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", ...)
.data | Output from the |
---|---|
.replace.zero.with.na | if T then replace all zeros with NAs, therefore letters with zero frequency wont appear at the plot. |
.width | 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. |
.scheme | Character. An argumentt passed to geom_logo specifying how to colour symbols. |
ggplot2 object
# NOT RUN { 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) # }