def layout(node):
if node.is_leaf():
pretty_name = names[node.name] if node.name in names else node.name
# derp = AttrFace("name", fsize=10, ftype="Arial", fgcolor="black")
pretty_name_face = faces.TextFace(pretty_name)
pretty_name_face.margin_left = 5
faces.add_face_to_node(pretty_name_face, node, column=0)
def layout(node):
## if node.is_leaf() and 'showname' in node.features:
## # Add node name to laef nodes
## N = AttrFace("name", fsize=14, fgcolor="black")
## faces.add_face_to_node(N, node, 0)
if "Rsize" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "Rsize"
C = CircleFace(radius=node.Rsize * 3,
color="RoyalBlue",
style="sphere")
# make the sphere transparent
C.opacity = 0.9
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
if "Rpearsize" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "Rpearsize"
C = CircleFace(radius=node.Rpearsize * 3,
color="lightgreen",
style="sphere")
# make the sphere transparent
C.opacity = 0.9
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def mylayout(node):
# Internal Node formatting
nstyle = NodeStyle()
nstyle["size"] = 0
nstyle["vt_line_width"] = 2
nstyle["hz_line_width"] = 2
if node.is_leaf():
circle_face = CircleFace(10, color_dict[node.name], style='circle')
faces.add_face_to_node(circle_face,
node,
position="branch-right",
column=0)
text_face = TextFace(meta_dict[node.name][0])
text_face.fgcolor = color_dict[node.name]
faces.add_face_to_node(text_face,
node,
position="branch-right",
column=1)
node.set_style(nstyle)
elif node.is_root():
node.dist = 0
node.set_style(nstyle)
else:
node.set_style(nstyle)
def my_layout(node):
N = None
# If user specified labels are specified add these:
if 'node_label' in tree_features:
for t in tree_features['node_label']:
node_attr = ifhasthenget(node, t)
if node_attr and to_string(node_attr):
if t == 'name' and hasattr(node, 'cl'):
continue
textface = to_string(node_attr)
N = TextFace(textface, fsize=12, fgcolor='black')
if 'e-' in textface and to_float(
textface
): # Stupid exception because ete3 rendering doesn't understand scientific notation
N = TextFace('%2.1e ' % to_float(textface),
fsize=12,
fgcolor='black')
# Add default values:
elif not no_default and node.frequency > 1 and not hasattr(node, 'cl'):
N = TextFace(
node.frequency, fsize=12,
fgcolor='black') # Default: use node frequency as TextFace
if N is not None:
N.rotation = -90
faces.add_face_to_node(N, node, 0, position='branch-top')
def layout(node):
"""
Helper function to annotate nodes with scientific name
:param node: A node instance of a ete3.Tree
:return: Annotated node with sci_name
"""
faces.add_face_to_node(TextFace(node.sci_name), node, 0)
def my_layout(node):
style = NodeStyle()
style["size"] = 0
style["vt_line_color"] = "#A0A0A0"
style["hz_line_color"] = "#A0A0A0"
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
node.set_style(style)
if node.is_leaf():
name_face = AttrFace("name", fsize=8, ftype="Times")
else:
name_face = TextFace(node.name, fsize=18, ftype="Times")
if node.node_type == Sum:
for child in node.children:
label = TextFace(round(child.support, 3), fsize=6)
child.add_face(label, column=1, position="branch-bottom")
if show_ids:
node.add_face(AttrFace("id", fsize=6),
column=1,
position="branch-top")
faces.add_face_to_node(name_face,
node,
column=1,
position="branch-right")
def treeLayout(self, node):
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0)
else:
node.img_style["size"] = 4
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#AA0000"
def barchart_layout(node, name='name',
width=20, height=40,
colors=None, min_value=0, max_value=1,
fsize=14, fgcolor="black"):
if colors is None:
