viewing 2D DNA walk with different colours

Question

I am interested in creating a form of RandomWalk, using DNA sequence to create the walk (eg T = up, A = down etc). I have created the code, however i am wanting to know if it is possible for each of the 4 base letters to be assigned a colour instead of the final plot graph only being in one colour?

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()

score 1 · Answer 1 · answered Jun 05 '21 at 21:22

You can use a dictionary to create a list of colors. Then, use plt.plot to plot the lines, and plt.scatter for coloured dots:

Adapted version of your code:

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()

score 0 · Accepted Answer · answered Jun 06 '21 at 15:59

A multicolored line based on this example can be used. The idea is to split the line into sequences and then plot the lines using a LineCollection. Each line of the collection can have is own color.

As the random walker uses a few segments more than once, some of the segments have to be shifted a bit.

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()

viewing 2D DNA walk with different colours

2 Answers2