| Title: | Visualize Alpha-Helical Peptide Sequences |
|---|---|
| Description: | Create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of alpha-helical oligopeptides. See Wadhwa RR, et al. (2018) <doi:10.21105/joss.01008> for more information. |
| Authors: | Raoul Wadhwa [cre, aut], Regina Stevens-Truss [aut], Vigneshwar Subramanian [aut] |
| Maintainer: | Raoul Wadhwa <[email protected]> |
| License: | GPL-3 |
| Version: | 1.0.1 |
| Built: | 2025-03-01 02:49:59 UTC |
| Source: | https://github.com/rrrlw/helixvis |
This function visualizes alpha-helical peptides as Wenxiang diagrams. Sequences between 2 and 18 (inclusive) characters can be visualized. The residue closest to the center represents the amino acid at the N-terminus (first in 'sequence').
draw_wenxiang(sequence, col = c("grey", "yellow", "blue", "red"), labels = FALSE, label.col = "black", fixed = TRUE, legend = FALSE)draw_wenxiang(sequence, col = c("grey", "yellow", "blue", "red"), labels = FALSE, label.col = "black", fixed = TRUE, legend = FALSE)
sequence |
character vector containing amino acid sequence from N-terminus to C-terminus |
col |
colors for each amino acid type in the following order: nonpolar residues, polar residues, basic residues, acidic residues |
labels |
logical value; if TRUE, one-letter residue codes are overlaid on the residue circles |
label.col |
character value for color of labels added if 'labels = TRUE' |
fixed |
if TRUE (default), ensures that residues will be circles (not ellipses) even if graphics device is rectangular |
legend |
if TRUE, adds legend to plot |
draw_wenxiang("GIGAVLKVLTTGLPALIS") draw_wenxiang("QQRKRKIWSILAPLGTTL")draw_wenxiang("GIGAVLKVLTTGLPALIS") draw_wenxiang("QQRKRKIWSILAPLGTTL")
This function visualizes alpha-helical peptides as helical wheels. Sequences between 2 and 18 (inclusive) characters can be visualized. The residue in the upper half of the wheel lying at the horizontal center representing the amino acid at the N-terminus (first in 'sequence').
draw_wheel(sequence, col = c("grey", "yellow", "blue", "red"), labels = FALSE, label.col = "black", fixed = TRUE, legend = FALSE)draw_wheel(sequence, col = c("grey", "yellow", "blue", "red"), labels = FALSE, label.col = "black", fixed = TRUE, legend = FALSE)
sequence |
character vector containing amino acid sequence from N-terminus to C-terminus |
col |
colors for each amino acid type in the following order: nonpolar residues, polar residues, basic residues, acidic residues |
labels |
logical value; if TRUE, one-letter residue codes are overlaid on the residue circles |
label.col |
character value for color of labels added if 'labels = TRUE' |
fixed |
if TRUE (default), ensures that residues will be circles (not ellipses) even if graphics device is rectangular |
legend |
if TRUE, adds legend to plot |
draw_wheel("GIGAVLKVLTTGLPALIS") draw_wheel("QQRKRKIWSILAPLGTTL")draw_wheel("GIGAVLKVLTTGLPALIS") draw_wheel("QQRKRKIWSILAPLGTTL")
The helixvis package allows visualization of alpha-helical peptide sequences in the form of helical wheels. Although online servers currently exist that do this, all currently require entering sequences and storing images individually. None known to us are completely open-source. This package allows users to create visualizations for entire databases of amino acid sequences without need for manual input.
A dataset containing the name and residue sequence of five antimicrobial peptides from the Antimicrobial Peptide Database (APD3).
sample_seqsample_seq
A data frame with 5 rows and 2 variables:
antimicrobial peptide name
antimicrobial residue sequence
See Wang et al. (2016) <doi:10.1093/nar/gkv1278> for more information.