs = len(HOG_groups_dict[intnodes[shortn]].keys())
number_of_gains = number_of_hogs
try:
number_of_losses = int(intnode_lossdict[shortn])
except:
number_of_losses = 0
#thisface = ete3.faces.BarChartFace([int(number_of_losses), int(number_of_gains)],
# colors=ete3.COLOR_SCHEMES["set1"],
# #["Tomato","DarkCyan"],
# labels=["#Losses","#Gains"],
# width=20, height=40, min_value=0, max_value=4100)
#thisface.opacity = 0.8
thisfaceA = ete3.faces.TextFace('L: ' + str(int(number_of_losses)) + '\n' + 'G: ' + str(int(number_of_gains)))
thisfaceA.opacity = 0.8
ete3.faces.add_face_to_node(thisfaceA, n, column=0, position="branch-right")
ete3.faces.add_face_to_node(ete3.AttrFace("name"), n, column=1)
else:
pass
def _align_leaf_name(tree):
attr_face = ete3.AttrFace('name')
text_face = ete3.TextFace(' ')
for leaf in tree:
leaf.add_face(text_face, column=0, position='aligned')
leaf.add_face(attr_face, column=1, position='aligned')
return 0
def CanSNPer_tree_layout(self, node):
'''Layout function for ETE3 trees.'''
# Adds the name face to the image at the top side of the branch
if not node.is_root():
ete3.faces.add_face_to_node(ete3.AttrFace("name"),
node,
column=0,
position="branch-top")
def layout(node):
N = ete3.AttrFace("name", fsize=30)
N.margin_right = 10
if node.is_leaf():
if node.name == "Orussus_abietinus":
N.background.color = "lightblue"
elif node.name == "Athalia_rosae":
N.background.color = "lightgreen"
ete3.faces.add_face_to_node(N, node, 0, position="aligned")
def tree_profile_layout(
node
): # prepare table and other node information (local function so mind the identation)
if "NORW" in (getattr(node, "submission_org_code")):
this_color = "darkred"
else:
this_color = "#080816"
node.img_style['hz_line_type'] = node.img_style[
'vt_line_type'] = 0 # 0=solid, 1=dashed, 2=dotted
node.img_style['hz_line_width'] = node.img_style['vt_line_width'] = 4
node.img_style['hz_line_color'] = node.img_style[
'vt_line_color'] = this_color
if node.is_leaf(
): # the aligned leaf is "column 0", thus traits go to column+1
node.img_style['size'] = 2
node.img_style['shape'] = "sphere"
node.img_style['fgcolor'] = this_color
ete3.add_face_to_node(ete3.AttrFace("name",
fsize=label_font_size,
text_suffix=" "),
node,
0,
position="aligned")
for column, (rgb_val, lab, wdt) in enumerate(
zip(d_seq_color[node.name], d_seq_label[node.name],
rect_width)):
label = {
"text": lab[:10],
"color": "Black",
"fontsize": label_font_size - 1
}
ete3.add_face_to_node(ete3.RectFace(wdt,
12,
fgcolor=rgb_val,
bgcolor=rgb_val,
label=label),
node,
2 * column + 1,
position="aligned")
ete3.add_face_to_node(ete3.RectFace(2,
12,
fgcolor="#ffffff",
bgcolor="#ffffff",
label=""),
node,
2 * column + 2,
position="aligned")
else:
node.img_style['size'] = 0
def tree_plot(phylo, Bsize=1.0):
T = phylo
ts = ete3.TreeStyle()
ts.show_leaf_name = False
for n in T.traverse():
if n.is_leaf():
Nlabel = ete3.AttrFace('name',
fsize=14,
ftype='Arial',
fstyle='italic')
n.add_face(face=Nlabel, column=0, position='aligned')
NOg = ete3.AttrFace('Total', fsize=10, ftype='Arial')
n.add_face(face=NOg, column=0, position='branch-bottom')
#Set node style
nstyle = ete3.NodeStyle()
nstyle["fgcolor"] = 'Red'
nstyle["shape"] = "circle"
nstyle["hz_line_color"] = "Gray"
nstyle["hz_line_width"] = 2
nstyle["vt_line_width"] = 2
nstyle["vt_line_color"] = "Gray"
nstyle["size"] = n.Total * Bsize
n.set_style(nstyle)
return ts
def mkEteHlaTree(newick_str, midpoint=False, colorfun=(lambda x: 'black')):
"""
Transform a Newick tree into the ETE format.
