plotAPCG: Plot All Protein Composition Graph

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

Description

A function that plots a comprehensive composition mapping given a protein list. The composition descriptors includes hydrophobicity, van der Waals volume, polarity, polarizability and desolvation. A hierarchical row and column clustering will also be displayed on the side to showing the similarity analysis

Usage

plotAPCG(file = "proSeq")

Arguments

file	input csv file containing the list of pdb id and sequence

Value

This function returns a matrix of composition descriptor infomation as well as a full composition graph given the proteins.

References

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

Examples

composition_plot <- plotAPCG(file = "proSeq")
composition_plot

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