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        "author": "Sander Bollen",
        "author_email": "a.h.b.bollen@lumc.nl",
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        "classifiers": [
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "|Build Status| |Coverage Status|\n\nafplot\n======\n\nThis is a tool to plot allele frequencies in VCF files.\n\nThe two main subcommands that are available are: \\* ``regions``: Plot\nsingle regions or regions from a bed file, optionally with a margin. \\*\n``whole-genome``: Create a single image for every chromosome on the\ngenome.\n\nBoth subcommands have three modes:\n\n-  ``histogram``: This will create a histogram with kernel density plot\n   of allele frequencies.\n-  ``scatter``: Create a scatter plot of allele frequencies, along the\n   region or chromosome.\n-  ``distance``: Create a scatter plot of distances to theoretical\n   allele frequencies, along the region or chromosome. This only makes\n   sense for autosomes of diploid organisms.\n\nBy default, colors correspond to call type (hom\\_alt/ref/hom\\_ref).\n\nMultiple VCF files can be supplied simultaneously for the\n``whole-genome`` subcommand, in which case they can be grouped by label.\nWhen multiple VCF files are supplied, plots will be colored on label per\nVCF file.\n\nOnly one sample per VCF file can be plotted.\n\nWe currently assume the presence of an ``AD`` column in the ``FORMAT``\nfield. This column should contain the depth per allele, with the\nreference allele being first.\n\nAll VCFs should be indexed with tabix, and should contain contigs in the\nheader.\n\nInstallation\n------------\n\nafplot is available through pypi with: ``pip install afplot``\n\nRequirements\n------------\n\n-  Python 3.4+\n-  click\n-  numpy\n-  matplotlib\n-  pandas\n-  seaborn\n-  progressbar2\n-  pysam\n-  pyvcf\n\nUsage\n-----\n\n.. code:: text\n\n    Usage: afplot [OPTIONS] COMMAND [ARGS]...\n\n      Plot allele frequencies in VCF files.\n\n      Two basic modes exist:\n        - regions: Plot histogram, scatter or distance plots per\n          user-specified region.\n        - whole-genome: Plot histogram, scatter or distance plots over the\n          entire genome.\n\n    Options:\n      --help  Show this message and exit.\n\n    Commands:\n      regions       Region plots\n      whole-genome  Whole-genome plots\n\nExamples\n--------\n\nSingle VCF on a single region\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n-  ``afplot regions histogram -v my.vcf.gz -o output_dir -R chr1:100-200``\n\nSingle VCF on a bed file\n~~~~~~~~~~~~~~~~~~~~~~~~\n\n-  ``afplot regions histogram -v my.vcf.gz -o output_dir -L regions.bed``\n\nSingle VCF whole genome\n~~~~~~~~~~~~~~~~~~~~~~~\n\n-  ``afplot whole-genome histogram -v my.vcf.gz -l my_label -s my_sample -o mysample.histogram.png``\n\nMultiple VCFs whole genome\n~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n-  ``afplot whole-genome histogram -v my1.vcf.gz -l my_label1 -s my_sample1 -v my2.vcf.gz -l my_label2 -s my_sample2 -o both_samples.histogram.png``\n\nGrouping samples can be achieved by supplying identical labels to\nsamples. E.g.\n\n-  ``afplot whole-genome histogram -v 1.vcf.gz -v 2.vcf.gz -v 3.vcf.gz -v 4.vcf.gz -l group1 -l group1 -l group2 -l group2 [...]``\n\nExcluding contigs on whole genome\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nIn certain cases, you may not want to plot all contigs. For instance,\nwhen your vcf header contains many small unplaced contigs. This can be\nachieved by supplying a regex pattern to the ``-e`` flag. For instance,\nall contigs containing \"gl\" can be filtered out by doing:\n\n-  ``afplot whole-genome [...] -e '.*gl.*'``\n\nChangelog\n---------\n\n0.2\n~~~\n\nThe entire command line interface was changed to use ``click``, instead\nof regular argparse. This allows a more complex CLI. In stead of having\nflags for plot mode, ``afplot`` now uses subcommands.\n\nWhile the CLI has changed, and the internals of ``afplot`` have been\nrefactored, the old-style (version 0.1) API remains in place for now.\nThis may be deprecated in the future.\n\nSupport for plotting regions was added. Region plotting outputs on a\ndirectory, rather than on a single file.\n\nLicense\n-------\n\nMIT\n\n.. |Build Status| image:: https://travis-ci.org/sndrtj/afplot.svg?branch=master\n   :target: https://travis-ci.org/sndrtj/afplot\n.. |Coverage Status| image:: https://coveralls.io/repos/github/sndrtj/afplot/badge.svg?branch=master\n   :target: https://coveralls.io/github/sndrtj/afplot?branch=master\n\n\n",
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        "license": "MIT",
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