scipy.cluster.hierarchy.dedrogram "above_threshold_color=above_threshold_color" 中的错误
Error in scipy.cluster.hierarchy.dedrogram "above_threshold_color=above_threshold_color"
我正在尝试使用 scipy 0.18.1（在 mac 上）在 Python 3.5 中可视化树状图，代码如下：
import numpy as np
import pandas as pd
import scipy as sci
from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram, linkage
from scipy.cluster.hierarchy import cophenet
from scipy.spatial.distance import pdist
data = pd.read_csv("data.csv", header = 0)
data_clean = data.dropna()
cluster = data_clean[['HI','GO', 'PA', 'TE', 'GC', 'FU', 'LA']]
cluster = np.array(cluster)
cluster
data_dist = pdist(cluster)
data_link = linkage(data_dist)
plt.figure(figsize=(25, 10))
plt.title('Hierarchical Clustering Dendrogram')
plt.xlabel('sample index')
plt.ylabel('distance')
dendrogram(data_link)
但是returns这个错误
---------------------------------------------------------------------------
RecursionError Traceback (most recent call last)
<ipython-input-14-57671852a042> in <module>()
1 plt.figure(figsize=(7, 5))
----> 2 dendrogram(data_link)#, labels= ('HI','GO', 'PA', 'TE', 'GC', 'FU', 'LA'))
3 plt.title('Hierarchical Clustering Dendrogram')#'Dendrograma de Clusterización Jerárquiza')
4 plt.xlabel('sample index')#'Islas')
5 plt.ylabel('distance')#'Disimilitud de Jaccard')
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in dendrogram(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, no_plot, no_labels, leaf_font_size, leaf_rotation, leaf_label_func, show_contracted, link_color_func, ax, above_threshold_color)
2289 contraction_marks=contraction_marks,
2290 link_color_func=link_color_func,
-> 2291 above_threshold_color=above_threshold_color)
2292
2293 if not no_plot:
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info
levellevel contraction_markscontraction_marks
link_color_funclink_color_func
实际上，在错误报告中，max_dist = max(uamd, ubmd, h)的块重复了太多次。分析似乎工作正常，但我无法绘制树状图。可能是什么错误？
我已经解决了。我只需要转置我的数据。错误是指我的集群中有太多组；因此，Python 没有足够的颜色来可视化它们。
我正在尝试使用 scipy 0.18.1（在 mac 上）在 Python 3.5 中可视化树状图，代码如下：
import numpy as np
import pandas as pd
import scipy as sci
from matplotlib import pyplot as plt
from scipy.cluster.hierarchy import dendrogram, linkage
from scipy.cluster.hierarchy import cophenet
from scipy.spatial.distance import pdist
data = pd.read_csv("data.csv", header = 0)
data_clean = data.dropna()
cluster = data_clean[['HI','GO', 'PA', 'TE', 'GC', 'FU', 'LA']]
cluster = np.array(cluster)
cluster
data_dist = pdist(cluster)
data_link = linkage(data_dist)
plt.figure(figsize=(25, 10))
plt.title('Hierarchical Clustering Dendrogram')
plt.xlabel('sample index')
plt.ylabel('distance')
dendrogram(data_link)
但是returns这个错误
---------------------------------------------------------------------------
RecursionError Traceback (most recent call last)
<ipython-input-14-57671852a042> in <module>()
1 plt.figure(figsize=(7, 5))
----> 2 dendrogram(data_link)#, labels= ('HI','GO', 'PA', 'TE', 'GC', 'FU', 'LA'))
3 plt.title('Hierarchical Clustering Dendrogram')#'Dendrograma de Clusterización Jerárquiza')
4 plt.xlabel('sample index')#'Islas')
5 plt.ylabel('distance')#'Disimilitud de Jaccard')
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in dendrogram(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, no_plot, no_labels, leaf_font_size, leaf_rotation, leaf_label_func, show_contracted, link_color_func, ax, above_threshold_color)
2289 contraction_marks=contraction_marks,
2290 link_color_func=link_color_func,
-> 2291 above_threshold_color=above_threshold_color)
2292
2293 if not no_plot:
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info(Z, p, truncate_mode, color_threshold, get_leaves, orientation, labels, count_sort, distance_sort, show_leaf_counts, i, iv, ivl, n, icoord_list, dcoord_list, lvs, mhr, current_color, color_list, currently_below_threshold, leaf_label_func, level, contraction_marks, link_color_func, above_threshold_color)
2577 level=level + 1, contraction_marks=contraction_marks,
2578 link_color_func=link_color_func,
-> 2579 above_threshold_color=above_threshold_color)
2580
2581 max_dist = max(uamd, ubmd, h)
/Users/Irbin/anaconda/lib/python3.5/site-packages/scipy/cluster/hierarchy.py in _dendrogram_calculate_info
levellevel contraction_markscontraction_marks
link_color_funclink_color_func
实际上，在错误报告中，max_dist = max(uamd, ubmd, h)的块重复了太多次。分析似乎工作正常，但我无法绘制树状图。可能是什么错误？
我已经解决了。我只需要转置我的数据。错误是指我的集群中有太多组；因此，Python 没有足够的颜色来可视化它们。