Plot mapping rate

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 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

Michael Steinbaugh, Rory Kirchner, Victor Barrera

Examples

data(bcb)

## bcbioRNASeq ====
plotMappingRate(bcb)