在远处从SciPy切割树状图/聚类树 [英] Cutting Dendrogram/Clustering Tree from SciPy at distance height
问题描述
我正在尝试使用SciPy
来学习如何在Python
中使用dendrograms
.我想获得集群并能够对其进行可视化;我听说hierarchical clustering
和dendrograms
是最好的方法.
I'm trying to learn how to use dendrograms
in Python
using SciPy
. I want to get clusters and be able to visualize them; I heard hierarchical clustering
and dendrograms
are the best way.
如何在特定距离处砍"树?
在此示例中,我只想将其剪切到距离1.6
In this example, I just want to cut it at distance 1.6
我在 https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-and-dendrogram-tutorial/#Inconsistency-Method ,但是这个家伙确实使用了一些令人困惑的包装器功能**kwargs
(他称其阈值为max_d
)
I looked up a tutorial on https://joernhees.de/blog/2015/08/26/scipy-hierarchical-clustering-and-dendrogram-tutorial/#Inconsistency-Method but the guy did some really confusing wrapper function using **kwargs
(he calls his threshold max_d
)
这是我的代码和下面的图;为了重现性,我尝试过尽其最大的注解:
Here is my code and plot below; I tried annotating it as best as I could for reproducibility:
from __future__ import print_function
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.cluster.hierarchy import dendrogram,linkage,fcluster
from scipy.spatial import distance
np.random.seed(424173239) #43984
#Dims
n,m = 20,7
#DataFrame: rows = Samples, cols = Attributes
attributes = ["a" + str(j) for j in range(m)]
DF_data = pd.DataFrame(np.random.random((n, m)), columns = attributes)
A_dist = distance.cdist(DF_data.as_matrix().T, DF_data.as_matrix().T)
#(i) . Do the labels stay in place from DF_data for me to do this?
DF_dist = pd.DataFrame(A_dist, index = attributes, columns = attributes)
#Create dendrogram
fig, ax = plt.subplots()
Z = linkage(distance.squareform(DF_dist.as_matrix()), method="average")
D_dendro = dendrogram(Z, labels = attributes, ax=ax) #create dendrogram dictionary
threshold = 1.6 #for hline
ax.axhline(y=threshold, c='k')
plt.show()
#(ii) How can I "cut" the tree by giving it a distance threshold?
#i.e. If I cut at 1.6 it would make (a5 : cluster_1 or not in a cluster), (a2,a3 : cluster_2), (a0,a1 : cluster_3), and (a4,a6 : cluster_4)
#link_1 says use fcluster
#This -> fcluster(Z, t=1.5, criterion='inconsistent', depth=2, R=None, monocrit=None)
#gives me -> array([1, 1, 1, 1, 1, 1, 1], dtype=int32)
print(
len(set(D_dendro["color_list"])), "^ # of colors from dendrogram",
len(D_dendro["ivl"]), "^ # of labels",sep="\n")
#3
#^ # of colors from dendrogram it should be 4 since clearly (a6, a4) and a5 are in different clusers
#7
#^ # of labels
link_1:如何从Python中的scipy中的链接/距离矩阵计算聚类分配?
推荐答案
对于更大的调色板,它应该可以工作:
For a bigger color palette this should work:
from scipy.cluster import hierarchy as hc
import matplotlib.cm as cm
import matplotlib.colors as col
#get a color spectrum "gist_ncar" from matplotlib cm.
#When you have a spectrum it begins with 0 and ends with 1.
#make tinier steps if you need more than 10 colors
colors = cm.gist_ncar(np.arange(0, 1, 0.1))
colorlst=[]# empty list where you will put your colors
for i in range(len(colors)): #get for your color hex instead of rgb
colorlst.append(col.to_hex(colors[i]))
hc.set_link_color_palette(colorlst) #sets the color to use.
将所有代码放在前面,它应该可以工作
Put all of that infront of your code and it should work
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