Sequence logo plots for amino acid profiles.

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 argument passed to geom_logo from ggseqlogo package specifying how to colour symbols.

Value

A ggplot2 object.

See also

getKmers, kmer_profile

Examples

# \dontrun{
data(immdata)
kmers <- getKmers(immdata$data[[1]], 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 or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`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 or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 93 rows containing missing values or values outside the scale range
#> (`geom_label_repel()`).

vis_seqlogo(d)

# }