In BradyAJohnston/plasmapR: Create Plasmid Maps in R

knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(
  fig.path = "man/figures/", 
  fig.width = 7, 
  fig.height = 7, 
  dpi = 300
)

plasmapR

This is an R package for making plasmid maps using {ggplot2}.

Installation

This package is still very early in development and the API may change. The parser for .gb files works most of the time but has not been tested extensively.

# install.packages("devtools")
devtools::install_github("bradyajohnston/plasmapr")

Example

plasmapR provides functions for parsing and plotting .gb plasmid files.

Once a plasmid has been exported in Genbank format it can be parsed and plotted.

library(plasmapR)

fl <- system.file('extdata', 'petm20.gb', package = "plasmapR")

fl |> 
  read_gb() |> 
  plot_plasmid(name = "pETM-20")

Access the features by turning the plasmid into a data.frame.

fl <- system.file('extdata', 'petm20.gb', package = "plasmapR")

plasmid <- fl |> 
  read_gb()

dat <- plasmid |> 
  as.data.frame()

head(dat)


dat[dat$type == "CDS", ] |> 
  plot_plasmid(name = "pETM-20")

It's not currently intended for linear display, but it can be used as such. I recommend checking out the gggenese package.

#| fig-height: 3
#| message: false
#| warning: false
dat[dat$type == "CDS", ] |> 
  plot_plasmid(name = NULL) + 
  ggplot2::coord_cartesian() + 
  ggplot2::scale_y_continuous(limits = NULL)

A {ggplot2} Object

The result of the call is just a {ggplot2} plot, which you can further customise to your liking with themes, etc.

fl <- system.file('extdata', '20.gb', package = "plasmapR")

plt <- fl |> 
  read_gb() |> 
  plot_plasmid()

plt + ggplot2::theme_bw()

BradyAJohnston/plasmapR documentation built on June 30, 2023, 5:28 p.m.