Args:
newick_str (str): a string representing the tree in the Newick format
Kwargs:
midpoint (bool): if True, find the midpoint of the tree and re-root.
colorfun (function): a rule for coloring faces (TODO)
Returns:
A tuple consisting of an ete3.Tree object and a list of integer node names
"""
tree = ete3.Tree(newick_str)
if midpoint:
tree.set_outgroup(
tree.get_leaves()[0]) ## make arbitrary leaf the outgroup
outgrp_node = tree.get_midpoint_outgroup() ## now use ete algorithm
tree.set_outgroup(outgrp_node) ## and re-define the outgroup
## give nodes a name to be used in Bayesian model
nodeNames = []
for i, node in enumerate(tree.traverse()):
if node.name != '':
hla = mhctools.MhcObject(node.name, fmt="Newick")
node.add_feature('hla', str(hla)) ## FIXME: use MhcObject
node.name = str(i)
nodeNames.append(i)
## set width and color of edges
size = 10
nstyle = ete3.treeview.NodeStyle()
nstyle["vt_line_width"] = size
nstyle[
"hz_line_width"] = size ## FIXME make sure that ultrametric trees are rendered properly
## make sure that ultrametric trees are rendered correctly
nstyle["size"] = 0 ## do not render nodes
node.set_style(nstyle)
## NB: colorEteTree overrides set_style
## set colors of the HLA tags
for leaf in tree:
N = ete3.AttrFace("hla", fsize=50, fgcolor=colorfun(leaf.hla))
leaf.add_face(N, 0)
return (tree, nodeNames)
def plot_tree(self, pdf_fn):
print("Plotting", pdf_fn, file=sys.stderr)
ts = ete3.TreeStyle()
ant = self.antibiotics.upper()
ts.title.add_face(ete3.TextFace("{}{}".format(18 * " ", ant),
fsize=60),
column=0)
ts.show_leaf_name = False
for n in self.tree.traverse():
taxid = n.name
nstyle = ete3.NodeStyle()
res_cat = self.res_dict[taxid]
nstyle["fgcolor"] = cat_to_color[res_cat]
nstyle["size"] = 15
n.set_style(nstyle)
if n.is_leaf():
N = ete3.AttrFace("name", fsize=20)
n.add_face(N, 0)
#add_face_to_node(N, n, 0, position="aligned")
#n.add_face_to_node(ete3.TextFace("XXX"))
self.tree.render(pdf_fn, tree_style=ts)
def layout(node):
if node.is_leaf():
N = ete3.AttrFace("name", fsize=30)
ete3.faces.add_face_to_node(N, node, 0, position="aligned")
tstyle.show_leaf_name = False
tstyle.show_branch_length = False
for branch in t:
if "N" in branch.name:
branch.delete()
for branch in t:
if "blood" in branch.name:
t.set_outgroup(branch)
root = t.get_tree_root()
root.dist = 2 * branch.dist
branch.delete()
root.get_children()[0].delete()
for branch in t.traverse():
if "_" in branch.name:
#Print the leaf names in our own font
name_face = ete3.AttrFace("name", fsize=vertical_margins[pid] + 10)
branch.add_face(name_face, column=0, position="branch-right")
branch.name = branch.name.split("_")[0]
# else:
if displaySVs:
displaySVsOnPhylogenies(pid, t, SVs)
else:
displayDriversOnPhylogenies(pid, t, drivers, deletions)
if displayCombo and displaySVs:
displayDriversOnPhylogenies(pid, t, drivers, deletions)
