Description Usage Arguments Value Author(s) Examples
plot sequence logo for MSA based 'ggolot2'
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msa |
Multiple sequence alignment file or object for representing either nucleotide sequences or peptide sequences. |
start |
Start position to plot. |
end |
End position to plot. |
font |
font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'DroidSansMono'. If font=NULL, only the background tiles is drawn. |
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'. |
adaptive |
A logical value indicating whether the overall height of seqlogo corresponds to the number of sequences. If FALSE, seqlogo overall height = 4,fixedly. |
top |
A logical value. If TRUE, seqlogo is aligned to the top of MSA. |
custom_color |
A data frame with two cloumn called "names" and "color".Customize the color scheme. |
ggplot object
Lang Zhou
1 2 3 | #plot sequence motif independently
nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa")
seqlogo(nt_sequence, color = "Chemistry_NT")
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