Plot a summary of alignments — plotAlignmentSummary • ngsReports

Plot a summary of alignments from a set of log files

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.

Value

A ggplot2 object, or a plotly object

Details

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

Examples


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