def my_layout(node):
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("name", ftype="Roboto", fgcolor='#191919')
name_face.margin_right = 10
name_face.margin_left = 10
else:
# If internal node, draws label with smaller font size
name_face = AttrFace("name",
fsize=10,
ftype="Roboto",
fgcolor='#191919')
name_face.margin_right = 10
name_face.margin_left = 10
# Adds the name face to the image at the preferred position
faces.add_face_to_node(name_face, node, column=0, position="branch-right")
def layout(node):
#print(node)
if (len(node.get_ancestors()) < 4):
print(node.name)
n = AttrFace("name", fsize=9)
n.margin_top = 10
n.margin_bottom = 0
n.margin_left = 10
faces.add_face_to_node(n, node, 0, position="float")
tf = TextFace(len(node.get_leaves()), fsize=12)
faces.add_face_to_node(tf, node, 0, position="float")
def ts_layout(node, fgcolor='#FF4ba6', fsize=12):
'''
Please set up as the following code shows:
```py
ts = TreeStyle()
ts.mode = 'r' # 'c'
ts.min_leaf_separation = 40
# ts.branch_vertical_margin = 20
# Do not add leaf names automatically
ts.show_leaf_name = False
ts.show_scale = False
ts.optimal_scale_level = 'mid'
ts.margin_top = 5
ts.margin_left = 5
ts.margin_right = 5
# Use my custom layout
ts.layout_fn = ts_layout
```
'''
node.img_style["size"] = 2
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = fgcolor
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("name", fsize=fsize) # fgcolor="royalblue"
name_face.margin_left = 3
faces.add_face_to_node(name_face,
node,
column=0,
position="branch-right")
elif not node.is_root():
# If internal node, draws label with smaller font size
name_face = AttrFace("name", fsize=fsize)
name_face.margin_left = 2
name_face.margin_bottom = 2
# Adds the name face to the image at the preferred position
faces.add_face_to_node(name_face,
node,
column=0,
position="branch-top")
def base_node_style(self):
from ete3 import NodeStyle, AttrFace
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 2
nstyle["fgcolor"] = "black"
for n in self.tree.traverse():
n.set_style(nstyle)
if re.match('.*fasta', n.name):
nf = AttrFace('name', fsize=8)
nf.margin_right = 150
nf.margin_left = 3
n.add_face(nf, column=0)
self.log.info("Applied base node style")
def layout(node):
node.img_style["size"] = 0
if not node.is_leaf():
boostFace = faces.TextFace(node.support, fgcolor="grey", fsize=34)
add_face_to_node(boostFace, node, column=0, position="branch-top")
if node.is_leaf():
taxid = (node.name.split('.')[0])
seq_name = (node.name.split('.')[1])
#add predicted name (eggnog 4.5)
try:
pred_name = predict_name[node.name]
predNameFace = faces.TextFace(pred_name,
fgcolor="salmon",
fsize=34)
predNameFace.margin_right = 20
predNameFace.margin_left = 20
add_face_to_node(predNameFace,
node,
column=2,
position="branch-right")
except:
predNameFace = faces.TextFace('--', fgcolor="salmon", fsize=34)
add_face_to_node(predNameFace,
node,
column=2,
position="branch-right")
seqNameFace = faces.TextFace(seq_name, fgcolor="grey", fsize=34)
add_face_to_node(seqNameFace, node, column=1, position="branch-right")
sp_name = ncbi.get_taxid_translator([(node.name.split('.')[0])])
node.name = sp_name[int(taxid)]
seqFace = SeqMotifFace(node.sequence, gap_format="blank")
add_face_to_node(seqFace, node, column=3, position="aligned")
lin = ncbi.get_lineage(taxid)
#metazoa
#if int('33208') in lin:
# N = AttrFace("name", fsize=34, fgcolor="blue")
# N.margin_left = 20
# N.margin_right= 20
# faces.add_face_to_node(N, node, column=0)
#cnidaria
if int('6073') in lin:
N = AttrFace("name", fsize=34, fgcolor="red")
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)
#ctenophora
elif int('10197') in lin:
N = AttrFace("name", fsize=34, fgcolor="orange")
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)
#bilateria
elif int('33213') in lin:
N = AttrFace("name", fsize=34, fgcolor="blue")
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)
#porifera
elif int('6040') in lin:
N = AttrFace("name", fsize=34, fgcolor="green")
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)
else:
N = AttrFace("name", fsize=34, fgcolor="black")
N.margin_left = 20
N.margin_right = 20
faces.add_face_to_node(N, node, column=0)