Plot annotated read structure examples

Forward and reverse barcode match counts are shown at each barcode start position across all inspected reads, above up to ten read examples. Only barcode types included in the inferred structure are annotated in the reads. Read examples are shown without barcode annotations if the structure is unknown.

Usage

plot_read_structure(fq, samples, all_constructs, nrec = 100000L)

Arguments

fq

Path to one FASTQ file

samples

A sample sheet as `data.frame` in tsv format. Requires the columns 'sample_id', 'minigenes', 'rep', 'origin', 'barcode'

all_constructs

A named list of all construct libraries

nrec

Number of FASTQ records to inspect

Value

A patchwork object containing barcode counts and read examples

Examples

if (interactive()) {
    samples = data.frame(sample_id="sample1", minigenes="pat1", rep="1",
        origin="library", barcode="GGG")
    constructs = list(pat1=data.frame(gene_name="GENE1", mut_id="GENE1_A1V",
        pep_id="GENE1_A1V", pep_type="alt", tiled="ATGGCCGCC", barcode_1="AAAA"))
    fq = tempfile(fileext=".fq")
    writeLines(c("@r1", "GGGAAAA", "+", "IIIIIII", "@r2", "GGGAAAA", "+", "IIIIIII"), fq)
    plot_read_structure(fq, samples, constructs, nrec=10)
}