colors = ['#0000FF']
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=fsize, fgcolor=fgcolor)
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"
if (isinstance(node.weight, int) or isinstance(node.weight, float)):
weight = [node.weight]
else:
weight = node.weight
C = BarChartFace(values=weight, width=width, height=height,
colors=['#0000FF'], min_value=min_value,
max_value=max_value)
# Let's make the sphere transparent
C.opacity = 0.5
# Rotate the faces by 270*
C.rotation = 270
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
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)
def tree_layout(node):
"""
TODO
"""
if node.is_leaf():
nameSize = 14
nameColor = '#009000'
relAbundSize = 10
else:
nameSize = 10
nameColor = '#303030'
relAbundSize = 8
nameFace = faces.TextFace(node.name, fsize=nameSize, fgcolor=nameColor)
nameFace.margin_bottom = 5
nameFace.margin_right = 10
nameFace.margin_left = 5
faces.add_face_to_node(nameFace, node, column=0, position='branch-top')
relAbundFace = faces.TextFace(node.rel_abund,
fsize=relAbundSize,
fgcolor='#2148c8')
relAbundFace.margin_top = 5
relAbundFace.margin_left = 5
faces.add_face_to_node(relAbundFace,
node,
column=0,
position='branch-bottom')
def master_ly(node):
if node.is_leaf():
# Create an ItemFAce. First argument must be the pointer to
# the constructor function that returns a QGraphicsItem. It
# will be used to draw the Face. Next arguments are arbitrary,
# and they will be forwarded to the constructor Face function.
F = faces.DynamicItemFace(ugly_name_face, 100, 50)
faces.add_face_to_node(F, node, 0, position="aligned")
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=10, fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
C = CircleFace(radius=node.weight, color="blue", style="sphere")
C.opacity = 0.3
faces.add_face_to_node(C, node, 0, position="float")
def master_ly(node):
if node.is_leaf():
# Create an ItemFAce. First argument must be the pointer to
# the constructor function that returns a QGraphicsItem. It
# will be used to draw the Face. Next arguments are arbitrary,
# and they will be forwarded to the constructor Face function.
F = faces.DynamicItemFace(ugly_name_face, 100, 50)
faces.add_face_to_node(F, node, 0, position="aligned")
def layout(node):
if not node.is_leaf():
size = random.randint(20,50)
F= faces.PieChartFace([10,20,60,10],
colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]],
width=size, height=size)
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="float")
def mylayout(node):
#if node.name != 'L':
file = 'tmp/%s.png' % node.name
new_face = faces.ImgFace(file)
new_face.rotable = True
new_face.rotation = -90
#new_face.margin_top = 50
new_face.margin_left = 15
faces.add_face_to_node(new_face, node, column=0 , position='branch-top')
def barchart_layout(node, name='name',
width=20, height=40,
colors=None, min_value=0, max_value=1,
fsize=14, fgcolor="black",
alpha=0.5,
rotation=270):
"""
Specifies the layout for the ete.TreeStyle object.
Parameters
----------
node: ete.Tree
Input node for specifying which attributes.
name: str, optional
Attribute to look up the name of the node.
width: int, optional
Width of the barchart.
height: int, optional
Height of the barchart.
colors: list of str, optional
List of HTML colors to color the barchart values.
min_value: int, optional
Minimum value to set the scale of the chart.
max_value: int, optional
Maximum value to set the scale of the chart.
fsize: int, optional
Font size on the leafs.
fgcolor: str, optional
Font color of the leafs.
alpha: float, optional
Transparency of the barchart.
rotation: int, optional
Orientation of the barchart.
