plotAlignmentSummary: Plot a summary of alignments

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

Plot a summary of alignments

Description

Plot a summary of alignments from a set of log files

Usage

plotAlignmentSummary(
  x,
  type = c("star", "bowtie", "bowtie2", "hisat2"),
  usePlotly = FALSE,
  stripPaths = TRUE,
  asPercent = FALSE,
  ...,
  fill = c("red", "yellow", "blue", rgb(0, 0.5, 1))
)

Arguments

x	Paths to one or more alignment log files
type	The aligner used. Can be one of star, bowtie, bowtie2 or hisat2
usePlotly	logical. If TRUE an interactive plot will be generated.
stripPaths	logical(1). Remove paths from the Filename column
asPercent	Show alignments as percentages, with the alternative (FALSE) being the total number of reads If FALSE a ggplot object will be output
...	Used to pass additional attributes to theme() and between methods
fill	Colours used to fill the bars. Passed to scale_fill_manual.

Details

Loads a set of alignment log files and creates a default plot. Implemented aligners are bowtie, bowtie2, Hisat2 and STAR.

Value

A ggplot2 object, or a plotly object

Examples

f <- c("bowtie2PE.txt", "bowtie2SE.txt")
bowtie2Logs <- system.file("extdata", f, package = "ngsReports")
plotAlignmentSummary(bowtie2Logs, "bowtie2")

UofABioinformaticsHub/fastqcReports documentation built on July 23, 2024, 3:26 p.m.