savefig 未保存树状图轴

Question

我正在尝试保存由大型 table（10000 多行，18 列）制成的大型树状图，我使用了这段代码

from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram, linkage
import numpy as np
import pandas as pd

data = pd.read_csv("Input.txt", header = 0, index_col = None,\
               sep = "\t", memory_map = True)
data = data.fillna(0)
Matrix = data.iloc[:,-18:]

Linkage_Matrix = linkage (Matrix, "ward")
fig=plt.figure(figsize=(20, 200))
#fig, ax = plt.subplots(1, 1, tight_layout=False)
ax = fig.add_axes([0.1,0.1,0.75,0.75])
#fig.title('Hierarchical Clustering Dendrogram')
ax.set_title("Hierarchical Clustering Dendrogram")
ax.set_xlabel("distance")
ax.set_xlabel("name")
dendrogram(
    Linkage_Matrix,
    orientation ="left",
    leaf_rotation=0., 
    leaf_font_size=12.,  
    labels = list(data.loc[:,"name"])
)    
ax.set_yticklabels(list(data.loc[:,"name"]), minor=False)
ax.yaxis.set_label_position('right')
ax.yaxis.tick_right()

plt.savefig("plt1.png", dpi = 320, format= "png", bbox_inches=None)

但不幸的是，它没有保存轴，而我留下了一些 space，如下所示：
Matplotlib savefig does not save axes
Why is my xlabel cut off in my matplotlib plot?
Matplotlib savefig image trim Plotting hierarchical clustering dendrograms for large data sets Dendrogram generated by scipy-cluster customisation 我在控制台中有一个正确的显示，我可以保存，但是 dpi 不好，理想情况下我也想切换到 svg 以便之后能够设置可读性级别。

任何见解将不胜感激

Answer 1

删除此行

ax = fig.add_axes([0.1,0.1,0.75,0.75])

并在 plt.savefig() 中设置 bbox_inches='tight' 使它对我有用。

此外，由于您使用 pandas 加载数据，请注意如何将 'name' 列声明为索引并将这些索引值用作标签。

from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram, linkage
import numpy as np
import pandas as pd


data = pd.read_csv('input.txt', header=0, index_col=['name'], sep="\t")
data = data.fillna(0)

link_matrix = linkage(data, 'ward')
fig, ax = plt.subplots(1, 1, figsize=(20,200))
ax.set_title('Hierarchical Clustering Dendrogram')
ax.set_xlabel('distance')
ax.set_ylabel('name')
dendrogram(
    link_matrix,
    orientation='left',
    leaf_rotation=0., 
    leaf_font_size=12.,  
    labels=data.index.values
)    
ax.yaxis.set_label_position('right')
ax.yaxis.tick_right()
plt.savefig('plt1.png', dpi=320, format='png', bbox_inches='tight')

savefig 未保存树状图轴

Dendrogram axes not saved by savefig

python

svg

matplotlib

labels

dendrogram