A Python framework for construction, analysis and visualization of trees.
# A virtual X-server XVFB is used in case you do not have X-server
from xvfbwrapper import Xvfb
vdisplay = Xvfb()
vdisplay.start()
# launch stuff inside virtual display here
#vdisplay.stop()
from ete3 import Tree, faces, TreeStyle, NodeStyle
from ete3 import ClusterTree, RectFace, AttrFace, ProfileFace, TextFace
from ete3.treeview.faces import add_face_to_node
import pandas as pd
import numpy as np
import colorsysThe most simple way of showing a tree.
t = Tree()
t.populate(7,names_library=['A','B','C','D','E','F','G'])
## %%liline is used for showing plots in ipythonnotebook.
## t.render(file_name="tree.pdf") # will save tree into pdf file
t.render(file_name="%%inline")Get the randomly generated tree in newick format and save to a string variable which can be read using Tree() function.
t_str = t.write(outfile=None, format=0)
t_str
'(((B:1,A:1)1:1,(G:1,F:1)1:1)1:1,(E:1,(D:1,C:1)1:1)1:1);'t = Tree(t_str)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
t.render(file_name="%%inline", tree_style=ts)Get the randomly generated tree in newick format and save to file which can also be read using Tree() function.
t.write(outfile="tree.nw", format=0)
t = Tree("tree.nw")
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
t.render(file_name="%%inline", w=500, tree_style=ts)设置根节点、叶节点和中间节点的属性
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
# Draws nodes as small red spheres of diameter equal to 10 pixels
for n in t.traverse(): # Traverse each node and set attribute for each type of nodes
if n.is_leaf(): # Decide if leaf node
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 10
nstyle["fgcolor"] = "darkred"
n.set_style(nstyle)
else:
nstyle = NodeStyle()
nstyle["shape"] = "square"
nstyle["size"] = 15
nstyle["fgcolor"] = "orange"
n.set_style(nstyle)
t.img_style["size"] = 30
t.img_style["fgcolor"] = "blue"
t.render(file_name="%%inline", w=500, tree_style=ts)修改节点的名字
t = Tree(t_str)
nameMap = {'A': 'American', 'B': 'Britain', 'C':'China',
'D':'Dutch', 'E':'Egypt','F':'France','G':'German'}
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
# Creates my own layout function. I will use all previously created
# faces and will set different node styles depending on the type of
# node.
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# We can also create faces on the fly
newName = nameMap.get(node.name, node.name)
newNameFace = faces.TextFace(newName)
faces.add_face_to_node(newNameFace, node, column=1, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
ts.layout_fn = mylayout
t.img_style["size"] = 30
t.img_style["fgcolor"] = "black"
t.render(file_name="%%inline", w=600, tree_style=ts)不同的节点设置不同的背景色，树枝的颜色
t = Tree(t_str)
nameMap = {'A': 'American', 'B': 'Britain', 'C':'China',
'D':'Dutch', 'E':'Egypt','F':'France','G':'German'}
colorMap = { 'American': '#ACFFFF',
'Britain': '#ACACFF',
'China': '#ACACAC',
'Dutch': '#59ACAC',
'Egypt': '#5959AC',
'France': '#595959',
'German': '#065959'}
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
# Creates my own layout function. I will use all previously created
# faces and will set different node styles depending on the type of
# node.
def mylayout(node):
#Change branch color
node.img_style["hz_line_color"] = 'orange' # change horizontal branch color
node.img_style["vt_line_color"] = 'red' # Change vertical branch color
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# We can also create faces on the fly
newName = nameMap.get(node.name, node.name)
newNameFace = faces.TextFace(newName)
faces.add_face_to_node(newNameFace, node, column=1, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
node.img_style["bgcolor"] = colorMap[newName]
node.img_style["hz_line_color"] = 'blue' # change branch color
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
ts.layout_fn = mylayout
t.img_style["size"] = 30
t.img_style["fgcolor"] = "black"
t.render(file_name="%%inline",tree_style=ts)自定义热图函数，同时该函数也支持替换或新增节点的名字。
nameFace = AttrFace("name", fsize=12) #Set leaf node attribute
def setup_heatmap(tree, tree_style, header, center_value=0.0, nameMap ={}, nameLabel = '',
color_up=0.7, color_down=0.2, color_center="white"):
DEFAULT_COLOR_SATURATION = 0.5
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex( tuple(map(lambda x: int(x*255),
colorsys.hls_to_rgb(h, l, s))))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
# Calculate max gradient value from the ClusterTree matrix
maxv = abs(center_value - tree.arraytable._matrix_max)
minv = abs(center_value - tree.arraytable._matrix_min)
if center_value <= tree.arraytable._matrix_min:
MAX_VALUE = minv + maxv
else:
MAX_VALUE = max(maxv, minv)
# Add heatmap colors to tree
cols_add_before_heat = 0
if nameMap:
cols_add_before_heat = 1
for lf in tree:
if nameMap:
longNameFace = faces.TextFace(nameMap.get(lf.name, lf.name))
lf.add_face(longNameFace, column=0, position="aligned")
for i, value in enumerate(getattr(lf, "profile", [])):
if value > center_value:
color = gradient_color(abs(center_value - value), MAX_VALUE,
