ggrama

The goal of ggrama is to make it easy to plot Ramachandran diagrams from a pdb file using ggplot2 graphics.

Installation

You can install the development version of ggrama:

devtools::install_github("missuse/ggrama")

Example

library(ggrama)

#download a pdb file
download.file("https://files.rcsb.org/download/2ADQ.pdb1.gz",
              dest = "2ADQ.pdb1.gz")

#plot by type of Ramachandran diagrams
ggrama("2ADQ.pdb1.gz") #general type the default

ggrama("2ADQ.pdb1.gz", "pre.pro") #pre-proline, additional options are glycine and proline

Or plot all four types in a grid

ggrama_all("2ADQ.pdb1.gz")

Using contours:

ggrama_all("2ADQ.pdb1.gz",
           contour = TRUE) #contours

ggrama_all("2ADQ.pdb1.gz",
           contour = TRUE, #contours
           smooth = TRUE) #use smoothed background

Bug reports

If you encounter undesired behavior in ggrama functions or have ideas how to improve the package please open an issue at: https://github.com/missuse/ggrama/issues

Citation

To cite ggrama in publications use:

Milan Dragićević (2021), ggrama: Ramachandran diagrams using ggplot2 graphics. url: https://github.com/missuse/ggrama. doi: 10.5281/zenodo.5660975

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {ggrama: Ramachandran diagrams using ggplot2 graphics},
    author = {Milan Dragićević},
    year = {2021},
    url = {https://github.com/missuse/ggrama},
    doi = {https://doi.org/10.5281/zenodo.5660975},
  }