tirganteanga / arg_ast

Program that perform phenotype genotype analysis with antibiotic resistance data

arg_ast : R code to visualize phenotype-genotype associations between resistance genes identified by whole genome sequencing and antibiotic susceptibility testing datasets.

Installation

git clone https://github.com/soda460/arg_ast

If need install these R libraries

install.packages('tidyverse')
install.packages('ggplot2')
install.packages('ggrepel')

# optional
install.packages('svglite')

Usage

Try to fit your phenotype and genotype data to the format of the csv files loaded by the main program : arg_ast.R

The script data_wrangling.R is highly specific to our datasets.

Contributors

• Jean-Simon Brouard, Ph.D.
  Biologist in bioinformatics, Science and Technology Branch
  Agriculture and Agri-Food Canada / Government of Canada
  [email protected]

• Dominic Poulin-Laprade, Ph.D.
  Research Scientist, Science and Technology Branch
  Agriculture and Agri-Food Canada / Government of Canada
  [email protected]

Notes

Technically, this script is also useful for me because it make use of quosure objects in R functions.