I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number

https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino-acid-sequence-logo

Here is an example sequence

seq <- "MGLRYSIYIENPLSSPSSSYKSINDPLFHSQHRSQKNVSFITYGCRHCKTHLSSSFQIIS
RDYRGRTGTAYLMNKVVNVVEGKVEQRRMLTGDYLVCDILCHWCKRNVGWKYLQSSNDDQ
QYKEGKFILELKNICKCT"

is there anyone who could help me plot it using this package or any other package

Is this a good way to show your sequence as a motif logo? It is not suggested. Whatever, you can try following code to plot your sequence.

seq <- "MGLRYSIYIENPLSSPSSSYKSINDPLFHSQHRSQKNVSFITYGCRHCKTHLSSSFQIIS
RDYRGRTGTAYLMNKVVNVVEGKVEQRRMLTGDYLVCDILCHWCKRNVGWKYLQSSNDDQ
QYKEGKFILELKNICKCT"
seq <- gsub("[^a-zA-Z]", "", seq)
seq <- strsplit(seq, "")[[1]]
rn <- sort(unique(seq))
mat <- matrix(0, nrow=length(rn), ncol=length(seq))
rownames(mat) <- rn
for(i in seq_along(seq)){mat[seq[i], i] <- 1 }
pfm <- new("pfm", mat=mat, name="your_seq_name")
plot(pfm) ##please make sure the canvas size: width >> height