Theme

In ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

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

 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")

library(ggmsa)
library(ggplot2)

Modify components of MSA theme

In this package, there are various powerful parameters to customize the non-data components of MSA plots: i.e. font size, background, sequence names, legends and border. Some parameters can be used to give MSA plots a consistent customized look.

Characters width

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

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

Background

If none_bg = TRUE, only show the character but not the colored background..

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

Sequence names

If seq_name = TRUE, the sequence name will be displayed.

ggmsa(protein_sequences, 164, 213, seq_name = TRUE)

Legend

If show.legend = TRUE, the legend of MSA plot will be displayed.

ggmsa(protein_sequences, 164, 213, font = NULL, show.legend = TRUE)

Border

Change or set colored block border. if border = NA, the border would be removed.

ggmsa(protein_sequences, 164, 213, font = NULL, border = NA)

Or, modify the border color by assign the color to border, like this： border = "white"

ggmsa(protein_sequences, 164, 213, font = NULL, border = "white")

Position Highlighted

Specified position can be highlighted but the block colors only assign by ggplot2 automatically.

ggmsa(protein_sequences, 164, 213, posHighligthed = c(185, 190), char_width = 0.5)

ggmsa documentation built on Aug. 3, 2021, 9:06 a.m.