Plot sequence logo plots for visualising of amino acid motif sequences / profiles.

vis_textlogo plots sequences in a text format - each letter has the same height. Useful when there are no big differences between occurences of amino acids in the motif.

vis_seqlogo is a traditional sequence logo plots. Useful when there are one or two amino acids with clear differences in their occurrences.

vis_textlogo(.data, .replace.zero.with.na = T, .width = 0.1, ...)

vis_seqlogo(.data, .scheme = "chemistry", ...)

## Arguments

.data Output from the kmer.profile function. if T then replace all zeros with NAs, therefore letters with zero frequency wont appear at the plot. Width for jitter, i.e., how much points will scatter around the verical line. Pass 0 (zero) to plot points on the straight vertical line for each position. Not used here. Character. An argumentt passed to geom_logo specifying how to colour symbols.

ggplot2 object

## Examples

if (FALSE) {
data(immdata)
kmers = getKmers(immdata\$data[[1]], 5)
ppm = kmer_profile(kmers, "prob")
vis(ppm, .plot="text")
vis(ppm, .plot="seq")

d <- kmer_profile(c('CASLL', 'CASSQ', 'CASGL'))
vis_textlogo(d)
vis_seqlog(d)
}