seqlogo.Rd
plot sequence logo for MSA based 'ggolot2'
seqlogo( msa, start = NULL, end = NULL, font = "DroidSansMono", color = "Chemistry_AA", adaptive = FALSE, top = FALSE, custom_color = NULL )
msa | Multiple sequence alignment file or object for representing either nucleotide sequences or peptide sequences. |
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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
#plot sequence motif independently nt_sequence <- system.file("extdata", "LeaderRepeat_All.fa", package = "ggmsa") seqlogo(nt_sequence, color = "Chemistry_NT")