"""
if colors is None:
colors = ['#0000FF']
if node.is_leaf():
# Add node name to leaf nodes
N = AttrFace("name", fsize=fsize, fgcolor=fgcolor)
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"
if (isinstance(node.weight, int) or isinstance(node.weight, float)):
weight = [node.weight]
else:
weight = node.weight
C = BarChartFace(values=weight, width=width, height=height,
colors=colors, min_value=min_value,
max_value=max_value)
# Let's make the sphere transparent
C.opacity = alpha
# Rotate the faces by 270*
C.rotation = rotation
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def _tree_layout(node):
try:
from ete3 import AttrFace, faces
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
if node.is_leaf():
nameFace = AttrFace("name", fsize=24, ftype="Nimbus Sans L")
faces.add_face_to_node(nameFace, node, 10, position="branch-right")
def layout(node):
global represent_lst
if node.is_leaf():
N = AttrFace("name", fsize=14, fgcolor="black") # can be "sci_name"
faces.add_face_to_node(N, node, 0)
if node.name in represent_lst:
C = CircleFace(radius=5, color="black", style="sphere")
faces.add_face_to_node(C, node, 1, position="aligned")
def tree_layout(node):
"""
side function for tree layouts (following ete3 manual)
:param node:
:return:
"""
if node.is_leaf():
color = get_color(node.name)
N = ete3.faces.TextFace(node.name, fsize=10, fgcolor=color)
faces.add_face_to_node(N, node, 0)
def layout(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)
if "weight" in node.features:
C = CircleFace(radius=node.weight, color="blue", style="sphere")
C.opacity = 0.3
faces.add_face_to_node(C, node, 0, position="float")
def _tree_layout(node):
try:
from ete3 import AttrFace, faces
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
if node.is_leaf():
nameFace = AttrFace("name", fsize=24, ftype="Nimbus Sans L")
faces.add_face_to_node(nameFace, node, 10, 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 layout(node):
if not node.is_leaf():
size = random.randint(20, 50)
F = faces.PieChartFace([10, 20, 60, 10],
colors=COLOR_SCHEMES[random.sample(
schema_names, 1)[0]],
width=size,
height=size)
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="float")
def 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="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.6
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
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)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.weight, 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, 0, position="float")
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
faces.add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
faces.add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
# If silhouette is good, creates a green bubble
if node.silhouette > 0:
validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"] = "#056600"
# Otherwise, use red bubbles
else:
validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
"Verdana", 10, "#940000")
node.img_style["fgcolor"] = "#940000"
# Sets node size proportional to the silhouette value.
node.img_style["shape"] = "sphere"
if node.silhouette <= 1 and node.silhouette >= -1:
node.img_style["size"] = 15 + int((abs(node.silhouette) * 10)**2)
# If node is very internal, draw also a bar diagram
# with the average expression of the partition
faces.add_face_to_node(validationFace, node, 0)
if len(node) > 100:
faces.add_face_to_node(cbarsFace, node, 1)
def layout(node):
if node.is_leaf():
if node.name=="A":
node.color="Blue"
node.attr2="Green"
elif node.name=="B":
node.color="Red"
node.attr2="Orange"
else:
node.color="Grey"
node.attr2="Yellow"
faces.add_face_to_node( CircleFace(radius=5, color=node.color), node, column=1)
faces.add_face_to_node( RectFace(width=10, height=10, fgcolor=node.attr2, bgcolor=node.attr2), node, column=2)
def phyparts_pie_layout(mynode):
if mynode.name in phyparts_pies:
pie = faces.PieChartFace(
phyparts_pies[mynode.name],
#colors=COLOR_SCHEMES["set1"],
colors=["blue", "green", "red", "dark gray"],
width=50,
height=50)
pie.border.width = None
pie.opacity = 0.5
faces.add_face_to_node(pie, mynode, 0, position="branch-right")
