hmm.logo: Plots the relative frequencies of each position for...

In grunwaldlab/effectR: Predicts Oomycete Effectors

Plots the relative frequencies of each position for hmmsearch table.

Description

This function plots the results from hmm.search as a barplot with amino acids in the x axis and the relative frequency of each amino acid in the y axis

Usage

hmm.logo(hmm.table)

Arguments

hmm.table

The HMM profile table resulting from hmm.search

Examples

## Not run: 

fasta.file <- system.file("extdata", "test_infestans.fasta", package = "effectR")
ORF <- seqinr::read.fasta(fasta.file)
REGEX <- regex.search(ORF, motif='RxLR')
candidate.rxlr <- hmm.search(original.seq = fasta.file, regex.seq=REGEX, num.threads = 2)
hmm.logo(candidate.rxlr$HMM_Table)

## End(Not run)

grunwaldlab/effectR documentation built on Sept. 9, 2023, 1:39 a.m.