def default_layout(node):
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=14, 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 "weight"
C = CircleFace(radius=node.weight, color="Red", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.5
# Rotate the faces by 90*
C.rotation = 90
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def my_layout(node):
circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
node.name]
text_color = 'black'
if isinstance(circle_color, str):
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': str(node.frequency),
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)
else:
P = PieChartFace(
[100 * x / node.frequency for x in circle_color.values()],
2 * 10 * scipy.sqrt(node.frequency),
2 * 10 * scipy.sqrt(node.frequency),
colors=[(color if color != 'None' else 'lightgray')
for color in list(circle_color.keys())],
line_color=None)
T = TextFace(' '.join(
[str(x) for x in list(circle_color.values())]),
tight_text=True)
T.hz_align = 1
T.rotation = -90
faces.add_face_to_node(P, node, 0, position='branch-right')
faces.add_face_to_node(T, node, 1, position='branch-right')
if idlabel:
T = TextFace(node.name, tight_text=True, fsize=6)
T.rotation = -90
T.hz_align = 1
faces.add_face_to_node(
T,
node,
1 if isinstance(circle_color, str) else 2,
position='branch-right')
def default_layout(node):
"""
Specifies the layout for the ete.TreeStyle object.
Parameters
----------
node: ete.Tree
Input node for specifying which attributes.
"""
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=14, 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 "weight"
C = CircleFace(radius=node.weight, color="Red", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.5
# Rotate the faces by 90*
C.rotation = 90
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def my_layout(node):
circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
node.name]
text_color = 'black'
if isinstance(circle_color, str):
if isolabel and hasattr(node, 'isotype'):
nl = ''.join(
sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
key=lambda x: ISO_TYPE_charORDER[x]))
else:
nl = str(node.frequency)
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': nl,
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)
else:
P = PieChartFace(
[100 * x / node.frequency for x in circle_color.values()],
2 * 10 * scipy.sqrt(node.frequency),
2 * 10 * scipy.sqrt(node.frequency),
colors=[(color if color != 'None' else 'lightgray')
for color in list(circle_color.keys())],
line_color=None)
T = TextFace(' '.join(
[str(x) for x in list(circle_color.values())]),
tight_text=True)
T.hz_align = 1
T.rotation = -90
faces.add_face_to_node(P, node, 0, position='branch-right')
faces.add_face_to_node(T, node, 1, position='branch-right')
if idlabel:
T = TextFace(node.name, tight_text=True, fsize=6)
T.rotation = -90
T.hz_align = 1
faces.add_face_to_node(
T,
node,
1 if isinstance(circle_color, str) else 2,
position='branch-right')
elif isolabel and hasattr(node, 'isotype') and False:
iso_name = ''.join(
sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
key=lambda x: ISO_TYPE_charORDER[x]))
#T = TextFace(iso_name, tight_text=True, fsize=6)
#T.rotation = -90
#T.hz_align = 1
#faces.add_face_to_node(T, node, 1 if isinstance(circle_color, str) else 2, position='branch-right')
C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
color=circle_color,
label={
'text': iso_name,
'color': text_color
} if node.frequency > 0 else None)
C.rotation = -90
C.hz_align = 1
faces.add_face_to_node(C, node, 0)