concord_text = faces.TextFace(str(int(concord_dict[mynode.name])) +
' ',
fsize=20)
conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name])) +
' ',
fsize=20)
faces.add_face_to_node(concord_text, mynode, 0, position="branch-top")
faces.add_face_to_node(conflict_text,
mynode,
0,
position="branch-bottom")
else:
F = faces.TextFace(mynode.name, fsize=20)
faces.add_face_to_node(F, mynode, 0, position="aligned")
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 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(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 my_layout(node):
"""Customise the layout of a tree node
Args:
node (node): tree node
"""
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("name")
else:
# If internal node, draws label with smaller font size
name_face = AttrFace("name", fsize=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 test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"] = False
if node.is_leaf():
if hasattr(node, "sequence"):
seqface = MySequenceFace(node.sequence,
"nt",
fsize=10,
col_w=11,
interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout(node):
if node.is_leaf():
if "Russia/" in node.name:
Rudesc = faces.AttrFace("name", fsize=10)
Rudesc.margin_left = 25
faces.add_face_to_node(Rudesc, node, 0, aligned=True)
else:
if "_" in node.name:
node.name = node.name.replace("_", " ")
countrydesc = faces.AttrFace("name", fsize=10)
countrydesc.margin_left = 5
countrydesc.margin_bottom = 10
countrydesc.margin_top = 5
countrydesc.margin_right = 5
faces.add_face_to_node(countrydesc, node, 0, aligned=False)
def test_layout_phylo_aa_motif(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "aa",
fsize=10,special_col=special_col,
alt_col_w=3,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout_idtree(node):
nstyle = NodeStyle()
nstyle["size"] = 1
node.set_style(nstyle)
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, position='aligned')
if not node.is_root():
# Creates a sphere face whose size is proportional to node's
# feature "weight"
TN = TextFace(str(node.ID), fsize=12)
faces.add_face_to_node(TN, node, 1, position="branch-right")
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 mylayout(node):
if node.is_leaf():
# faces.add_face_to_node(nameFace, node, column=0)
node.img_style["size"] = 80
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#000000"
L = node.name.split(' ')
if len(L) > 1:
img_name = os.path.join(g_suncg_object_path, L[1], "rgb_img",
"8_rotation.png")
objectFace = faces.ImgFace(img_name)
faces.add_face_to_node(objectFace, node, column=0)
else:
node.img_style["size"] = 80
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#AA0000"
def layout(node):
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
F = faces.DynamicItemFace(scientific_name_face)
if F.node == "DAR34208_Raffaelea_kilii_sp._nov.":
F.background = "Black"
faces.add_face_to_node(
F,
node,
0,
)
F.margin_left = 10
faces.add_face_to_node(
F,
node,
0,
)
def aligned_faces(node):
if node.is_leaf():
for i in xrange(3):
F = faces.TextFace("ABCDEFGHIJK"[0:random.randint(1,11)])
F.border.width = 1
F.border.line_style = 1
F.inner_background.color = "lightgreen"
F.border.width = 1
F.inner_border.width = 1
F.background.color = "darkgreen"
F.border.width = 2
F.vt_align = random.randint(0,4)
F.hz_align = random.randint(0,4)
F.margin_bottom = random.randint(1, 20)
F.margin_right = random.randint(1, 20)
F.margin_left = random.randint(1, 20)
F.margin_top = random.randint(1, 20)
faces.add_face_to_node(F, node, i, position="aligned")
if random.randint(0, 1):
faces.add_face_to_node(F, node, i, position="aligned")
def layout(node):
if node.is_leaf():
F = faces.PieChartFace(
[10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6], colors=COLOR_SCHEMES["set3"], width=50, height=50
)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
F = faces.PieChartFace(
[10, 20, 5, 5, 60], colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]], width=100, height=40
)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
else:
F = faces.BarChartFace(
[40, 20, 70, 100, 30, 40, 50, 40, 70, -12],
