In dxjasmine/Rppsc: R package for Plotting Protein Sequence Compositon

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(Rppsc)

Introduction

Rppsc is a R package for plotting protein sequence composition. The package benefits from the protr package and its determination on the chemical proterty of amino acid.

To start, the lattest version of Rppsc package can be installed via github

require("devtools")
install_github("dxjasmine/Rppsc", build_vignettes = TRUE)
library(Rppsc)

Plotting sequence composition for multiple proteins.

Rppsc provide visualization of protein sequence composition with regard to 5 aspects. They are hydrophobiciy, van der Waals volume, polarity polarizability, and desolvation. The 5 attributes are frequently used evaluate the surface and structure property. This distribution of each attributes is useful in assessment of protein sequence including domain, structure, and function analysis.

#user can use their own csv file providing pdbid and seuquence
#Default data --"proSeq" are also provided
hydrophobicity_plot <- plotCG(file = "proSeq", type= 1, circular_plot = TRUE)
hydrophobicity_plot #call to view the plot

Plotting sequence composition with 5 chemical attributes.

PlotAPCG() function combine the information from 5 chemical attributes and show a heatmap of the whole sequence composition.

#user can use their own csv file providing pdbid and seuquence
#Default data --"proSeq" are also provided
five_attribute_map <- plotAPCG(file= "proSeq")
five_attribute_map #call to view the plot

Rppsc shiny app

Rppsc can also be accessed as a shiny ap to interactively view the features mentioned above. The app aims to show the visualization of the protein sequence composition with regard to 5 attributes.

runRppsc()

Reference

Xiao, N., Cao, D.-S., Zhu, M.-F., & Xu, Q.-S. (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics, 31(11), 1857–1859. https://doi.org/10.1093/bioinformatics/btv042

dxjasmine/Rppsc documentation built on Dec. 8, 2019, 11:40 a.m.