{ "info": { "author": "Philipp Schlegel", "author_email": "pms70@cam.ac.uk", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "tanglegram\n==========\nUses scipy and matplotlib to plot simple tanglegrams. Inspired by the amazing [dendextend](https://github.com/talgalili/dendextend) by Tal Galili.\n\n## Installation\nI recommend using [Python Packaging Index (PIP)](https://pypi.python.org/pypi) to install the package.\nFirst, get [PIP](https://pip.pypa.io/en/stable/installing/) and then run in terminal:\n\n`pip install git+git://github.com/schlegelp/tanglegram@master`\n\nThis command should also work to update the package.\n\n**Attention**: on Windows, the dependencies (i.e. Numpy, Pandas and SciPy) will likely fail to install automatically. Your best bet is to get a Python distribution that already includes them (e.g. [Anaconda](https://www.continuum.io/downloads)).\n\nIf your default distribution is Python 2, you have to explicitly tell [PIP](https://pip.pypa.io/en/stable/installing/) to install for Python 3:\n\n`pip3 install git+git://github.com/schlegelp/tanglegram@master`\n\n#### External libraries used:\nInstalling via [PIP](https://pip.pypa.io/en/stable/installing/) should install all external dependencies. You may run into problems on Windows though. In that case, you need to install dependencies manually, here is a list of dependencies (check out `install_requires` in [setup.py](https://raw.githubusercontent.com/schlegelp/PyMaid/master/setup.py) for version info):\n\n- [Pandas](http://pandas.pydata.org/)\n- [SciPy](http://www.scipy.org)\n- [Numpy](http://www.scipy.org)\n- [Matplotlib](http://www.matplotlib.org)\n- [Tqdm](https://pypi.python.org/pypi/tqdm)\n\n## Quickstart:\n\n```python\nimport tanglegram as tg\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport pandas as pd\n\n# Generate two distance matrices and just switch labels in one\nlabelsA= ['A', 'B', 'C', 'D']\nlabelsB= ['B', 'A', 'C', 'D']\ndata = [[ 0, .1, .4, .3],\n [.1, 0, .5, .6],\n [ .4, .5, 0, .2],\n [ .3, .6, .2, 0]]\n\nmat1 = pd.DataFrame(data,\n columns=labelsA,\n index=labelsA)\n\nmat2 = pd.DataFrame(data,\n columns=labelsB,\n index=labelsB)\n\n# Plot tanglegram\nfig = tg.gen_tangle(mat1, mat2, optimize_order=False)\nplt.show()\n\n# Plot again but this time try minimizing cross-over\nfig = tg.gen_tangle(mat1, mat2, optimize_order=1000)\nplt.show()\n```\n\n\n\n## Known Issues:\n* layout does not scale well, i.e. small dendrograms look weird\n\n## License:\nThis code is under GNU GPL V3\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/schlegelp/tanglegram", "keywords": "python tanglegram dendrogram", "license": "GNU GPL V3", "maintainer": "", "maintainer_email": "", "name": "tanglegram", "package_url": "https://pypi.org/project/tanglegram/", "platform": "", "project_url": "https://pypi.org/project/tanglegram/", "project_urls": { "Homepage": "https://github.com/schlegelp/tanglegram" }, "release_url": "https://pypi.org/project/tanglegram/0.1.0/", "requires_dist": [ "scipy (>=0.18.1)", "numpy (>=1.12.1)", "pandas", "matplotlib (>=2.0.0)", "tqdm" ], "requires_python": ">=3", "summary": "Plots simple tanglegrams 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