{
    "info": {
        "author": "FEI YUAN",
        "author_email": "yuanfeifuzzy@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "plottree\n========\n\n``plottree`` is a command line tool written in Python, building on to of\n``matplotlib`` and ``Biopython.Phylo`` module. It is designed for\nquickly visualize phylogenetic tree via a single command in terminal. Both\ntext file or string (surrounded by double quotes) in NEWICK format is\naccepted as input. Several optional parameters are also accepted for\nfine tuning the tree figure a little bit. If you just want to take a quick view\nof a phylogenetic relationships of a tree file or from a tree string,\n``plottree`` is the right tool for you, otherwise, please consider to use other\nvisualization tools (e.g., TreeView, iTOL, ...) if you care more about real\nvisualization and want to make more fancy figures.\n\nUsage\n=====\n\nOnce ``plottree`` was successfully installed and its executable can be found in\nyou system's search path, you can type ``plottree`` or ``plottree -h`` in\nterminal to check the short help message for how to use ``plottree``. If you\nneed more examples of how to use ``plottree``, after reading the help message,\nyou can jump to the ``Examples`` part to learn more about efficently using\n``plottree``.\n\n::\n\n    $ plottree\n    PLOTTREE - Plot a phylogenetic tree with just a single line of code.\n\n    Usage: plottree TREE [options]\n\n    positional arguments:\n      TREE                  A tree in NEWCIK format file or string (surrounded by\n                            double quotes).\n\n    optional arguments:\n      -h, --help            show this help message and exit.\n      -a, --axes            Display ticks for x and y axes.\n      -b, --box             Display the tree inside a box.\n      -m TOP BOTTOM LEFT RIGHT, --margin TOP BOTTOM LEFT RIGHT\n                            Set the margins of the figure, four numbers in the\n                            order of top bottom left and right.\n      -s SIZE, --size SIZE  Set the fontsize of leaf and node names.\n      -x MIN MAX, --xlim MIN MAX\n                            Set the limits for x-axis, two numbers for min and max.\n      -y MIN MAX, --ylim MIN MAX\n                            Set the limits for y-axis, two numbers for min and max.\n      -o OUTPUT, --output OUTPUT\n                            Save the figure into a file.\n\n\nExamples\n========\n\nPlot a tree in a NEWICK file::\n\n    $ plottree <newick_tree_file>\n\n    Plotting tree using the following setting:\n          fontsize (-s): 10.0\n          width (-w): 6.4\n          height (-l): 4.8\n          xlim(-x): -0.10, 2.50\n          ylim(-y): 5.80, 0.20\n      Feel free to modify them to tune the figure nice.\n\n``plottree`` will plot the tree from the file and show the tree figure in a\nwindow. In the terminal, it will display the parameters and their\ncorresponding values used for plotting the current figure. If you want to tune\nthe figure a little bit, just close the figure window and you will get your\nterminal back. Inside the terminal, retrieve the last command, add some\nadditional parameters and run the command again. Repeat and try the optional\nparameters until you get a ideal figure.\n\nPlot a tree in a NEWICK string::\n\n    $ plottree \"(((A:0.2, B:0.3):0.3,(C:0.5, D:0.3):0.2):0.3, E:0.7):1.0;\"\n\n      Plotting tree using the following setting:\n          fontsize (-s): 10.0\n          width (-w): 6.4\n          height (-l): 4.8\n          xlim(-x): -0.10, 2.50\n          ylim(-y): 5.80, 0.20\n      Feel free to modify them to tune the figure nice.\n\nSimilar as plot tree from a NEWICK file, pass a double quote surrounded NEWICK\nstring will allow you to plot tree in a even more easier way. After running the\ncommand you will see the tree was plotted in a window:\n\n.. figure:: https://raw.githubusercontent.com/iBiology/plottree/master/figures/SimpleTree.png\n    :alt: Simple tree\n    :align: center\n\n.. Note::\n\n    Double quote surrounded NEWICK string as input is required. Depending on\n    the setting of your system (more specifically, the setting of\n    ``matplotlib``), the displayed parameters may be different from what you\n    are seeing from here. No need to worry about that, just play around with\n    them, you should be easily figure out how to tune the tree figure.