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Python package to plot sequence logos

Home Page: https://www.saket-choudhary.me/pyseqlogo/

License: MIT License

Makefile 0.27% Python 99.73%

sequence-logo motif motif-analysis tfs

pyseqlogo's Introduction

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.

pyseqlogo's People

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stella-gao grassking100 nrkssa mrlgb aerijman zhou-ran ruixiangliu qw12563 rochoa85 shanring biogeek dchandran ram-nagar y9c netratvasheel danyunghsu hjanime

pyseqlogo's Issues

Hello, can't the position weight matrix be 0?

counts = {'A' : [0,4,5,0], 'C': [2,3,5,0], 'T': [2,1,0,1], 'G': [0,2,1,2]}
fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability')
fig.tight_layout()
plt.show()

Hello, can't the position weight matrix be 0? When I run a file containing 0 matrix, I get the following warning. What should I do ? ? ?

warning is this

RuntimeWarning: divide by zero encountered in log2
-pfm[b][l] * np.nan_to_num(np.log2(pfm[b][l])) for b in bases

Failure to plot logos when using pdf renderer

pyseqlogo version: commit bda975f
Python version: Python 3.7.9
Operating System: MX Linux 17 (Debian-based distribution)

Description

I wanted to try draw_logo from within an automated pipeline, where, for some reason, I had to set a pdf renderer for matplotlib, and draw_logo crashed on line 127 of pyseqlogo.py:

    126             window_ext = txt.get_window_extent(
--> 127                 txt._renderer)  #(fig.canvas.renderer) #txt._renderer)

What I Did

Here is a minimum example to reproduce the crash:

>>> import matplotlib as mpl
>>> mpl.use("PDF")
>>> from pyseqlogo.pyseqlogo import draw_logo
>>> data = {"A": [5, 5, 5, 5], "C": [5, 5, 5, 5], "G": [5, 5, 5, 5], "T": [5, 5, 5, 5]}
>>> fig, axes = draw_logo(data, data_type="counts")
RuntimeError                              Traceback (most recent call last)
<ipython-input-5-5a59f0cf5a0b> in <module>
----> 1 fig, axes = draw_logo(data, data_type="counts")

/usr/local/lib/python3.7/site-packages/pyseqlogo/pyseqlogo.py in draw_logo(data, data_type, seq_type, yaxis, colorscheme, nrow, ncol, padding, draw_range, coordinate_type, draw_axis, fontfamily, debug, ax)
    364         else:
    365             xshifts_list = _draw_text_data_coord(
--> 366                 ic, ax, fontfamily, colorscheme, draw_axis=draw_axis)
    367     else:
    368         if yaxis == 'probability':

/usr/local/lib/python3.7/site-packages/pyseqlogo/pyseqlogo.py in _draw_text_data_coord(height_matrix, ax, fontfamily, colorscheme, scalex, draw_axis, debug)
    125             fig.canvas.draw()
    126             window_ext = txt.get_window_extent(
--> 127                 txt._renderer)  #(fig.canvas.renderer) #txt._renderer)
    128             if basescore > 0.3:
    129                 yshift = window_ext.height * basescore  #- fontsize/10# fontsize/4#/1.20 #*.85 #* fig.dpi/72.0

/usr/local/lib/python3.7/site-packages/matplotlib/text.py in get_window_extent(self, renderer, dpi)
    895             self._renderer = self.figure._cachedRenderer
    896         if self._renderer is None:
--> 897             raise RuntimeError('Cannot get window extent w/o renderer')
    898 
    899         with cbook._setattr_cm(self.figure, dpi=dpi):

RuntimeError: Cannot get window extent w/o renderer

Unable to draw all seqlogo

When I draw the diagram, I can’t draw all of the sequence, only the first four letters can be displayed

counts = {'A': [1, 10, 17, 13, 3, 7, 0, 27, 27, 27, 0, 27, 16, 7], 'G': [10, 7, 4, 5, 11, 0, 0, 0, 0, 0, 25, 0, 4, 4], 'C': [7, 5, 2, 5, 8, 20, 0, 0, 0, 0, 0, 0, 2, 6], 'T': [9, 5, 4, 5, 0, 0, 27, 0, 0, 0, 2, 0, 5, 10]}
fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability')
fig.tight_layout()

##warning
UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations.
fig.tight_layout()

[feature] Add support for amino acid

It's seemed only support 'ATCG', if can support amino acid will be very benefited

set up a dynamic y-axis for applicable data

Hello, pyselogo is very suitable for my drawing needs. I am very happy to be able to quote pygenome. What is the function to change the y-axis scale range? I want to set up a dynamic y-axis for applicable data. I hope to get your help. Thank you very much!

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

installing：ERROR: No matching distribution found for pyseqlogo

When installing the pyseqlogo package, I encountered a problem:
ERROR: No matching distribution found for pyseqlogo