hue=color_up)
elif value < center_value:
color = gradient_color(abs(center_value - value), MAX_VALUE,
hue=color_down)
else:
color = color_center
lf.add_face(RectFace(20, 20, color, color), position="aligned",
column=i+cols_add_before_heat)
# Uncomment to add numeric values to the matrix
#lf.add_face(TextFace("%0.2f "%value, fsize=5), position="aligned", column=i)
lf.add_face(nameFace, column=i+cols_add_before_heat+1, position="aligned")
if nameMap and nameLabel:
nameF = TextFace(nameLabel, fsize=7)
#nameF.rotation = -90
tree_style.aligned_header.add_face(nameF, column=0)
# Add header
for i, name in enumerate(header):
nameF = TextFace(name, fsize=7)
nameF.rotation = -90
tree_style.aligned_header.add_face(nameF, column=i+cols_add_before_heat)
#-------------END setup_heatmap----------------------------------------------读入矩阵 （可把文后的测试矩阵存储到文件中读入）
矩阵需满足三个条件：
data = pd.read_table("matrix", header=0, index_col=0)
data.index.name = "#Names" #修改第一行的名字使其符合ETE的要求
data_mat = data.to_csv(None, sep=" ", float_format="%.2f")
header = list(data.columns.values) #获取列的名字用于标记
datacol1 | col2 | col3 | col4 | col5 | col6 | col7 | |
#Names | |||||||
A | -1.23 | -0.81 | 1.79 | 0.78 | -0.42 | -0.69 | 0.58 |
B | -1.76 | -0.94 | 1.16 | 0.36 | 0.41 | -0.35 | 1.12 |
C | -2.19 | 0.13 | 0.65 | -0.51 | 0.52 | 1.04 | 0.36 |
D | -1.22 | -0.98 | 0.79 | -0.76 | -0.29 | 1.54 | 0.93 |
E | -1.47 | -0.83 | 0.85 | 0.07 | -0.81 | 1.53 | 0.65 |
F | -1.04 | -1.11 | 0.87 | -0.14 | -0.80 | 1.74 | 0.48 |
G | -1.57 | -1.17 | 1.29 | 0.23 | -0.20 | 1.17 | 0.26 |
data_mat'#Names col1 col2 col3 col4 col5 col6 col7
A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58
B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12
C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36
D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93
E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65
F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48
G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26
'header['col1', 'col2', 'col3', 'col4', 'col5', 'col6', 'col7']调用函数绘制热图
t = ClusterTree(t_str, data_mat)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
setup_heatmap(t, ts, header, center_value=0, color_up=0.9, color_down=0.3, color_center="white")
t.render(file_name="%%inline", tree_style=ts)绘制热图时修改Layout
def mylayout_only(node):
#Change branch color
node.img_style["hz_line_color"] = 'orange' # change horizontal branch color
node.img_style["vt_line_color"] = 'red' # Change vertical branch color
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
newName = nameMap.get(node.name)
node.img_style["size"] = 12
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "blue"
node.img_style["bgcolor"] = colorMap[newName]
node.img_style["hz_line_color"] = 'blue' # change branch color
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 1
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "darkred"
t = ClusterTree(t_str, data_mat)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = True
ts.show_branch_support = True
ts.layout_fn = mylayout_only
setup_heatmap(t, ts, header, center_value=0, color_up=0.9, color_down=0.3,
color_center="white", nameMap=nameMap, nameLabel="Full")
t.render(file_name="%%inline", tree_style=ts)测试矩阵
## 矩阵为TAB键分割
## 矩阵每一行第一列为行名字，与树的节点对应
## 矩阵可以存储于一个文件中，也可以是如下的字符串
matrix = """
#Names col1 col2 col3 col4 col5 col6 col7
A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58
B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12
C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36
D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93
E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65
F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48
G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26
"""产生颜色的辅助函数，给定一个列表，这个函数会自动返回一个字典包含每个字段对应的颜色。
def hex2rgb(hexcolor):
return [(hexcolor>>16) & 0xff, (hexcolor>>8) & 0xff, hexcolor & 0xff]
def rgb2hex(rgbcolor):
r, g, b = rgbcolor
rgb = hex((r << 16) + (g << 8) +b)[2:].upper()
zero = '0'* (6-len(rgb))
return '#'+zero+rgb
#----------------------------------
def generateColor(labelL):
labelL = list(set(labelL))
labelL.sort()
colorD = {}
r = 255
g = 255
b = 255
len_label = int(len(labelL) / 3 + 1)
step = int(250 / len_label)
cnt = 1
for labels in labelL:
if cnt % 3 == 1:
r = r - step
elif cnt % 3 == 2:
g = g -step
else:
b = b - step
cnt += 1
color = rgb2hex([r, g, b])
colorD[labels] = color
return colorD
clan_colorD = generateColor(nameMap.values())
clan_colorD
{'American': '#ACFFFF',
'Britain': '#ACACFF',
'China': '#ACACAC',
'Dutch': '#59ACAC',
'Egypt': '#5959AC',
'France': '#595959',
'German': '#065959'}带有Support value的Newick树，供测试不同的属性使用
nw = """
(((Dre:0.008339,Dme:0.300613)1.000000:0.596401,
(Cfa:0.640858,Hsa:0.753230)1.000000:0.182035)1.000000:0.106234,
((Dre:0.271621,Cfa:0.046042)1.000000:0.953250,
(Hsa:0.061813,Mms:0.110769)1.000000:0.204419)1.000000:0.973467);关闭Virtual X-server
vdisplay.stop()https://github.com/Tong-Chen/notebook/blob/master/ETE.ipynb
原文链接 http://blog.genesino.com/2016/07/ete/
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