zhou-ran/pyseqlogo

Python package to plot sequence logos

pyseqlogo

Python package to plot sequence logos

• Free software: MIT license
• Documentation: http://saketkc.github.io/pyseqlogo
• Example Notebook: https://github.com/saketkc/pyseqlogo/blob/master/notebooks/Example01.ipynb

from pyseqlogo.pyseqlogo import draw_logo, setup_axis

ALL_SCORES1 = [[('C', 0.02247014831444764),
              ('T', 0.057903843733384308),
              ('A', 0.10370837683591219),
              ('G', 0.24803586793255664)],
             [('T', 0.046608227674354567),
              ('G', 0.048827667087419063),
              ('A', 0.084338697696451109),
              ('C', 0.92994511407402669)],
             [('G', 0.0),
              ('T', 0.011098351287382456),
              ('A', 0.022196702574764911),
              ('C', 1.8164301607015951)],
             [('C', 0.020803153636453006),
              ('T', 0.078011826136698756),
              ('G', 0.11268374886412044),
              ('A', 0.65529933954826969)],
             [('T', 0.017393530660176126),
              ('A', 0.030438678655308221),
              ('G', 0.22611589858228964),
              ('C', 0.45078233627623127)],
             [('G', 0.022364103549245576),
              ('A', 0.043412671595594352),
              ('T', 0.097349627214363091),
              ('C', 0.1657574733649966)],
             [('C', 0.03264675899941203),
              ('T', 0.045203204768416654),
              ('G', 0.082872542075430544),
              ('A', 1.0949220710572034)],
             [('C', 0.0),
              ('T', 0.0076232429756614498),
              ('A', 0.011434864463492175),
              ('G', 1.8867526364762088)],
             [('C', 0.0018955903000026028),
              ('T', 0.0094779515000130137),
              ('A', 0.35637097640048931),
              ('G', 0.58005063180079641)],
             [('A', 0.01594690817903021),
              ('C', 0.017541598996933229),
              ('T', 0.2774762023151256),
              ('G', 0.48638069946042134)],
             [('A', 0.003770051401807444),
              ('C', 0.0075401028036148881),
              ('T', 0.011310154205422331),
              ('G', 1.8624053924928772)],
             [('C', 0.036479877757360731),
              ('A', 0.041691288865555121),
              ('T', 0.072959755514721461),
              ('G', 1.1517218549109602)],
             [('G', 0.011831087684038642),
              ('T', 0.068620308567424126),
              ('A', 0.10174735408273231),
              ('C', 1.0009100180696691)],
             [('C', 0.015871770937774379),
              ('T', 0.018757547471915176),
              ('A', 0.32176408355669878),
              ('G', 0.36505073156881074)],
             [('A', 0.022798100897300954),
              ('T', 0.024064662058262118),
              ('G', 0.24571286522646588),
              ('C', 0.34070495229855319)]]

Default mode is bits

plt.rcParams['figure.dpi'] = 300
fig, axarr = draw_logo(ALL_SCORES1)
fig.tight_layout()

Colorscheme

plt.rcParams['figure.dpi'] = 300
fig, axarr = draw_logo(ALL_SCORES1, data_type='bits', colorscheme='meme')
fig.tight_layout()

Counts as input

counts = {'A' : [3,4,5,6], 'C': [2,3,1,1], 'T': [2,1,3,1], 'G': [3,2,1,2]}
fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability')
fig.tight_layout()

Different font!

fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability', fontfamily='Comic Sans MS')
fig.tight_layout()

Plot conservation scores

ALL_SCORES = [[('G', 0.1),
              ('A', 0.1),
              ('C', 0.31312908494534769),
              ('T', 0.84220926295645249)]] * 4
stem_scores = np.random.rand(4)
fig, axarr = draw_logo(ALL_SCORES, data_type='bits', nrow= 2,ncol=1)
axarr[1,0].stem(range(1, len(ALL_SCORES)+1), stem_scores)
setup_axis(axarr[1,0], axis='y', majorticks=1, minorticks=0.1)
fig.tight_layout()

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.