min_value=-12,
colors=COLOR_SCHEMES["spectral"],
labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","),
label_fsize=10,
scale_fsize=10,
)
faces.add_face_to_node(F, node, 0, position="branch-top")
F.background.color = "#eee"
def phyparts_pie_layout(mynode):
if mynode.name in phyparts_pies:
pie= faces.PieChartFace(phyparts_pies[mynode.name],
#colors=COLOR_SCHEMES["set1"],
colors = args.colors,
width=50, height=50)
pie.border.width = None
pie.opacity = 1
faces.add_face_to_node(pie,mynode, 0, position="branch-right")
concord_text = faces.TextFace(str(int(concord_dict[mynode.name]))+' ',fsize=20)
conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name]))+' ',fsize=20)
faces.add_face_to_node(concord_text,mynode,0,position = "branch-top")
faces.add_face_to_node(conflict_text,mynode,0,position="branch-bottom")
else:
F = faces.TextFace(mynode.name,fsize=20)
faces.add_face_to_node(F,mynode,0,position="aligned")
def layout(node):
node.img_style['size'] = 0
node.img_style['vt_line_width'] = 0
node.img_style['hz_line_width'] = 0
if "bgcolor" in node.features:
node.img_style['bgcolor'] = node.bgcolor
if node.is_leaf():
if not args.no_names:
name = faces.TextFace(node.sci_name, fsize=12, fstyle='italic')
faces.add_face_to_node(name, node, 0, aligned=True)
fake = faces.TextFace(" ")
fake.background.color = "white"
faces.add_face_to_node(fake, node, 1, aligned=True) # fake
else:
if not args.no_internal_names and node.get_distance(tNCBI, topology_only=True) < 3:
name = faces.TextFace(node.sci_name, fsize=12, fstyle='italic')
faces.add_face_to_node(name, node, 0, position='branch-top')
def layout(node):
'''
The layout function for exporting treees
'''
# Label the leaves
if node.is_leaf():
faces.add_face_to_node(TextFace(
getattr(node, TAXA_FEATURE)[-1],
fgcolor=('blue'
if getattr(node, GROUP_FEATURE) == interest_group
else 'black')),
node, column=0)
pval = float(getattr(node, CORRECTED_P_VAL_FEATURE))
pval_color = get_color(pval)
faces.add_face_to_node(RectFace(10, 10, fgcolor='Black',
bgcolor=pval_color),
node, column=1, aligned=True)
faces.add_face_to_node(
TextFace(' {0:0.5f} {1}'.format(
float(getattr(node, CORRECTED_P_VAL_FEATURE)),
getattr(node, OTU_FEATURE))),
node, column=2, aligned=True)
def layout(node):
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0)
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=30)
faces.add_face_to_node(N, node, 0, position="aligned")
def node_text_layout(mynode): F = faces.TextFace(mynode.name,fsize=20) faces.add_face_to_node(F,mynode,0,position="branch-right")
def sphere_map(node):
# Creates a random color sphere face that will be floating over nodes
bubble = faces.CircleFace(random.randint(5,40), random_color(), "sphere")
bubble.opacity = 0.7
faces.add_face_to_node(bubble, node, 0, position="float")
def leaf_name(node):
if node.is_leaf():
nameF = faces.AttrFace("name")
nameF.border.width = 1
faces.add_face_to_node(nameF, node, 0, position="branch-right")
def layout(node):
faces.add_face_to_node(AttrFace("name"), node, column=0,
position="branch-right")
def test(node):
if node.is_leaf():
faces.add_face_to_node(faces.AttrFace("name"), node, 0, position="aligned")
def custom_layout(self,node):
if node.is_leaf():
aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=12)
aligned_name_face.margin_top = 5
aligned_name_face.margin_right = 5
aligned_name_face.margin_left = 5
aligned_name_face.margin_bottom = 5
aligned_name_face.hz_align = 0 #0 = left, 1 = center, 2 = right
add_face_to_node(aligned_name_face, node, column=2, position='aligned')
#name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
#name_face.margin_top = 3
#name_face.margin_right = 3
#name_face.margin_left = 3
#name_face.margin_bottom = 3
#add_face_to_node(name_face, node, column=2, position='branch-right')
node.img_style['size'] = 0
#---------------------------------------------
#displaying extra categorical and numeric data
if (node.name in self._tip2info):
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_data = self._tip2info[node.name][headerIndex]
if isinstance( extra_data, ( int, float ) ):
