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, = T, .width = 0.1, ...)

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



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

See also


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) }