[python] 基于matplotlib实现树形图的绘制

树形图Tree diagram (代码下载)

本文旨在描述如何使用Python实现基本的树形图。要实现这样的树形图，首先需要有一个数值矩阵。每一行代表一个实体（这里是一辆汽车）。每列都是描述汽车的变量。目标是将实体聚类以了解谁与谁有共同点。python下通过scipy中hierarchy.linkage进行聚类，hierarchy.dendrogram画树形图。参考文档：https://python-graph-gallery.com/dendrogram/
该章节主要内容有：

1. 数据处理 data processing
2. 基础树形图 basic dendrogram
3. 自定义树形图 customised dendrogram
4. 彩色树形图标签 color dendrogram labels

1. 数据处理 data processing

画树形图，往往第一列是数据实体名字，即物体种类。其他列分别为物体变量。

# 导入库
import pandas as pd
from matplotlib import pyplot as plt
from scipy.cluster import hierarchy
import numpy as np

# Import the mtcars dataset from the web + keep only numeric variables
url = 'https://python-graph-gallery.com/wp-content/uploads/mtcars.csv'
df = pd.read_csv(url)
df

	model	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
0	Mazda RX4	21.0	6	160.0	110	3.90	2.620	16.46	0	1	4	4
1	Mazda RX4 Wag	21.0	6	160.0	110	3.90	2.875	17.02	0	1	4	4
2	Datsun 710	22.8	4	108.0	93	3.85	2.320	18.61	1	1	4	1
3	Hornet 4 Drive	21.4	6	258.0	110	3.08	3.215	19.44	1	0	3	1
4	Hornet Sportabout	18.7	8	360.0	175	3.15	3.440	17.02	0	0	3	2
5	Valiant	18.1	6	225.0	105	2.76	3.460	20.22	1	0	3	1
6	Duster 360	14.3	8	360.0	245	3.21	3.570	15.84	0	0	3	4
7	Merc 240D	24.4	4	146.7	62	3.69	3.190	20.00	1	0	4	2
8	Merc 230	22.8	4	140.8	95	3.92	3.150	22.90	1	0	4	2
9	Merc 280	19.2	6	167.6	123	3.92	3.440	18.30	1	0	4	4
10	Merc 280C	17.8	6	167.6	123	3.92	3.440	18.90	1	0	4	4
11	Merc 450SE	16.4	8	275.8	180	3.07	4.070	17.40	0	0	3	3
12	Merc 450SL	17.3	8	275.8	180	3.07	3.730	17.60	0	0	3	3
13	Merc 450SLC	15.2	8	275.8	180	3.07	3.780	18.00	0	0	3	3
14	Cadillac Fleetwood	10.4	8	472.0	205	2.93	5.250	17.98	0	0	3	4
15	Lincoln Continental	10.4	8	460.0	215	3.00	5.424	17.82	0	0	3	4
16	Chrysler Imperial	14.7	8	440.0	230	3.23	5.345	17.42	0	0	3	4
17	Fiat 128	32.4	4	78.7	66	4.08	2.200	19.47	1	1	4	1
18	Honda Civic	30.4	4	75.7	52	4.93	1.615	18.52	1	1	4	2
19	Toyota Corolla	33.9	4	71.1	65	4.22	1.835	19.90	1	1	4	1
20	Toyota Corona	21.5	4	120.1	97	3.70	2.465	20.01	1	0	3	1
21	Dodge Challenger	15.5	8	318.0	150	2.76	3.520	16.87	0	0	3	2
22	AMC Javelin	15.2	8	304.0	150	3.15	3.435	17.30	0	0	3	2
23	Camaro Z28	13.3	8	350.0	245	3.73	3.840	15.41	0	0	3	4
24	Pontiac Firebird	19.2	8	400.0	175	3.08	3.845	17.05	0	0	3	2
25	Fiat X1-9	27.3	4	79.0	66	4.08	1.935	18.90	1	1	4	1
26	Porsche 914-2	26.0	4	120.3	91	4.43	2.140	16.70	0	1	5	2
27	Lotus Europa	30.4	4	95.1	113	3.77	1.513	16.90	1	1	5	2
28	Ford Pantera L	15.8	8	351.0	264	4.22	3.170	14.50	0	1	5	4
29	Ferrari Dino	19.7	6	145.0	175	3.62	2.770	15.50	0	1	5	6
30	Maserati Bora	15.0	8	301.0	335	3.54	3.570	14.60	0	1	5	8
31	Volvo 142E	21.4	4	121.0	109	4.11	2.780	18.60	1	1	4	2

