ggmsa
Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.
ggmsa( msa, start = NULL, end = NULL, font = "helvetical", color = "Chemistry_AA", custom_color = NULL, order = NULL, char_width = 0.9, none_bg = FALSE, by_conservation = FALSE, posHighligthed = NULL, seq_name = NULL, border = NULL, consensus_views = FALSE, use_dot = FALSE, disagreement = TRUE, ignore_gaps = FALSE, ref = NULL )
msa |
Multiple aligned sequence files or objects representing either nucleotide sequences or AA sequences. |
start |
a numeric vector. Start position to plot. |
end |
a numeric vector. End position to plot. |
font |
font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. If font = NULL, only plot the background tile. |
color |
a Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER', 'CN6', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'. |
custom_color |
A data frame with two cloumn called "names" and "color".Customize the color scheme. |
order |
vectors.Specified sequences order. |
char_width |
a numeric vector. Specifying the character width in the range of 0 to 1. Defaults is 0.9. |
none_bg |
a logical value indicating whether background should be disaplayed. Defaults is FALSE. |
by_conservation |
a logical value. The most conserved regions have the brightest colors. |
posHighligthed |
A numeric vector of the position that need to be highlighted. |
seq_name |
a logical value indicating whether seqence names should be displayed. 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 in any case. If 'seq_name = FALSE' the sequence name will not be displayed under any circumstances. |
border |
a character string. The border color. |
consensus_views |
a logical value that opeaning consensus views. |
use_dot |
a logical value. Displays characters as dots instead of fading their color in the consensus view. |
disagreement |
a logical value. Displays characters that disagreememt to consensus(excludes ambiguous disagreements). |
ignore_gaps |
a logical value. When selected TRUE, gaps in column are treated as if that row didn't exist. |
ref |
a character string. Specifying the reference sequence which should be one of input sequences when 'consensus_views' is TRUE. |
ggplot object
Guangchuang Yu
#plot multiple sequences by loading fasta format
fasta <- system.file("extdata", "sample.fasta", package = "ggmsa")
ggmsa(fasta, 164, 213, color="Chemistry_AA")
#XMultipleAlignment objects can be used as input in the 'ggmsa'
#AAMultipleAlignment <- Biostrings::readAAMultipleAlignment(fasta)
#ggmsa(AAMultipleAlignment, 164, 213, color="Chemistry_AA")
#XStringSet objects can be used as input in the 'ggmsa'
#AAStringSet <- Biostrings::readAAStringSet(fasta)
#ggmsa(AAStringSet, 164, 213, color="Chemistry_AA")
#Xbin objects from 'seqmagick' can be used as input in the 'ggmsa'
#AAbin <- seqmagick::fa_read(fasta)
#ggmsa(AAbin, 164, 213, color="Chemistry_AA")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.