extra_face = BarChartFace([extra_data], width=100,height=25,colors=[self._tip2color[node.name][headerIndex]],labels=[dataheader],min_value=0.0,max_value=self._tip_max)
else:
extra_face = TextFace(extra_data, fsize=11, fgcolor='black')
extra_face.background.color = self._tip2color[node.name][headerIndex]
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
#add_face_to_node(extra_face, node, column=column_no, aligned = True, position='branch-right')
column_no += 1
else:
#print "No data available"
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_face = TextFace("No data available", fsize=10, fgcolor='black')
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
column_no += 1
image_col_no = column_no
#----------------------------------------------
if (node.name in self._img_chk_list):
if self._img_data_dic[node.name] is not None:
img_face = ImgFace(self._img_data_dic[node.name], is_url=True)
#img_face = ImgFace(self._tip2info[node.name][0], is_url=True)
#img_path = os.path.join("file:///home/tayeen/TayeenFolders/TreeViewer/WebTreeApp/newplugin_test/data/", "328653.jpg")
#img_face = ImgFace(img_path, is_url=True)
img_face.margin_top = 10
img_face.margin_right = 10
img_face.margin_left = 10
img_face.margin_bottom = 10
#add_face_to_node(img_face, node, column=3, position='branch-right')
#add_face_to_node(img_face, node, column=3, aligned= True, position='branch-right')
else:
img_path = os.path.join("file://"+image_path, "ina.jpg")
img_face = ImgFace(img_path, is_url=True)
#add_face_to_node(img_face, node, column=5, position='branch-right')
add_face_to_node(img_face, node, column=image_col_no, position='aligned')
else: #node is not a leaf
node.img_style['size'] = 4
node.img_style['shape'] = 'square'
if node.name and self._custom_options["draw_internal"]:
name_face = TextFace(node.name, fgcolor='grey', fsize=10)
name_face.margin_top = 4
name_face.margin_right = 4
name_face.margin_left = 4
name_face.margin_bottom = 4
add_face_to_node(name_face, node, column=0, position='branch-top')
if node.name in self._node2label:
label_face = TextFace(self._node2label[node.name], fgcolor='DarkGreen', fsize=10)
label_face.margin_top = 4
label_face.margin_right = 4
label_face.margin_left = 4
label_face.margin_bottom = 4
add_face_to_node(label_face, node, column=0, position="branch-top")
if node.support and self._custom_options["draw_support"]:
support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
support_face.margin_top = 4
support_face.margin_right = 4
support_face.margin_left = 4
support_face.margin_bottom = 4
add_face_to_node(support_face, node, column=0, position='branch-bottom')
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"]= False
collapsed_face = faces.TextFace(" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
# Parse node features features and conver them into styles. This must be done like this, since current ete version
#does not allow modifying style outside the layout function.
if hasattr(node, "bsize"):
node.img_style["size"]= int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"]= node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"]= node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"]= node.fgcolor
#parse all nodes features
if hasattr(node, "bh_bgcolor"):
node.img_style["bgcolor"]= node.bh_bgcolor
if hasattr(node, "bh_size"):
node.img_style["size"]= node.bh_size
if hasattr(node, "lh_color"):
node.img_style['hz_line_color'] = node.lh_color
node.img_style["vt_line_color"] = node.lh_color
if hasattr(node, "lh_width"):
node.img_style['hz_line_width'] = node.lh_width
node.img_style['vt_line_width'] = node.lh_width
if hasattr(node, "lh_width") and hasattr(node, "lh_color"):
for n in node.iter_descendants():
n.img_style['hz_line_color'] = node.lh_color
n.img_style["vt_line_color"] = node.lh_color
n.img_style['hz_line_width'] = node.lh_width
n.img_style['vt_line_width'] = node.lh_width
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# Add an static face that handles the node name
faces.add_face_to_node(nameFace, node, column=0)
# We can also create faces on the fly
longNameFace = faces.TextFace(code2name[node.name])
faces.add_face_to_node(longNameFace, node, column=0)
# text faces support multiline. We add a text face
# with the whole description of each leaf.
descFace = faces.TextFace(code2desc[node.name], fsize=10)
descFace.margin_top = 10
descFace.margin_bottom = 10
descFace.border.margin = 1
# Note that this faces is added in "aligned" mode
faces.add_face_to_node(descFace, node, column=0, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "circle"
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 6
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "#000000"
# If an internal node contains more than 4 leaves, add the
# images of the represented species sorted in columns of 2
# images max.
if len(node)>=4:
col = 0
for i, name in enumerate(set(node.get_leaf_names())):
if i>0 and i%2 == 0:
col += 1
# Add the corresponding face to the node
if name.startswith("Dme"):
faces.add_face_to_node(flyFace, node, column=col)
elif name.startswith("Dre"):
faces.add_face_to_node(fishFace, node, column=col)
elif name.startswith("Mms"):
faces.add_face_to_node(mouseFace, node, column=col)
elif name.startswith("Ptr"):
faces.add_face_to_node(chimpFace, node, column=col)
elif name.startswith("Hsa"):
faces.add_face_to_node(humanFace, node, column=col)
elif name.startswith("Cfa"):
faces.add_face_to_node(dogFace, node, column=col)
# Modifies this node's style
node.img_style["size"] = 16
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#AA0000"
# If leaf is "Hsa" (h**o sapiens), highlight it using a
# different background.
if node.is_leaf() and node.name.startswith("Hsa"):
node.img_style["bgcolor"] = "#9db0cf"
def main_layout(node):
''' Main layout function. It controls what is shown in tree
images. '''
# Add faces to leaf nodes. This allows me to add the faces from
# the global variable LEAVE_FACES, which is set by the application
# controler according to the arguments passed through the URL.
if node.is_leaf():
for f, fkey, pos in LEAVE_FACES:
if hasattr(node, fkey):
faces.add_face_to_node(f, node, column=pos, position="branch-right")
else:
# Add special faces on collapsed nodes
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"]= False
collapsed_face = faces.TextFace(\
" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
# Set node aspect. This controls which node features are used to
# control the style of the tree. You can add or modify this
# features, as well as their behaviour
if node.is_leaf():
node.img_style["shape"] = "square"
node.img_style["size"] = 4
else:
node.img_style["size"] = 8
node.img_style["shape"] = "sphere"
# Evoltype: [D]uplications, [S]peciations or [L]osess.
if hasattr(node,"evoltype"):
if node.evoltype == 'D':
node.img_style["fgcolor"] = "#1d176e"
node.img_style["hz_line_color"] = "#1d176e"
node.img_style["vt_line_color"] = "#1d176e"
elif node.evoltype == 'S':
node.img_style["fgcolor"] = "#FF0000"
node.img_style["line_color"] = "#FF0000"
elif node.evoltype == 'L':
node.img_style["fgcolor"] = "#777777"
node.img_style["vt_line_color"] = "#777777"
node.img_style["hz_line_color"] = "#777777"
node.img_style["line_type"] = 1
# If no evolutionary information, set a default style
else:
node.img_style["fgcolor"] = "#000000"
node.img_style["vt_line_color"] = "#000000"
node.img_style["hz_line_color"] = "#000000"
# Parse node features features and conver them into styles. This
# must be done like this, since current ete version does not allow
# modifying style outside the layout function.
if hasattr(node, "bsize"):
node.img_style["size"]= int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"]= node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"]= node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"]= node.fgcolor