R: Sequence logo plots for amino acid profiles.

vis_textlogo {immunarch} | R Documentation

## 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)

[Package immunarch version 0.6.5 Index]