Hello everyone,
I need plot, which visualize percentage of nucletides per base in R. I have a percentage of bases but now I don't know how to visualize them. 

    fastq <- readDNAStringSet("https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq","fastq")
    freq <- alphabetFrequency(fastq)
    perc <- freq/width(fastq)*100
    perc <- as.data.frame(perc)
    perc

Any help? Thanks.
    library(Biostrings)
    fastq <- readDNAStringSet("test.fa","fasta")
    fastq
    af=alphabetFrequency(fastq, as.prob = T,baseOnly=T)
    barplot(af)

No need to convert per and as.prob=T will convert it percentages and you can bar plot directly without converting it data frame.