Skip to contents

fastq_plot

fastq_plot.Rd

Function to plot nucleotide sequences from a raw `.fastq` file in a grid format

Usage

fastq_plot(patient_id, output_dir = tempdir(), n, read_length)

Arguments

patient_id

A character string representing the patient ID.

output_dir

A character string specifying the directory where the plot file will be saved.

n

An integer specifying the number of reads to plot.

read_length

An integer specifying the length of each read. It should be a multiple of 4. Default is 8.

Details

The function reads a `.fastq` file and plots the sequences in a grid format. Each base is represented by a different color:

  • A: Green

  • T: Red

  • G: Blue

  • C: Orange

  • N: Gray

The plot is saved as a PNG file in the specified output directory.

Examples

# Plot nucleotide sequences for patient ID "patient_123" with 2 reads of length 8
fastq_plot("patient_123", output_dir = tempdir(), n = 2, read_length = 8)
#> Plot saved to: /tmp/RtmpCk48DO/fastq_plot_patient_123.png