man_qq_annotate

Creates Manhattan and QQ plots with annotated peaks for sequencing-based GWAS outputs, by thinning the dataset to what the eye can see.

Installation

Install using devtools (in R):

# Install devtools if you don't have it
install.packages('devtools')
library(devtools)
install_github("hmgu-itg/man_qq_annotate")

Usage

You can either use the CLI or load the package into your R environment.

Command Line Interface (CLI)

Once installed, you can use the manqq_cli script in the base of the repository as a command line tool.
For a GCTA output, use the following:

./manqq_cli --chr-col Chr --pval-col p --pos-col bp --a1 A1 --a2 A2 --build 38 --image png --af-col Freq input.assoc.txt.gz output.prefix

You can add manqq_cli to your PATH variable for convenient execution:

export PATH="/path/to/man_qq_annotate:$PATH"
# Or to make this permanent:
echo 'export PATH="/path/to/man_qq_annotate:$PATH"' >> ~/.bashrc

Input files can be gzipped or plain. Run without arguments for a list of options, run with --help for detailed options:

usage: ./manqq_cli   [-h] [--chr-col [character]] [--pval-col [character]]
                     [--pos-col [character]] [--a1 [character]]
                     [--a2 [character]] [--build [integer]]
                     [--image [character]] [--af-col [character]]
                     [--maf-filter [double]] [--sig [double]]
                     [--maxpeaks [integer]] [--no-qq] [--no-man] [--no-annot]
                     [--no-distance] [--man-height [integer]]
                     [--upper-margin [double]] [--annot-cex [double]]
                     [--axes-cex [double]] [--ylim [double]]
                     infile outfile

A program to plot Manhattan and QQ plots

positional arguments:
  infile                Input file name, must be gzip file
  outfile               Output file name (with no file extension)

optional arguments:
  -h, --help            show this help message and exit
  --chr-col [character]
                        The column NAME for the chromosome column, default chr
  --pval-col [character]
                        The column NAME for the chromosome column, default
                        p_score
  --pos-col [character]
                        The column NAME for the chromosome column, default ps
  --a1 [character]      The column NAME for the effect allele column, default
                        allele1
  --a2 [character]      The column NAME for the non-effect column, default
                        allele0
  --build [integer]     The genome build the positions refer to
  --image [character]   The filetype to save plots to (png or pdf)
  --af-col [character]  The column NAME for the allele frequency column,
                        default af
  --maf-filter [double]
                        The significance threshold for MAF filter, default
                        0.0.
  --sig [double]        The significance threshold to use for peak annotation
  --maxpeaks [integer]  The maximum number of peaks to annotate
  --no-qq               Don't plot QQ.
  --no-man              Don't plot Manhattan.
  --no-annot            Disable peak annotation even if peaks are present.
  --no-distance         Don't add very useful distance to gene info.
  --man-height [integer]
                        Force height of Manhattan in inches. Can have
                        unpredictable consequences (some of which you may
                        regret).
  --upper-margin [double]
                        Y limit of Manhattan plot in units of maximum data
                        points. Even more unpredictable than the above.
  --annot-cex [double]  Size factor for annotations.
  --axes-cex [double]   Size factor for axes and labels.
  --ylim [double]       The y-axis limit (-log10(p))

Loading the package

You can load the package into your R environment and use the available functions.

library(manqq)
ls('package:manqq')

[1] "manqq_cli"      "fastqq"

Currently, only two functions are exported and available for users. The other functions are all hidden and only used internally within the package. If there are any particular functionality you wish to use from the package, please make a request in the issue page.

Creating a QQ-plot

## example using a simulated null GWAS with 10,000 SNPs
library(manqq)
fastqq(runif(10000))

Development

You can use devtools to load all the functions into your environment for development/debugging:

library(devtools)
setwd('/base/of/the/repo/man_qq_annotate')
load_all()
test() # Use testthat's test function to run the testsuite