plot_trimmomatic_paired: Trimmomatic statistics histograms

In bryancquach/omixjutsu: Utilities for omics analysis tasks

Trimmomatic statistics histograms

Description

Create a histograms for read retention and filtering rates.

Usage

plot_trimmomatic_paired(
  data,
  binsize = c(2.5, 0.5),
  fill = c("gray10", "goldenrod2", "steelblue4"),
  alpha = 0.5,
  ids = NULL,
  invert = F
)

Arguments

data	A data frame with sequencing depth data in the same format as trimmomatic returned by load_paired_end_qc_data.
binsize	A 2-item numeric vector that denotes the bin width for histogram bars. The first value is for the excluded plot, and the other value corresponds to the retained plot.
fill	A 3-item vector of strings that denotes the colors for histogram bars. The first color is for the excluded plot, and the other colors correspond to R1 and R2 reads in the retained plot.
alpha	A numeric. The alpha level for histogram bars.
ids	A vector of rownames for subsetting data for plotting.
invert	A logical. Should ids be used for excluding rows from plotting instead?

Details

Uses output generated by MultiQC on Trimmomatic output for paired-end sequencing data to produce sample frequency histograms of read retention and filtering rates. Note: this function only works with Trimmomatic output for paired-end sequencing data.

Value

A list with two ggplot objects, excluded and retained that correspond to ggplot objects for reads excluded and retained after Trimmomatic respectively.

See Also

load_paired_end_qc_data

bryancquach/omixjutsu documentation built on Jan. 29, 2023, 3:47 p.m.