Question

我正在尝试保存一个由大表（10000多行，18列）制成的大型树形图，我附带了这段代码

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，而我留下了一些空间，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dpi不好，理想情况下我也想切换到svg以便能够设置后续的可读性水平。

非常感谢任何见解

Answer 1

删除此行

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

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

此外，由于您要使用pandas加载数据，请注意如何声明＆＃39; name＆＃39;列作为索引，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')

树形图轴未由savefig保存

1 个答案: