ggmsa: Plot multiple sequence alignment using ggplot2

Introduction

Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.

Supports visualizing multiple sequence alignment of DNA and protein sequences using ggplot2 It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other ‘ggplot2’ plots, such as aligning a phylogenetic tree produced by ‘ggtree’ with multiple sequence alignment.

Installation

This R package (ggmsa, current version: 0.0.6) is avalable via CRAN. The way to install the package is the following:

## installing the package
install.packages("ggmsa")
## loading the package
library("ggmsa")

The development version from github:

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/ggmsa")

Load sample data

Three sample data are shipped with the ggmsa package. Note that ggmsa supports not only fasta files but other objects as well. available_msa()can be used to list MSA objects currently available.

 available_msa()
#> files currently available:
#> .fasta
#> XStringSet objects from 'Biostrings' package:
#> DNAStringSet RNAStringSet AAStringSet BStringSet DNAMultipleAlignment RNAMultipleAlignment AAMultipleAlignment
#> bin objects:
#> DNAbin AAbin

 protein_sequences <- system.file("extdata", "sample.fasta", package = "ggmsa")
 miRNA_sequences <- system.file("extdata", "seedSample.fa", package = "ggmsa")
 nt_sequences <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa")
 

Visualizing Multiple Sequence Alignments

The most simple code to use ggmsa:

ggmsa(protein_sequences, start = 265, end = 300)

Colour Schemes

Several classic color schemes for MSA are shipped in the package. In the same ways, you can use available_msa() to list colour schemes currently available. Note that Amino acids and nucleotides have different colour schemes.

 available_colors()
#> color schemes for nucleotide sequences currently available:
#> Chemistry_NT Shapely_NT Taylor_NT Zappo_NT
#> color schemes for AA sequences currently available:
#> Clustal Chemistry_AA Shapely_AA Zappo_AA Taylor_AA LETTER CN6 Hydrophobicity

Clustal X Colour Scheme

This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type.

ggmsa(protein_sequences, start = 320, end = 360, color = "Clustal")

Color by Chemistry(Default)

Amino acids are colored according to their side chain chemistry:

ggmsa(protein_sequences, start = 320, end = 360, color = "Chemistry_AA")

Color by Shapely

This color scheme matches the RasMol amino acid and RasMol nucleotide color schemes, which are, in turn, based on Robert Fletterick’s “Shapely models”.

ggmsa(protein_sequences, start = 320, end = 360, color = "Shapely_AA")

Color by Taylor

This color scheme is taken from Taylor(Taylor 1997) and is also used in JalView(Waterhouse et al. 2009).

ggmsa(protein_sequences, start = 320, end = 360, color = "Taylor_AA")

Color by Zappo

This scheme colors residues according to their physico-chemical properties, and is also used in JalView(Waterhouse et al. 2009).

ggmsa(protein_sequences, start = 320, end = 360, color = "Zappo_AA")

Color by LETTER

Thanks to ShixiangWang for the color scheme suggestions.

https://en.wikipedia.org/wiki/Help:Distinguishable_colors

ggmsa(protein_sequences, start = 320, end = 360, color = "LETTER")

Font

Several classic font for MSA are shipped in the package. In the same ways, you can use available_fonts() to list font currently available

 available_fonts()
#> font families currently available:
#> helvetical mono TimesNewRoman DroidSansMono

ggmsa(protein_sequences, start = 320, end = 360, font = "helvetical", color = "Chemistry_AA")

ggmsa(protein_sequences, start = 320, end = 360, font = "TimesNewRoman", color = "Chemistry_AA")

ggmsa(protein_sequences, start = 320, end = 360, font = "DroidSansMono", color = "Chemistry_AA")

If you specify font = NULL, only tiles will be plot.

ggmsa(protein_sequences, start = 320, end = 360, font = NULL, color = "Chemistry_AA")

Other params

Characters width can be specified by char_width. Defaults is 0.9.

ggmsa(protein_sequences, start = 320, end = 360, char_width = 0.5, color = "Chemistry_AA")

Background can be specified by none_bg. If none_bg = TRUE, only the character will be plot.

ggmsa(protein_sequences, start = 320, end = 360, none_bg = TRUE) + theme_void()

Position Highligthed can be specified by posHighligthed. The none_bg = FALSE when you specified position Highligthed by posHighligthed

ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA", 
      posHighligthed = c(185, 190))

Sequence names Defaults is ‘NULL’ which indicates that the sequence name is displayed when font = NULL, but ‘font = char’ will not be displayed.

If seq_name = TRUE the sequence name will be displayed when you need it.

ggmsa(protein_sequences, 164, 213, color = "Chemistry_AA", seq_name = TRUE)

If seq_name = FALSE the sequence name will not be displayed in any case.

ggmsa(protein_sequences, 164, 213, font = NULL, color = "Chemistry_AA", seq_name = FALSE)

Reference

Taylor, W R. 1997. “Residual Colours: A Proposal for Aminochromography.” Protein Eng 10 (7): 743–46.

Waterhouse, A. M., J. B. Procter, D. M. Martin, M Clamp, and G. J. Barton. 2009. “Jalview Version 2–a Multiple Sequence Alignment Editor and Analysis Workbench.” Bioinformatics 25 (9): 1189.