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 = TRUE, .width = 0.1, ...) vis_seqlogo(.data, .scheme = "chemistry", ...)
Output from the
if TRUE 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.
A ggplot2 object.
data(immdata) kmers <- getKmers(immdata$data[], 5) ppm <- kmer_profile(kmers, "prob") #> Warning: Warning: removed 5 non-amino acid symbol(s): A #> Please make sure your data doesn't have them in the future. vis(ppm, .plot = "text") #> Warning: Removed 5 rows containing missing values (geom_point). #> Warning: Removed 5 rows containing missing values (geom_label_repel). #> Warning: ggrepel: 21 unlabeled data points (too many overlaps). Consider increasing max.overlaps vis(ppm, .plot = "seq") d <- kmer_profile(c("CASLL", "CASSQ", "CASGL")) #> Warning: Warning: removed 1 non-amino acid symbol(s): A #> Please make sure your data doesn't have them in the future. vis_textlogo(d) #> Warning: Removed 93 rows containing missing values (geom_point). #> Warning: Removed 93 rows containing missing values (geom_label_repel). vis_seqlogo(d)