/plasmapAMR

Creating plasmid maps inside ggplot.

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plasmapAMR

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

This repo is forked from bradyajohnston/plasmapr and edited to visualise AMR genes on plasmids. It is my first time releasing a package so is experimental and only involves a few small tweeks. It still needs more work.

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.

For the original package:

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

For the new AMR gene package:

# install.packages("devtools")
devtools::install_github("melparker101/plasmapamr", ref = "ctx-m_plasmids")

Conda package in progress...

The code below is for the original package:

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)
##   index                    name         type start  end direction
## 1     1 synthetic DNA construct       source     1 7700         1
## 2     2                 f1 orim   rep_origin    12  467         1
## 3     3           AmpR promoter     promoter   494  598         1
## 4     4                    AmpR          CDS   599 1459         1
## 5     5                     ori   rep_origin  1630 2218         1
## 6     6                     bom misc_feature  2404 2546         1

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.

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()