{"id":17278240,"url":"https://github.com/saketkc/pyseqlogo","last_synced_at":"2025-04-14T08:34:41.497Z","repository":{"id":49863959,"uuid":"106945416","full_name":"saketkc/pyseqlogo","owner":"saketkc","description":"Python package to plot sequence 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figure:: https://img.shields.io/pypi/v/pyseqlogo.svg\n        :target: https://pypi.python.org/pypi/pyseqlogo\n\n.. figure:: https://img.shields.io/travis/saketkc/pyseqlogo.svg\n        :target: https://travis-ci.org/saketkc/pyseqlogo\n\n.. figure:: https://pyup.io/repos/github/saketkc/pyseqlogo/shield.svg\n     :target: https://pyup.io/repos/github/saketkc/pyseqlogo/\n     :alt: Updates\n\n\nPython package to plot sequence logos\n\n\n* Free software: MIT license\n* Documentation: http://saketkc.github.io/pyseqlogo\n* Example Notebook: https://github.com/saketkc/pyseqlogo/blob/master/notebooks/Example01.ipynb\n\n.. code:: python\n\n    from pyseqlogo.pyseqlogo import draw_logo, setup_axis\n\n\n.. code:: python\n\n    ALL_SCORES1 = [[('C', 0.02247014831444764),\n                  ('T', 0.057903843733384308),\n                  ('A', 0.10370837683591219),\n                  ('G', 0.24803586793255664)],\n                 [('T', 0.046608227674354567),\n                  ('G', 0.048827667087419063),\n                  ('A', 0.084338697696451109),\n                  ('C', 0.92994511407402669)],\n                 [('G', 0.0),\n                  ('T', 0.011098351287382456),\n                  ('A', 0.022196702574764911),\n                  ('C', 1.8164301607015951)],\n                 [('C', 0.020803153636453006),\n                  ('T', 0.078011826136698756),\n                  ('G', 0.11268374886412044),\n                  ('A', 0.65529933954826969)],\n                 [('T', 0.017393530660176126),\n                  ('A', 0.030438678655308221),\n                  ('G', 0.22611589858228964),\n                  ('C', 0.45078233627623127)],\n                 [('G', 0.022364103549245576),\n                  ('A', 0.043412671595594352),\n                  ('T', 0.097349627214363091),\n                  ('C', 0.1657574733649966)],\n                 [('C', 0.03264675899941203),\n                  ('T', 0.045203204768416654),\n                  ('G', 0.082872542075430544),\n                  ('A', 1.0949220710572034)],\n                 [('C', 0.0),\n                  ('T', 0.0076232429756614498),\n                  ('A', 0.011434864463492175),\n                  ('G', 1.8867526364762088)],\n                 [('C', 0.0018955903000026028),\n                  ('T', 0.0094779515000130137),\n                  ('A', 0.35637097640048931),\n                  ('G', 0.58005063180079641)],\n                 [('A', 0.01594690817903021),\n                  ('C', 0.017541598996933229),\n                  ('T', 0.2774762023151256),\n                  ('G', 0.48638069946042134)],\n                 [('A', 0.003770051401807444),\n                  ('C', 0.0075401028036148881),\n                  ('T', 0.011310154205422331),\n                  ('G', 1.8624053924928772)],\n                 [('C', 0.036479877757360731),\n                  ('A', 0.041691288865555121),\n                  ('T', 0.072959755514721461),\n                  ('G', 1.1517218549109602)],\n                 [('G', 0.011831087684038642),\n                  ('T', 0.068620308567424126),\n                  ('A', 0.10174735408273231),\n                  ('C', 1.0009100180696691)],\n                 [('C', 0.015871770937774379),\n                  ('T', 0.018757547471915176),\n                  ('A', 0.32176408355669878),\n                  ('G', 0.36505073156881074)],\n                 [('A', 0.022798100897300954),\n                  ('T', 0.024064662058262118),\n                  ('G', 0.24571286522646588),\n                  ('C', 0.34070495229855319)]]\n\nDefault mode is bits\n====================\n\n.. code:: python\n\n    plt.rcParams['figure.dpi'] = 300\n    fig, axarr = draw_logo(ALL_SCORES1)\n    fig.tight_layout()\n\n.. figure:: examples/output_3_0.png\n   :align: center\n   :width: 100%\n   :figclass: align center\n\n\nColorscheme\n===========\n\n.. code:: python\n\n    plt.rcParams['figure.dpi'] = 300\n    fig, axarr = draw_logo(ALL_SCORES1, data_type='bits', colorscheme='meme')\n    fig.tight_layout()\n\n.. figure:: docs/images/output_5_0.png\n   :align: center\n   :width: 100%\n   :figclass: align center\n\n\nCounts as input\n===============\n\n.. code:: python\n\n    counts = {'A' : [3,4,5,6], 'C': [2,3,1,1], 'T': [2,1,3,1], 'G': [3,2,1,2]}\n    fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability')\n    fig.tight_layout()\n\n.. figure:: docs/images/output_7_0.png\n   :align: center\n   :width: 100%\n   :figclass: align center\n\n\nDifferent font!\n===============\n\n.. code:: python\n\n    fig, axarr = draw_logo(counts, data_type='counts', yaxis='probability', fontfamily='Comic Sans MS')\n    fig.tight_layout()\n\n.. figure:: docs/images/output_9_0.png\n   :align: center\n   :width: 100%\n   :figclass: align center\n\nPlot conservation scores\n========================\n\n.. code:: python\n\n    ALL_SCORES = [[('G', 0.1),\n                  ('A', 0.1),\n                  ('C', 0.31312908494534769),\n                  ('T', 0.84220926295645249)]] * 4\n    stem_scores = np.random.rand(4)\n    fig, axarr = draw_logo(ALL_SCORES, data_type='bits', nrow= 2,ncol=1)\n    axarr[1,0].stem(range(1, len(ALL_SCORES)+1), stem_scores)\n    setup_axis(axarr[1,0], axis='y', majorticks=1, minorticks=0.1)\n    fig.tight_layout()\n\n.. figure:: docs/images/output_11_0.png\n   :align: center\n   :width: 100%\n   :figclass: align center\n\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _notebook: notebooks/Example01.ipynb\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaketkc%2Fpyseqlogo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaketkc%2Fpyseqlogo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaketkc%2Fpyseqlogo/lists"}