# else:
# branch.add_feature(stuff="I'm internal!")
# upper = ete3.AttrFace("stuff", fsize=vertical_margins[pid])
# lower = ete3.TextFace("below", fsize=vertical_margins[pid])
if leaf.genome_name in recipient_branch.get_leaf_names()
]
donor_branch_in_reticulation = reticulation.get_common_ancestor(
donor_intersection)
recipient_branch_in_reticulation = reticulation.get_common_ancestor(
recipient_intersection)
reticulation.set_style(reticulation_style)
donor_branch_in_reticulation.set_style(donor_style)
recipient_branch_in_reticulation.set_style(recipient_style)
##color palette: blue, red, green , orange, purple, black
#color_palette = '#2e2be2 #e22e2b #2be22e #f9a82c #8a2be2 #000000'
nameFaces = {}
nameFaces[1117] = ete3.AttrFace("name", fsize=10, fgcolor='#000000')
nameFaces[1224] = ete3.AttrFace("name", fsize=10, fgcolor='#a20417')
def myLayout(node):
if node.is_leaf():
node.img_style['size'] = 0
genome_name, gene_name = node.name.split('_')
node.name = genome_table.loc[genome_name, 'organism_name']
ete3.add_face_to_node(nameFaces[genome_table.loc[genome_name,
'phylum']],
node,
2,
aligned=True)
elif node.is_root():
node.img_style['size'] = 0
def main(treefile,
outfile=None,
cladelistfile=None,
datafile=None,
prune=False,
log_dist=False,
values=None,
quoted_node_names=False,
startmatch=False):
global tot_clades
tot_clades = 0
tree = ete3.Tree(treefile, format=1, quoted_node_names=quoted_node_names)
if cladelistfile:
with open(cladelistfile) as f:
cladelist = set((line.rstrip().split('\t')[0] for line in f if \
not line.startswith('#')))
else:
cladelist = set()
if datafile:
assert values
data = pd.read_csv(datafile, sep='\t', index_col=0, header=0)
assert all(val in data.columns for val in values)
value_face = {
val: ete3.AttrFace(val,
formatter=' %.2f ',
fgcolor='grey',
fsize=8)
for val in values
}
max_val = data[values].max().max()
min_val = data[values].min().min()
average_val = data[values].mean().mean()
alt_col = ['#7FD09C', '#4cbdad']
ns = [ete3.NodeStyle(bgcolor=col) for col in alt_col]
default_ns = ete3.NodeStyle(size=0)
labelface = ete3.AttrFace('name')
if startmatch:
test = lambda node: any(
node.name.startswith(clade) for clade in cladelist) and not prune
else:
test = lambda node: node.name in cladelist and not prune
#for node in tree.traverse():
def mylayout(node):
global tot_clades
if log_dist:
node.add_feature('orig_dist', node.dist)
node.dist = log10(
node.dist
) if node.dist > 0 else -log10(-node.dist) if node.dist < 0 else 0
if test(node):
node.set_style(ns[0])
ns.insert(0, ns.pop()) #Cycle through colors
if not node.is_leaf():
ete3.add_face_to_node(labelface,
node,
column=0,
position='branch-right')
tot_clades += 1
else:
node.set_style(default_ns)
if datafile and node.is_leaf():
node.add_feature('profile',
[data[val][node.name] for val in values])
node.add_feature('deviation', [0.0] * len(values))
heatface = ete3.ProfileFace(max_val,
min_val,
average_val,
width=20 * len(values),
height=20,
style='heatmap')
ete3.add_face_to_node(heatface, node, column=1, aligned=True)
for i, val in enumerate(values, start=2):
node.add_feature(val, data[val][node.name])
ete3.add_face_to_node(value_face[val],
node,
column=i,
aligned=True)
if prune:
tree.prune(cladelist, preserve_branch_length=True)
tree.dist = 0
if outfile:
tree.render(outfile, mylayout)
else:
tree.show(layout=mylayout)
# Print summary
print("Found %d clades" % tot_clades)