def mylayout(node):
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = ProfileFace(matrix_max,matrix_min,matrix_avg,200,70,"cbars")
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=0
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 = TextFace("Silh=%0.2f" %node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"]="#056600"
# Otherwise, use red bubbles
else:
validationFace = 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
add_face_to_node(validationFace, node, 0)
if len(node)>100:
add_face_to_node(cbarsFace, node, 1)
def ColorCodedNode (node):
if node.is_leaf():
ColorCode=PhenoDict[node.name]
if ColorCode == '1':
#Name=faces.AttrFace('name',fsize='20',fgcolor="Blue")
#NameFace=TextFace(Name)
faces.add_face_to_node(AttrFace('name',fsize=20,fgcolor='blue'), node, column=0,aligned=True)
#faces.add_face_to_node(TextFace(text='marker1',fsize=10,fgcolor='black'), node, column=1,position='aligned')
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
elif ColorCode == '2':
#Name=faces.AttrFace('name',fsize='20',fgcolor="Red")
#NameFace=TextFace(Name)
faces.add_face_to_node(AttrFace("name",fsize=20,fgcolor='red'), node, column=0,aligned=True)
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
elif ColorCode == '-9':
faces.add_face_to_node(AttrFace("name",fsize=20,fgcolor='black'), node, column=0,aligned=True)
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
def mylayout(node):
if node.is_leaf():
if node.name == "Danio_rerio":
# import pudb; pudb.set_trace()
pass
# profile_face = ProfileFace(data_max[1], data_min[1], 0.0, 100, 14, "heatmap")
profile_face = ProfileFace(data_max[0], data_min[0], 0.0, 100, 14,
"heatmap")
ete3.treeview.faces.add_face_to_node(profile_face,
node,
0,
aligned=True)
def create_circle(self,
filename,
title,
name2color=None,
name2class_dic=None,
class2color_dic=None,
vector=None,
ignore_branch_length=True):
plt.clf()
axis_font = {'size': '3'}
plt.rc('xtick', labelsize=0.1)
plt.rc('ytick', labelsize=0.1)
plt.rc({'font.size': 0.1})
# legend creation
if name2class_dic and class2color_dic:
leg = []
for cls, color in class2color_dic.items():
leg.append(mpatches.Patch(color=color, label=cls))
t = Tree(self.nwk)
# iterate over tree leaves only
for l in t.iter_leaves():
ns = NodeStyle()
if name2color:
ns["bgcolor"] = name2color[
l.name] if l.name in name2color else 'white'
elif name2class_dic and class2color_dic:
ns["bgcolor"] = class2color_dic[name2class_dic[
l.name]] if l.name in name2class_dic else 'white'
# Gray dashed branch lines
#ns["hz_line_type"] = 1
#ns["hz_line_color"] = "#cccccc"
#
l.img_style = ns
F = TextFace(l.name)
F.ftype = 'Times'
#if vector:
# if l.name in vector:
l.add_features(profile=[random.random()
for x in range(10)]) #vector[l.name])
l.add_features(deviation=[0 for x in range(10)
]) #len(vector[l.name]))])
l.add_face(ProfileFace(max_v=1,
min_v=0.0,
center_v=0.5,
width=200,
height=40,
style='heatmap',
colorscheme=5),
column=0,
position='aligned')
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = VisualizeCircularTree.layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
ts.force_topology = ignore_branch_length
ts.title.add_face(TextFace(title, fsize=20, ftype='Times'), column=15)
# legend creation
if name2class_dic and class2color_dic:
for k, (cls, col) in enumerate(class2color_dic.items()):
x = RectFace(8, 8, 'black', col)
#x.opacity=0.5
ts.legend.add_face(x, column=8)
ts.legend.add_face(TextFace(' ' + cls + ' ',
fsize=9,
ftype='Times'),
column=9)
t.render(filename + '.pdf', tree_style=ts, dpi=5000)
t = ClusterTree(PATH + "diauxic.nw", PATH + "diauxic.array")
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 70, "cbars")
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
def create_circle(self, filename, title, ignore_branch_length=True):
plt.clf()
axis_font = {'size': '29'}
plt.rc('xtick', labelsize=0.1)
plt.rc('ytick', labelsize=0.1)
plt.rc({'font.size': 0.2})
plt.rc('text', usetex=True)
# legend creation
if self.motif2struct and self.struct2color_dic:
leg = []
for cls, color in self.struct2color_dic.items():
leg.append(mpatches.Patch(color=color, label=str(cls)))
t = Tree(self.nwk)
node_to_keep = []
for l in t.iter_leaves():
if len(l.name) > 1:
node_to_keep.append(l.name)
t.prune(tuple(node_to_keep))
# iterate over tree leaves only
for l in t.iter_leaves():
ns = NodeStyle()
if self.motif2struct and self.struct2color_dic:
ns["bgcolor"] = self.struct2color_dic[self.motif2struct[
l.
