plotAlignmentSummary: Plot a summary of alignments

View source: R/plotAlignmentSummary.R

plotAlignmentSummaryR Documentation

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.