.ipynb .pdf

Binder

Logo

import numpy as np
import pandas as pd

pfm = pd.DataFrame(np.random.randint(10,1000,(10,4)),columns=list('ACGT'))

pfm = [[0,0.8,0.2,0,],
      [0,0.2,0.8,0,],
       [0,0.8,0.2,0,],
       [0.3,0.3,0.4,0,],
      [0.2,0.4,0.3,0.1,],
      [0.0,0.2,0.8,0.0,],
      [0.0,0.8,0.2,0.0,],
      [0.0,0.2,0.8,0.0,],]
pfm = pd.DataFrame(pfm,columns=list('ACGT'))

pfm

	A	C	G	T
0	0.0	0.8	0.2	0.0
1	0.0	0.2	0.8	0.0
2	0.0	0.8	0.2	0.0
3	0.3	0.3	0.4	0.0
4	0.2	0.4	0.3	0.1
5	0.0	0.2	0.8	0.0
6	0.0	0.8	0.2	0.0
7	0.0	0.2	0.8	0.0

import seqlogo
def logo(a):
    pfm = a.copy()
    a = pfm.sum(axis=1)
    for allele in 'ACGT':
        pfm[allele] = pfm[allele]/a
    pwm = seqlogo.pfm2pwm(pfm.values)
    pwm = seqlogo.Pwm(pwm)
    ppm = seqlogo.pwm2ppm(pwm)
    ppm = seqlogo.Ppm(ppm.values)
    a = seqlogo.seqlogo(ppm, ic_scale = True, format = 'png', size = 'large')
    cpm = seqlogo.CompletePm(ppm = ppm)
    print(cpm.consensus)
    return a

logo(pfm)

CGCGCGCG

logo(pfm[:4])

CGCG

Manhattan & QQ plot