plotAlignmentSummary {ngsReports} | R 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")

[Package ngsReports version 1.6.1 Index]