tr_qc_plots: Create ggplot2 figures from MultiQC results
In travis-m-blimkie/tRavis: tRavis: an R package by Travis Blimkie

tr_qc_plots

R Documentation

Create ggplot2 figures from MultiQC results

Description

Creates four ggplot2 figures from MultiQC results, and returns the data along with the plot objects. The plots are for FastQC (read counts and Phred scores), STAR, and HTSeq. See Details for more information.

Usage

tr_qc_plots(directory, font_size = 18, threshold_line = 1e+07, limits = NULL)

Arguments

`directory`	Folder containing all the data files generated by MultiQC, e.g. "multiqc_data/"
`font_size`	Base font size (defaults to 18)
`threshold_line`	Provide a number to draw a red dashed line at the indicated number of reads for FastQC read, STAR, and HTSeq plots. Defaults to 10e6; set to NULL to disable.
`limits`	Override the upper limit of FastQC read, STAR, and HTSeq plots. Supply a single number to give all three plots the same limit, or a vector of three values to modify each individually. Defaults to NULL, which sets automatic limits.

Details

For the Phred scores, one must open the MultiQC HTML report, and export the data for "fastqc_per_base_sequence_quality_plot" as a tab- delimited file (TSV), placing it inside the same directory as the rest.