\n\nYou can added a black boarded for the tree figure by adding ``-b`` flag::\n\n    $ plottree \"(((A:0.2, B:0.3):0.3,(C:0.5, D:0.3):0.2):0.3, E:0.7):1.0;\"\n\n      Plotting tree using the following setting:\n          fontsize (-s): 10.0\n          width (-w): 6.4\n          height (-l): 4.8\n          xlim(-x): -0.10, 2.50\n          ylim(-y): 5.80, 0.20\n          Plot a box surrounding the tree: -b\n      Feel free to modify them to tune the figure nice.\n\nIt will show you a figure like this:\n\n.. figure:: https://raw.githubusercontent.com/iBiology/plottree/master/figures/BoxedTree.png\n    :alt: Boxed tree\n    :align: center\n\nFor big trees (or trees with several leaves), tree branches will be crowded or\neven overlapped with each other, you can tune the tree figure by several ways,\nlike decreasing fontsize (-s), increasing width (-w) and/or height (-l).\n\nAssume you plot a tree in a file (``tree.newick``) using the following command::\n\n    $ plottree tree.newick\n\nAnd the tree displayed like this:\n\n.. figure:: https://raw.githubusercontent.com/iBiology/plottree/master/figures/CrowedTree.png\n    :alt: Crowded tree\n    :align: center\n\nThen you can try to decrease the fontsize to make it looks better::\n\n    $ plottree tree.newick -s 8\n\nThis will make the tree looks like this:\n\n.. figure:: https://raw.githubusercontent.com/iBiology/plottree/master/figures/FontsizeTree.png\n    :alt: Small fontsize tree\n    :align: center\n\nYou can also try to increase the height (-l) to make the tree looks better::\n\n    $ python plottree/plottree.py tree.newick -l 8.4\n\n.. figure:: https://raw.githubusercontent.com/iBiology/plottree/master/figures/HeightTree.png\n    :alt: Figure height increased tree\n    :align: center\n\nOnce you think the tree figure is good enough, you can save it by hit the\nsave icon in the figure windows or re-run the command with ``-o <output>``\noption to save it.\n\nFeel free to tune the figure with other options to make it even better.\nHowever, ``plottree`` is not designed for generating fancy tree figures, if you\nwant to polish the tree figure and want it to be more fancy, I strongly suggest\nyou use other tree visualization tools and do not waste your time on\n``plottree``, because it is only designed for quickly visualize phylogenetic\nrelationships.\n\nInstallation\n============\n\n``plottree`` can be easily installed using ``pip``::\n\n    $ pip install plottree\n\nThis will install ``plottree`` and generate its executable script. See Q&A for\ndetails, if you run into any problem during installation.\n\nQ&A\n===\n\nQ: Do I need to have Python to use ``plottree``:\n\nA: Yes, ``plottree`` is not a standalone program, it is a Python package with an\nexecutable script made available for user once the package was installed.\n\nQ: Which Python version do I need to use? Python 2 or 3?\n\nA: It does not matter, it works well under both version. However, I do\nrecommend you to use Python 3 for future compatibility.\n\nQ: Is there any dependency for ``plottree``?\n\nA: Yes, ``plottree`` was built on top of ``matplotlib`` and ``Biopython.Phylo``\nmodule. If you install ``plottree`` using ``pip``, they will be automatically\ninstalled if they are not installed yet.\n\nQ: Why it tells me \"'plottree' is not recognized as an internal or external\ncommand, operable program or batch file\"?\n\nA: Make sure you successfully installed ``plottree`` first. Then, make sure\n``C:PythonX\\\\Scripts`` folder was added to your system path, if you installed\nPython with the default options. If you installed Python with other options,\nfind the Scripts folder under Python installation folder and make sure the\nfolder was added to your system path and try again.\n\nQ: Why it tells me \"-bash: plottree: command not found\"?\n\nA: Make sure you successfully installed ``plottree`` first. Then, make sure the\nexecutable script generated during ``plottree`` installation was installed to a\nlocation that included into your ``PATH``, if not, add the location to PATH.\n\nQ: After I run the command, why it does not release the prompt even I append\n\"&\" after the command and try to put it running background?\n\nA: It was intentionally designed like this. If you want to take your prompt\nback, just close the figure window, and the prompt will come back\nautomatically. Once you need to see the figure again, just re-run the command.\n\n\n",
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