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Overview of drawProteins

This package has been created to allow the visualisation of protein schematics based on the data obtained from the Uniprot Protein Database.

The basic workflow is:

  • to provide one or more Uniprot IDs
  • get a list of features from the Uniprot API
  • draw the basic chains of these proteins
  • add features as desired

    drawProteins uses the package httr to interact with the Uniprot API and extract a JSON object into R. The JSON object is used to create a data.table.

    The graphing package ggplot2 is then used to create the protein schematic.

    The Vignette gives a good overview of the package.

    Sample script on R for Biochemists blog

    The master version of this package is available through Bioconductor. The development version is currently available here through GitHub.

    To install and use development branch:

    This package is available through Bioconductor. Installation instructions and documentation are available.

    To install from Github:

    if (!require(devtools)) {
        install.packages('devtools')
    }
    dev_mode(on=TRUE)
    devtools::install_github('brennanpincardiff/drawProteins')
    

    Please cite the following article when using drawProteins:

    Brennan P. drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics [version 1; referees: 2 approved]. F1000Research 2018, 7:1105


    Feedback is very welcome. Please raise Github issues to provide bug reports, give feedback or request features.