BradyAJohnston / plasmapR

Creating plasmid maps inside ggplot.

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)

##   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()