plotBindingMotif: Plot an MHC Binding Motif

In EpitopePrediction: Predict Binding Between Peptides and MHC Molecules

Description

Visualizes the set of peptides which are predicted to bind to a certain MHC molecule.

Usage

plotBindingMotif(mhc = "HLA-A-02:01", l = 9, motif.matrix = NULL,
  width = 0.5, space = 1, col = rainbow(20), main = paste(mhc, ", ", l,
  "-mers", sep = ""), ...)

Arguments

mhc	name of the MHC molecule.
l	length of the peptide.
motif.matrix	a matrix. If this is not NULL, then the parameters mhc and l are ignored and the supplied matrix is used instead. This makes it possible to use this function for plotting sequence logos unrelated to MHC-peptide binding. The supplied matrix must have row names to indicate the letters out of which the sequence logo is made.
width	bar width for profile per position.
space	amount of space left before each bar, as a fraction of the bar width.
col	vector of colors to use for the amino acids (given in alphabetical order in single-letter coding).
main	title for the plot.
...	further options to be passed on to barplot

Examples

## Compare binding motifs of HLA-A02 at all supported peptide lengths
par( mfrow=c(2,2) )
for( l in 8:11 ){
   plotBindingMotif( "HLA-A-02:01", l )
}

EpitopePrediction documentation built on May 2, 2019, 6:18 p.m.