# 通常获得数据表格需要将车名设置行标题，这里model代表车的类型
df = df.set_index('model')
df

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
model
Mazda RX4	21.0	6	160.0	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160.0	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108.0	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258.0	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360.0	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225.0	105	2.76	3.460	20.22	1	0	3	1
Duster 360	14.3	8	360.0	245	3.21	3.570	15.84	0	0	3	4
Merc 240D	24.4	4	146.7	62	3.69	3.190	20.00	1	0	4	2
Merc 230	22.8	4	140.8	95	3.92	3.150	22.90	1	0	4	2
Merc 280	19.2	6	167.6	123	3.92	3.440	18.30	1	0	4	4
Merc 280C	17.8	6	167.6	123	3.92	3.440	18.90	1	0	4	4
Merc 450SE	16.4	8	275.8	180	3.07	4.070	17.40	0	0	3	3
Merc 450SL	17.3	8	275.8	180	3.07	3.730	17.60	0	0	3	3
Merc 450SLC	15.2	8	275.8	180	3.07	3.780	18.00	0	0	3	3
Cadillac Fleetwood	10.4	8	472.0	205	2.93	5.250	17.98	0	0	3	4
Lincoln Continental	10.4	8	460.0	215	3.00	5.424	17.82	0	0	3	4
Chrysler Imperial	14.7	8	440.0	230	3.23	5.345	17.42	0	0	3	4
Fiat 128	32.4	4	78.7	66	4.08	2.200	19.47	1	1	4	1
Honda Civic	30.4	4	75.7	52	4.93	1.615	18.52	1	1	4	2
Toyota Corolla	33.9	4	71.1	65	4.22	1.835	19.90	1	1	4	1
Toyota Corona	21.5	4	120.1	97	3.70	2.465	20.01	1	0	3	1
Dodge Challenger	15.5	8	318.0	150	2.76	3.520	16.87	0	0	3	2
AMC Javelin	15.2	8	304.0	150	3.15	3.435	17.30	0	0	3	2
Camaro Z28	13.3	8	350.0	245	3.73	3.840	15.41	0	0	3	4
Pontiac Firebird	19.2	8	400.0	175	3.08	3.845	17.05	0	0	3	2
Fiat X1-9	27.3	4	79.0	66	4.08	1.935	18.90	1	1	4	1
Porsche 914-2	26.0	4	120.3	91	4.43	2.140	16.70	0	1	5	2
Lotus Europa	30.4	4	95.1	113	3.77	1.513	16.90	1	1	5	2
Ford Pantera L	15.8	8	351.0	264	4.22	3.170	14.50	0	1	5	4
Ferrari Dino	19.7	6	145.0	175	3.62	2.770	15.50	0	1	5	6
Maserati Bora	15.0	8	301.0	335	3.54	3.570	14.60	0	1	5	8
Volvo 142E	21.4	4	121.0	109	4.11	2.780	18.60	1	1	4	2

# 同时需要删除行标索引的标题名
del df.index.name
df

	mpg	cyl	disp	hp	drat	wt	qsec	vs	am	gear	carb
Mazda RX4	21.0	6	160.0	110	3.90	2.620	16.46	0	1	4	4
Mazda RX4 Wag	21.0	6	160.0	110	3.90	2.875	17.02	0	1	4	4
Datsun 710	22.8	4	108.0	93	3.85	2.320	18.61	1	1	4	1
Hornet 4 Drive	21.4	6	258.0	110	3.08	3.215	19.44	1	0	3	1
Hornet Sportabout	18.7	8	360.0	175	3.15	3.440	17.02	0	0	3	2
Valiant	18.1	6	225.0	105	2.76	3.460	20.22	1	0	3	1
Duster 360	14.3	8	360.0	245	3.21	3.570	15.84	0	0	3	4
Merc 240D	24.4	4	146.7	62	3.69	3.190	20.00	1	0	4	2
Merc 230	22.8	4	140.8	95	3.92	3.150	22.90	1	0	4	2
Merc 280	19.2	6	167.6	123	3.92	3.440	18.30	1	0	4	4
Merc 280C	17.8	6	167.6	123	3.92	3.440	18.90	1	0	4	4
Merc 450SE	16.4	8	275.8	180	3.07	4.070	17.40	0	0	3	3
Merc 450SL	17.3	8	275.8	180	3.07	3.730	17.60	0	0	3	3
Merc 450SLC	15.2	8	275.8	180	3.07	3.780	18.00	0	0	3	3
Cadillac Fleetwood	10.4	8	472.0	205	2.93	5.250	17.98	0	0	3	4
Lincoln Continental	10.4	8	460.0	215	3.00	5.424	17.82	0	0	3	4
Chrysler Imperial	14.7	8	440.0	230	3.23	5.345	17.42	0	0	3	4
Fiat 128	32.4	4	78.7	66	4.08	2.200	19.47	1	1	4	1
Honda Civic	30.4	4	75.7	52	4.93	1.615	18.52	1	1	4	2
Toyota Corolla	33.9	4	71.1	65	4.22	1.835	19.90	1	1	4	1
Toyota Corona	21.5	4	120.1	97	3.70	2.465	20.01	1	0	3	1
Dodge Challenger	15.5	8	318.0	150	2.76	3.520	16.87	0	0	3	2
AMC Javelin	15.2	8	304.0	150	3.15	3.435	17.30	0	0	3	2
Camaro Z28	13.3	8	350.0	245	3.73	3.840	15.41	0	0	3	4
Pontiac Firebird	19.2	8	400.0	175	3.08	3.845	17.05	0	0	3	2
Fiat X1-9	27.3	4	79.0	66	4.08	1.935	18.90	1	1	4	1
Porsche 914-2	26.0	4	120.3	91	4.43	2.140	16.70	0	1	5	2
Lotus Europa	30.4	4	95.1	113	3.77	1.513	16.90	1	1	5	2
Ford Pantera L	15.8	8	351.0	264	4.22	3.170	14.50	0	1	5	4
Ferrari Dino	19.7	6	145.0	175	3.62	2.770	15.50	0	1	5	6
Maserati Bora	15.0	8	301.0	335	3.54	3.570	14.60	0	1	5	8
Volvo 142E	21.4	4	121.0	109	4.11	2.780	18.60	1	1	4	2

