Metadata-Version: 1.1
Name: afplot
Version: 0.2
Summary: Plot allele frequencies in VCF files
Home-page: https://github.com/sndrtj/afplot
Author: Sander Bollen
Author-email: a.h.b.bollen@lumc.nl
License: MIT
Description: afplot
        ======
        
        This is a tool to plot allele frequencies in VCF files.
        
        The two main subcommands that are available are: \* ``regions``: Plot
        single regions or regions from a bed file, optionally with a margin. \*
        ``whole-genome``: Create a single image for every chromosome on the
        genome.
        
        Both subcommands have three modes:
        
        -  ``histogram``: This will create a histogram with kernel density plot
           of allele frequencies.
        -  ``scatter``: Create a scatter plot of allele frequencies, along the
           region or chromosome.
        -  ``distance``: Create a scatter plot of distances to theoretical
           allele frequencies, along the region or chromosome. This only makes
           sense for autosomes of diploid organisms.
        
        By default, colors correspond to call type (hom\_alt/ref/hom\_ref).
        
        Multiple VCF files can be supplied simultaneously for the
        ``whole-genome`` subcommand, in which case they can be grouped by label.
        When multiple VCF files are supplied, plots will be colored on label per
        VCF file.
        
        Only one sample per VCF file can be plotted.
        
        We currently assume the presence of an ``AD`` column in the ``FORMAT``
        field. This column should contain the depth per allele, with the
        reference allele being first.
        
        All VCFs should be indexed with tabix, and should contain contigs in the
        header.
        
        Installation
        ------------
        
        afplot is available through pypi with: ``pip install afplot``
        
        Requirements
        ------------
        
        -  Python 3.4+
        -  click
        -  numpy
        -  matplotlib
        -  pandas
        -  seaborn
        -  progressbar2
        -  pysam
        -  pyvcf
        
        Usage
        -----
        
        .. code:: text
        
            Usage: afplot [OPTIONS] COMMAND [ARGS]...
        
              Plot allele frequencies in VCF files.
        
              Two basic modes exist:
                - regions: Plot histogram, scatter or distance plots per
                  user-specified region.
                - whole-genome: Plot histogram, scatter or distance plots over the
                  entire genome.
        
            Options:
              --help  Show this message and exit.
        
            Commands:
              regions       Region plots
              whole-genome  Whole-genome plots
        
        Examples
        --------
        
        Single VCF on a single region
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``afplot regions histogram -v my.vcf.gz -o output_dir -R chr1:100-200``
        
        Single VCF on a bed file
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``afplot regions histogram -v my.vcf.gz -o output_dir -L regions.bed``
        
        Single VCF whole genome
        ~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``afplot whole-genome histogram -v my.vcf.gz -l my_label -s my_sample -o mysample.histogram.png``
        
        Multiple VCFs whole genome
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``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``
        
        Grouping samples can be achieved by supplying identical labels to
        samples. E.g.
        
        -  ``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 [...]``
        
        Excluding contigs on whole genome
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        In certain cases, you may not want to plot all contigs. For instance,
        when your vcf header contains many small unplaced contigs. This can be
        achieved by supplying a regex pattern to the ``-e`` flag. For instance,
        all contigs containing "gl" can be filtered out by doing:
        
        -  ``afplot whole-genome [...] -e '.*gl.*'``
        
        Changelog
        ---------
        
        0.2
        ~~~
        
        The entire command line interface was changed to use ``click``, instead
        of regular argparse. This allows a more complex CLI. In stead of having
        flags for plot mode, ``afplot`` now uses subcommands.
        
        While the CLI has changed, and the internals of ``afplot`` have been
        refactored, the old-style (version 0.1) API remains in place for now.
        This may be deprecated in the future.
        
        Support for plotting regions was added. Region plotting outputs on a
        directory, rather than on a single file.
        
        License
        -------
        
        MIT
        
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
