查看不同颜色的 2D DNA 行走

Question

我有兴趣创建一种 RandomWalk 形式，使用 DNA 序列创建行走（例如 T = 向上，A = 向下等）。我已经创建了代码，但是我想知道是否可以为 4 个基本字母中的每一个都分配一种颜色，而不是最终的绘图图只有一种颜色？

import matplotlib.pyplot as plt 

x = y = 0

x_values = [0]
y_values = [0]

dna_seq =  ('GGACTTCCCTATGGTGCTAACAAAGAGGCAGACAAA')


for base in dna_seq:
    if base == 'T':
        y += 1
    elif base == 'A':
        y -= 1
    elif base == 'G':
        x += 1
    elif base == 'C':
        x -= 1 
    x_values.append(x)
    y_values.append(y)
    
            

fig, ax = plt.subplots()
ax.plot(x_values, y_values, c='g')
plt.show()

Answer 1

您可以使用字典来创建颜色列表。然后，使用 plt.plot 绘制线条，使用 plt.scatter 绘制彩色点：

您的代码的改编版本：

import matplotlib.pyplot as plt 

x = y = 0

x_values = [0]
y_values = [0]

color_lookup = {'A': 'red',
         'T':'green',
         'G': 'blue',
         'C': 'orange'}


dna_seq =  ('GGACTTCCCTATGGTGCTAACAAAGAGGCAGACAAA')

colors = ['k'] # initialise starting point with black

for base in dna_seq:
    if base == 'T':
        y += 1
    elif base == 'A':
        y -= 1
    elif base == 'G':
        x += 1
    elif base == 'C':
        x -= 1 
    x_values.append(x)
    y_values.append(y)
    colors.append(color_lookup[base])
    
            

fig, ax = plt.subplots()
ax.plot(x_values, y_values, c='k')
ax.scatter(x_values, y_values, c=colors)
plt.show()

Answer 2

基于this example can be used. The idea is to split the line into sequences and then plot the lines using a LineCollection 的彩色线条。集合的每一行都可以有自己的颜色。

由于随机游走程序不止一次使用几个片段，因此必须稍微移动一些片段。

import matplotlib.pyplot as plt 

x = y = 0.
x_values = [0.]
y_values = [0.]
colors = []

dna_seq =  ('GGACTTCCCTATGGTGCTAACAAAGAGGCAGACAAA')#
color_lookup = {'A': 'red',
         'T':'green',
         'G': 'blue',
         'C': 'orange'}

for base in dna_seq:
    if base == 'T':
        y += 1
    elif base == 'A':
        y -= 1
    elif base == 'G':
        x += 1
    elif base == 'C':
        x -= 1 
    x_values.append(x)
    y_values.append(y)
    colors.append(color_lookup[base])

import numpy as np
from matplotlib.collections import LineCollection

points = np.array([x_values, y_values]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)

#handle collisions (algorithm could probably be improved :-) )
delta = 0.1
changed=True
while changed:
    changed=False
    for idx, segment in enumerate(segments):
        if idx > 0:
            cur_seg = segment.tolist()
            if cur_seg in segments[:idx-1].tolist() or [cur_seg[1], cur_seg[0]] in segments[:idx].tolist():
                if(cur_seg[0][0] == cur_seg[1][0]):
                    segment[0][0] += delta
                    segment[1][0] += delta
                else:
                    segment[0][1] += delta
                    segment[1][1] += delta
                changed=True

fig, ax = plt.subplots()
lc = LineCollection(segments, colors=colors)
lc.set_linewidth(2)
ax.add_collection(lc)

ax.set_aspect('equal')
ax.set_xlim(min(x_values)-.1, max(x_values)+.1)
ax.set_ylim(min(y_values)-.1, max(y_values)+.1)

plt.show()

查看不同颜色的 2D DNA 行走

viewing 2D DNA walk with different colours

matplotlib

random-walk