name]] if l.name in self.motif2struct and self.motif2struct[
l.name] in self.struct2color_dic else 'white'
# Gray dashed branch lines
#ns["hz_line_type"] = 1
#ns["hz_line_color"] = "#cccccc"
#
l.img_style = ns
if self.propVec:
if l.name in self.propVec:
l.add_features(profile=self.propVec[l.name])
l.add_features(deviation=[
0 for x in range(len(self.propVec[l.name]))
])
l.add_face(ProfileFace(max_v=1,
min_v=-1,
center_v=0,
width=200,
height=40,
style='heatmap',
colorscheme=2),
column=3,
position='aligned')
l.name = " " + l.name + " "
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = VisualizeTreeOfMotifs.layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = False
ts.show_branch_support = False
ts.force_topology = ignore_branch_length
ts.title.add_face(TextFace(title, fsize=20, ftype='Times'), column=15)
# legend creation
if self.motif2struct and self.struct2color_dic:
for k, (cls, col) in enumerate(self.struct2color_dic.items()):
x = RectFace(15, 15, 'black', col)
#x.opacity=0.5
ts.legend.add_face(x, column=8)
ts.legend.add_face(TextFace(' ' + str(cls) + ' ',
fsize=30,
ftype='Times'),
column=9)
ts.legend.add_face(TextFace('--- Properties vector order ↓',
fsize=30,
ftype='Times'),
column=10)
for y in [
'Mean molecular weight of amino acids',
'Mean flexibility of amino acids',
'Mean DIWV instability index of sequence',
'Mean surface accessibility of amino acids',
'Mean KD hydrophobicity', 'Mean hydrophilicity of amino acids'
]:
x = RectFace(5, 5, 'black', 'black')
#x.opacity=0.5
ts.legend.add_face(x, column=11)
ts.legend.add_face(TextFace(' ' + y + ' ',
fsize=25,
ftype='Times'),
column=12)
t.render(filename + '.pdf', tree_style=ts, dpi=5000)
def plot_heat_tree_V0(heatmap_file, tree_file, output_file=None):
'''
Plot heatmap next to a tree. The order of the heatmap **MUST** be the same,
as order of the leafs on the tree. The tree must be in the Newick format. If
*output_file* is specified, then heat-tree will be rendered as a PNG,
otherwise interactive browser will pop-up with your heat-tree.
Parameters
----------
heatmap_file: str
Path to the heatmap file. The first row must have '#Names' as first
element of the header.
e.g. #Names, A, B, C, D
row1, 2, 4, 0, 4
row2, 4, 6, 2, -1
tree_file: str
Path to the tree file in Newick format. The leaf node labels should
be the same as as row names in the heatmap file. E.g. row1, row2.
output_file: str, optional
If specified the heat-tree will be rendered in that file as a PNG image,
otherwise interactive browser will pop-up. **N.B.** program will wait
for you to exit the browser before continuing.
'''
import numpy
from ete3.treeview.faces import add_face_to_node
from ete3 import ClusterTree, TreeStyle, AttrFace, ProfileFace
# To operate with numbers efficiently
# Loads tree and array
t = ClusterTree(tree_file, heatmap_file)
t.ladderize()
R = t.get_midpoint_outgroup()
t.set_outgroup(R)
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(1., 0., 0.5, 1000, 14, "heatmap", colorscheme=1)
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
t.render("test.svg", tree_style=ts)
'''