vis_textlogo: Sequence logo plots for amino acid profiles.

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Sequence logo plots for amino acid profiles.

Description

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.

Usage

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

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

Arguments

.data	Output from the kmer.profile function.
.replace.zero.with.na	if TRUE 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.

Value

A ggplot2 object.

See Also

getKmers, kmer_profile

Examples

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_seqlogo(d)

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.