def layout(node):
node.img_style["size"] = 5
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
if node.is_leaf():
f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
faces.add_face_to_node(f, node, 0, position="aligned")
f = faces.AttrFace("name", fsize=15)
faces.add_face_to_node(f, node, 0, position="branch-right")
else:
f = faces.TextFace("uno", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-top")
f = faces.TextFace("otromassssssssssss", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-bottom")
f = faces.CircleFace(20, "red")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float")
f = faces.CircleFace(23, "blue")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float-behind")
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=7)
faces.add_face_to_node(faces.AttrFace("name", "Arial", 10, None),
node,
0,
position='branch-right')
def layout(node):
if node.is_leaf():
#######################################################
#~ Taxon Label Size and Margin Adjustment
N = AttrFace("name", fsize=1200, fgcolor="#000000")
N.margin_top = 250
N.margin_right = 100 #outside
N.margin_left = 1000 #inside
N.margin_bottom = 250
#######################################################
#######################################################
#~ Taxon Label Background Color Setting
tmp = "<myTaxaonLabel>"
#~ if not(node.name.find(tmp)) : N.background.color="#FF9999"
#######################################################
faces.add_face_to_node(N, node, 0, position="aligned")
if (not node.is_leaf()):
S = faces.AttrFace("support", fsize=200, fgcolor="#000000")
S.margin_top = 20
S.margin_right = 10
S.margin_left = 20
S.margin_bottom = 20
faces.add_face_to_node(S, node, column=0, position="float")
if "support" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.support * 20,
color="RoyalBlue",
style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, position="float", column=1)
style = NodeStyle()
style["size"] = 0
style["vt_line_width"] = 150
style["hz_line_width"] = 150
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
bgcol1 = "#FFCCCC"
bgcol2 = "#FFE5CC"
bgcol3 = "#FFFFCC"
bgcol4 = "#E5FFCC"
bgcol5 = "#CCFFCC"
bgcol6 = "#CCFFE5"
bgcol7 = "#FFCCE5"
bgcol8 = "#CCFFFF"
bgcol9 = "#CCE5FF"
bgcol10 = "#CCCCFF"
bgcol11 = "#E5CCFF"
def _colorize(self, palette):
"""
Assigns faces and colours to the locus trees for pretty rendering.
:param palette: list
List of strings representing colours in hexadecimal format.
:return:
"""
from ete2 import NodeStyle, faces
if not self.L:
self.locus_tree() # computes & stores the tree
ncol = len(palette)
iFace = faces.AttrFace("I", fsize=8, text_suffix='/')
pFace = faces.AttrFace("P", fsize=8)
# idFace = faces.AttrFace("id", fsize=8)
# suppFace = faces.AttrFace("support", text_suffix=" ", formatter="%.2f", fsize=8)
coloured = dict((i, False) for i, g in enumerate(self.L.traverse(strategy="postorder")))
current_colour = -1
for g in self.L.traverse(strategy="postorder"):
if not g.is_leaf():
# g.add_face(suppFace, position="branch-bottom", column=-2)
g.add_face(iFace, position="branch-top", column=-1)
g.add_face(pFace, position="branch-top", column=0)
if g.source:
current_colour += 1
current_colour %= ncol
style = NodeStyle()
style['vt_line_color'] = palette[current_colour]
style['hz_line_color'] = palette[current_colour]
style['size'] = 0
style['fgcolor'] = '#000000'
style["vt_line_width"] = 2
style["hz_line_width"] = 2
for gg in g.traverse():
if not coloured[gg.nid]:
gg.set_style(style)
coloured[gg.nid] = True
def test_ultrametric():
t = Tree()
# Creates a random tree (not ultrametric)
t.populate(100)
# Convert tree to a ultrametric topology in which distance from
# leaf to root is always 100. Two strategies are available:
# balanced or fixed
convert_to_ultrametric(t, 1.0, "balanced")
# Print distances from all leaves to root. Due to precision issues
# with the float type. Branch lengths may show differences at
# high precision levels, that's way I round to 6 decimal
# positions.
print "distance from all leaves to root:", \
set([round(l.get_distance(t), 6)for l in t.iter_leaves()])
nameFace = faces.AttrFace("name")
t.show(ultrametric_layout)
