Plot annotated read structure examples

Plot annotated read structure examples

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', 'patient', 'rep', 'origin', 'barcode'

all_constructs

A named list of all construct libraries

nrec

Number of FASTQ records to inspect

Value

A `ggplot2` object

Examples

if (interactive()) {
    samples = data.frame(sample_id="sample1", patient="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)
}