region-plot - A tool to plot significant regions of GWAS

region-plot is a bioinformatics pipeline to plot significant regions found by genome-wide association studies (GWAS). It works on both Python 2 and 3 versions.

The following figure (low resolution) is an example from Tardif et al. (2015) (doi:10.1161/CIRCGENETICS.114.000663). The difference with the original figure is the inclusion of the annotation from the HAVANA project in this example.

Dependencies

The tool requires a standard Python installation with the following packages:

1. numpy version 1.9.1 or latest
2. pandas version 0.17.0 or latest
3. six version 1.9.0 or latest
4. matplotlib version 1.4.3 or latest
5. gepyto version 0.9.2 or latest

The tool has been tested on Linux only, but should also work on both Mac OSX and Windows.

Usage

For Linux users, make sure that the script is executable (using the chmod command).

$ launch-region-plot --help
usage: launch-region-plot [-h] [-v] [--log-level {INFO,DEBUG}]
                          [--log-file LOGFILE] --assoc FILE --bfile PREFIX
                          [--imputed-sites FILE] [--significant FLOAT]
                          [--plot-p-lower FLOAT] [--snp-col COL]
                          [--chr-col COL] [--pos-col COL] [--p-col COL]
                          --genetic-map FILE [--genetic-chr-col COL]
                          [--genetic-pos-col COL] [--genetic-rate-col COL]
                          [--plot-format {png,pdf}] [--build {GRCh37,GRCh38}]
                          [--region-padding FLOAT] [--whole-dataset]

Plots significant regions of GWAS.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --log-level {INFO,DEBUG}
                        The logging level [INFO]
  --log-file LOGFILE    The log file [region-plot.log]

Input Files:
  --assoc FILE          The association file containing the hits
  --bfile PREFIX        The prefix of the binary PEDFILE to compute LD with
                        best hit
  --imputed-sites FILE  The file containing the imputed sites (if absent, all
                        points will have the same darkness)

Association Options:
  --significant FLOAT   The significant association threshold [<5.000000e-08]
  --plot-p-lower FLOAT  Plot markers with p lower than value [<5.000000e-08]
  --snp-col COL         The name of the SNP column [snp]
  --chr-col COL         The name of the chromosome column [chr]
  --pos-col COL         The name of the pos column [pos]
  --p-col COL           The name of the p-value column [p]

Genetic Map Options:
  --genetic-map FILE    The file containing the genetic map
  --genetic-chr-col COL
                        The name of chromosome column for the genetic map
                        [chromosome]
  --genetic-pos-col COL
                        The name of the position column for the genetic map
                        [position]
  --genetic-rate-col COL
                        The name of the recombination rate column for the
                        genetic map [rate]

Plot Options:
  --plot-format {png,pdf}
                        The format of the output file containing the plot
                        (might be 'png' or 'pdf') [png]
  --build {GRCh37,GRCh38}
                        The build to search the overlapping genes [GRCh37]
  --region-padding FLOAT
                        The amount of base pairs to pad the region (on each
                        side of the best hit [500000.0]
  --whole-dataset       Plot all markers (no padding) (WARNING this might take
                        a lot of memory)