Question

我有以下工作代码。

from matplotlib import pyplot as plt
import numpy as np
from matplotlib_venn import venn3, venn3_circles
Gastric_tumor_promoters = set(['DPEP1', 'CDC42BPA', 'GNG4', 'RAPGEFL1', 'MYH7B', 'SLC13A3', 'PHACTR3', 'SMPX', 'NELL2', 'PNMAL1', 'KRT23', 'PCP4', 'LOX', 'CDC42BPA'])

Ovarian_tumor_promoters = set(['ABLIM1','CDC42BPA','VSNL1','LOX','PCP4','SLC13A3'])

Gastric_tumor_suppressors = set(['PLCB4', 'VSNL1', 'TOX3', 'VAV3'])
#Ovarian_tumor_suppressors = set(['VAV3', 'FREM2', 'MYH7B', 'RAPGEFL1', 'SMPX', 'TOX3'])
venn3([Gastric_tumor_promoters,Ovarian_tumor_promoters, Gastric_tumor_suppressors], ('GCPromoters', 'OCPromoters', 'GCSuppressors'))

venn3([Gastric_tumor_promoters,Ovarian_tumor_promoters, Gastric_tumor_suppressors], ('GCPromoters', 'OCPromoters', 'GCSuppressors'))
plt.show()

如何在这3个圈子中显示每个组的内容？颜色alpha为0.6。圆圈必须更大才能容纳所有符号。

Answer 1

我不确定是否有一种简单的方法可以自动完成任何可能的组合组合。如果您准备在特定示例中进行一些手动调整，请从以下内容开始：

A = set(['DPEP1', 'CDC42BPA', 'GNG4', 'RAPGEFL1', 'MYH7B', 'SLC13A3', 'PHACTR3', 'SMPX', 'NELL2', 'PNMAL1', 'KRT23', 'PCP4', 'LOX', 'CDC42BPA'])
B = set(['ABLIM1','CDC42BPA','VSNL1','LOX','PCP4','SLC13A3'])
C = set(['PLCB4', 'VSNL1', 'TOX3', 'VAV3'])

v = venn3([A,B,C], ('GCPromoters', 'OCPromoters', 'GCSuppressors'))

v.get_label_by_id('100').set_text('\n'.join(A-B-C))
v.get_label_by_id('110').set_text('\n'.join(A&B-C))
v.get_label_by_id('011').set_text('\n'.join(B&C-A))
v.get_label_by_id('001').set_text('\n'.join(C-A-B))
v.get_label_by_id('010').set_text('')
plt.annotate(',\n'.join(B-A-C), xy=v.get_label_by_id('010').get_position() +
             np.array([0, 0.2]), xytext=(-20,40), ha='center',
             textcoords='offset points', 
             bbox=dict(boxstyle='round,pad=0.5', fc='gray', alpha=0.1),
             arrowprops=dict(arrowstyle='->',              
                             connectionstyle='arc',color='gray'))

请注意，像v.get_label_by_id('001')这样的方法会返回matplotlib Text对象，您可以根据自己的喜好自由配置它们（例如，您可以通过调用set_fontsize(8)等来更改字体大小）。

Answer 2

这是一个使整个过程自动化的示例。它会创建一个临时词典，其中包含venn所需的id作为键以及该id的所有参与集的交集。

如果您不希望对标签进行排序，请删除倒数第二行中的sorted（）调用。

import math
from matplotlib import pyplot as plt
from matplotlib_venn import venn2, venn3
import numpy as np

# Convert number to indices into binary
# e.g. 5 -> '101' > [2, 0]
def bits2indices(b):
    l = []
    if b == 0:
        return l
    for i in reversed(range(0, int(math.log(b, 2)) + 1)):
        if b & (1 << i):
            l.append(i)
    return l

# Make dictionary containing venn id's and set intersections
# e.g. d = {'100': {'c', 'b', 'a'}, '010': {'c', 'd', 'e'}, ... }
def set2dict(s):
    d = {}
    for i in range(1, 2**len(s)):
        # Make venn id strings
        key = bin(i)[2:].zfill(len(s))
        key = key[::-1]
        ind = bits2indices(i)
        # Get the participating sets for this id
        participating_sets = [s[x] for x in ind] 
        # Get the intersections of those sets
        inter = set.intersection(*participating_sets)
        d[key] = inter
    return d

# Define some sets
a = set(['a', 'b', 'c']) 
b = set(['c', 'd', 'e'])
c = set(['e', 'f', 'a'])
s = [a, b, c]

# Create dictionary from sets
d = set2dict(s)

# Plot it
h = venn3(s, ('A', 'B', 'C'))
for k, v in d.items():
    l = h.get_label_by_id(k)
    if l:
        l.set_text('\n'.join(sorted(v)))
plt.show()

/编辑对不起，我刚刚发现以上代码并未删除重复的标签，因此是错误的。 venn表示的元素数和标签数不同。这是一个新版本，可从其他路口删除错误的重复项。我想有一种更聪明，更实用的方法来执行此操作，而不是遍历所有路口两次……

import math, itertools
from matplotlib import pyplot as plt
from matplotlib_venn import venn2, venn3
import numpy as np

# Generate list index for itertools combinations
def gen_index(n):
    x = -1
    while True:       
        while True:
            x = x + 1
            if bin(x).count('1') == n:
                break
        yield x

# Generate all combinations of intersections
def make_intersections(sets):
    l = [None] * 2**len(sets)
    for i in range(1, len(sets) + 1):
        ind = gen_index(i)
        for subset in itertools.combinations(sets, i):
            inter = set.intersection(*subset)
            l[next(ind)] = inter
    return l

# Get weird reversed binary string id for venn
def number2venn_id(x, n_fill):
    id = bin(x)[2:].zfill(n_fill)
    id = id[::-1]
    return id

# Iterate over all combinations and remove duplicates from intersections with
# more sets
def sets2dict(sets):
    l = make_intersections(sets)
    d = {}
    for i in range(1, len(l)):
        d[number2venn_id(i, len(sets))] = l[i]
        for j in range(1, len(l)):
            if bin(j).count('1') < bin(i).count('1'):
                l[j] = l[j] - l[i]
                d[number2venn_id(j, len(sets))] = l[j] - l[i]
    return d

# Define some sets
a = set(['a', 'b', 'c', 'f']) 
b = set(['c', 'd', 'e'])
c = set(['e', 'f', 'a'])
sets = [a, b, c]

d = sets2dict(sets)

# Plot it
h = venn3(sets, ('A', 'B', 'C'))
for k, v in d.items():
   l = h.get_label_by_id(k)
   if l:
       l.set_fontsize(12)
       l.set_text('\n'.join(sorted(v)))

# Original for comparison
f = plt.figure(2)
venn3(sets, ('A', 'B', 'C'))  
plt.show()

Python：维恩图：如何显示图表内容？

2 个答案: