RoaRyVis is an R package that processes output data from the pangenome software, Roary (“Roary: Rapid large-scale prokaryote pan genome analysis”, AJ Page et al., 2015.). In a pangenome study, the genomic DNA a population of a certain species is sequenced, and the genes are predicted in silico. Roary compares the predicted genes of each genome, examines if certain genes are similar enough to be considered as the same gene, and outputs a table containing the presence and absence of each predicted gene in all genomes.
Version 1.1: RoaRyViz is available on shiny app: https://davidtong28.shinyapps.io/RoaRyViz/
The new RoaRyViz features an accessory genome heatmap, which is able to infer gene gain and loss between sublineages.
Install the development version from GitHub with:
install.packages("devtools")
devtools::install_github("davidtong28/RoaRyVis")The github repository for RoaRyVis is https://github.com/davidtong28/RoaRyVis.
So far there is only one visuallization function wrapped by RoaRyVis, namely the distributionplot function, which returns a plot showing the distribution of genes present in a given number of genomes in a population.
RoaRyVis::distributionplot("testdata/campylobacter.csv","con","test_campy")
How I implemented the package components:
# Opened up github repository
# Opened new project and linked the project to this repository via "version control"-"git"
library (devtools)
create_package(~/RoaRyVis)
use_git()
use_r()
# Created `distributionplot.R` file. Added Roxigen 2 skeleton. Imported dplyr and ggplot2 (since I will use these packages extensively, they will go to NAMESPACE after document(), and no "::" colons will be needed to call functions from them)
# Created `input_csv.R` file as an internal function
# Created the "testdata" folder and "results" folder. Added two previous test data in /testdata folder
document()
use_pipe()
# Edited description file.
use_package(grDevices)
use_package(utils)
use_package(stringr)
use_package(here)
use_mit_license()
use_testthat()
use_test()
# Specified test "distributionplot test".
test() #No errors, all passed
library(here)
check(check_dir=here())# 0 Errors, 0 warnings
#When I run test(), it's returning 3 passed tests. But when I run check(), it returns with errors because the here::here directory changed. Since I use the relative path of the input file as the first argument of distributionplot, the input file I use for my test is not found since the here director changed. To change the check() path, I used the `check_dir=here::here()` argument