2. 基础树形图 basic dendrogram

# 执行分层聚类
Z = hierarchy.linkage(df, 'ward')
# 函数原型如下：
# scipy.cluster.hierarchy.linkage(y, method='single', metric='euclidean', optimal_ordering=False)
# y输入矩阵，method聚类方法，metric距离计算方法。通常ward比较靠谱
# optimal_ordering重新排序链接矩阵，以使连续叶之间的距离最小，这样树形结构更为直观，但是计算速度变慢。
# 参数选择见：https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html

# Make the dendrogram
plt.title('Hierarchical Clustering Dendrogram')
plt.xlabel('sample index')
plt.ylabel('distance (Ward)')
# 画聚类图，常用参数labels设定横坐标下标，leaf_rotation标题旋转
# 详细使用见：https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.cluster.hierarchy.dendrogram.html
hierarchy.dendrogram(Z, labels=df.index, leaf_rotation=90);

3. 自定义树形图 customised dendrogram

• 叶标签 leaf label
• 聚类簇数 number of clusters
• 颜色 color
• 截减 truncate
• 方向 orientation

# 叶标签 leaf label
# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')
 
# Plot with Custom leaves
# 常用参数labels设定横坐标下标，leaf_rotation标题旋转，leaf_font_size设置字号
hierarchy.dendrogram(Z, leaf_rotation=90, leaf_font_size=8, labels=df.index);

# 聚类簇数 number of clusters
# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')
 
# Control number of clusters in the plot + add horizontal line.
# color_threshold设定颜色阈值，小于olor_threshold根据簇节点为一簇
hierarchy.dendrogram(Z, color_threshold=240)
# 画水平线，y纵坐标，c颜色，lw线条粗细，linestyle线形
plt.axhline(y=240, c='grey', lw=1, linestyle='dashed');

# 颜色 color
# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')

# Set the colour of the cluster here: 设置聚类颜色
hierarchy.set_link_color_palette(['#b30000','#996600', '#b30086'])
 
# Make the dendrogram and give the colour above threshold
# above_threshold_color设置color_threshold上方链接的颜色
hierarchy.dendrogram(Z, color_threshold=240, above_threshold_color='grey')
 
# Add horizontal line.
plt.axhline(y=240, c='grey', lw=1, linestyle='dashed');

# 截减 truncate
# 原始观察矩阵很大时，树形图很难读取。截断用于压缩树形图。有几种模式：
# 1 None 不执行截断
# 2 lastp lastp设置叶子节点数，最底层节点数
# 3 level 根据level设置图中层最大数
# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')
  
# method 1: lastp
# you will have 4 leaf at the bottom of the plot  
hierarchy.dendrogram(Z, truncate_mode = 'lastp', p=4);

# method 2: level
# No more than ``p`` levels of the dendrogram tree are displayed.
hierarchy.dendrogram(Z, truncate_mode = 'level', p=2);

# 方向 orientation

# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')
 
# Orientation of the dendrogram
# 设置层次树的朝向，orientation可选"top", "left", "bottom", "right"，默认top
hierarchy.dendrogram(Z, orientation="right", labels=df.index);

# Orientation of the dendrogram
hierarchy.dendrogram(Z, orientation="bottom", labels=df.index);

4. 彩色树形图标签 color dendrogram labels

# Calculate the distance between each sample
Z = hierarchy.linkage(df, 'ward')

# Make the dendro
# 画树状图
hierarchy.dendrogram(Z, labels=df.index, leaf_rotation=0, orientation="left", color_threshold=240, above_threshold_color='grey')

# Create a color palette with 3 color for the 3 cyl possibilities
# 设置渐变颜色，共三种颜色
my_palette = plt.cm.get_cmap("Accent", 3)

# transforme the 'cyl' column in a categorical variable. It will allow to put one color on each level.
# 根据cyl设置颜色参数，对参数进行分类
df['cyl']=pd.Categorical(df['cyl'])
# 获得每种汽车cyl对应的颜色
my_color=df['cyl'].cat.codes

# Apply the right color to each label
ax = plt.gca()
# 获得y轴坐标标签
xlbls = ax.get_ymajorticklabels()
num=-1
for lbl in xlbls:
    num+=1
    val=my_color[num]
    # 设置颜色
    lbl.set_color(my_palette(val))