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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 --genotypes FILE
                          [--imputed-sites FILE] [--genotypes-format FORMAT]
                          [--keep FILE] [--significant FLOAT]
                          [--plot-p-lower FLOAT] [--snp-col COL]
                          [--chr-col COL] [--pos-col COL] [--p-col COL]
                          [--a1-col ALLELE] [--a2-col ALLELE] --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] [--output-directory DIR]

Plots significant regions of GWAS (0.1.3).

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.
  --genotypes FILE      The file containing the genotypes (available format
                        are VCF, IMPUTE2, BGEN or Plink binary files.
  --imputed-sites FILE  The file containing the imputed sites (if absent, all
                        points will have the same darkness).

Genotypes Options:
  --genotypes-format FORMAT
                        The genotype file format. If not specified, the tool
                        will try to guess the format and parse the file
                        accordingly.
  --keep FILE           The list of samples to keep for the LD calculation.

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]
  --a1-col ALLELE       The name of the column containing the first allele.
                        [minor]
  --a2-col ALLELE       The name of the column containing the second allele.
                        [major]

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).

Output Options:
  --output-directory DIR
                        The output directory. [.]