Description Usage Arguments Value Author(s) Examples
Plot multiple sequence alignment using ggplot2 with multiple color schemes supported.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ggmsa(
msa,
start = NULL,
end = NULL,
font = "helvetical",
color = "Chemistry_AA",
custom_color = 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,
show.legend = FALSE
)
|
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. |
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. |
show.legend |
logical. Should this layer be included in the legends? |
ggplot object
Guangchuang Yu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | #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")
|
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