plot.fastqc.R

Description

Create a PDF file summarizing FastQC output for a batch of samples.

Usage

plot.fastqc.R <file> <outputfile> <integer> <integer>

Dependencies

# R packages
fastqcr
ggplot2

Arguments

# Required
1) file with paths to `*_fastqc.zip` files to process


# Optional
2) PDF name [DEFAULT: "fastqc.pdf"]
3) PDF height [DEFAULT: 12 inches]
4) PDF width [DEFAULT: 12 inches]

Details

FastQC already provides a visualization of the results via .html files. However, if you work with many samples, you'd need to inspect dozens or hundreds of such files manually. CaptureAl provides a concise visualization of up to hundred or more *_fastqc.zip result files, in a single PDF file of 18 pages. Some plots show the distribution of key statistics across all samples, while other plots show detailled statistics on a per-sample basis using ggplot2 and facets for a direct comparison across samples.

Value

A PDF file with ggplot2-type visualizations for all samples.

Examples

ls -1 fastqc/*_fastqc.zip > samples.fastqc.txt
plot.fastqc.R samples.fastqc.txt fastqc_raw.pdf 18 18