plotMappingRate: Plot mapping rate

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Plot mapping rate

Description

The genomic mapping rate represents the percentage of reads mapping to the reference genome. Low mapping rates are indicative of sample contamination, poor sequencing quality or other artifacts.

Usage

plotMappingRate(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotMappingRate(
  object,
  interestingGroups = NULL,
  limit = 0.7,
  labels = list(title = "Mapping rate", subtitle = NULL, sampleAxis = NULL, metricAxis =
    "mapping rate (%)"),
  flip = getOption(x = "acid.flip", default = TRUE)
)

Arguments

object	Object.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
limit	numeric(1). Threshold limit.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
flip	logical(1). Flip x and y axes. Recommended for plots containing many samples.
...	Additional arguments.

Value

ggplot.

Note

Updated 2022-05-09.

Author(s)

Michael Steinbaugh, Rory Kirchner, Victor Barrera

Examples

data(bcb)

## bcbioRNASeq ====
plotMappingRate(bcb)

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.