Plot ribosomal RNA (rRNA) mapping rate

Clean, high-quality samples should have an rRNA mapping rate below 10%. Higher rates are likely indicative of the polyA enrichment or ribo depletion protocol not having removed all ribosomal RNA (rRNA) transcripts. This will reduce the number of biologically meaningful reads in the experiment and is best avoided.

Usage

plotRrnaMappingRate(object, ...)

# S4 method for bcbioRNASeq
plotRrnaMappingRate(
  object,
  interestingGroups = NULL,
  limit = 0.1,
  labels = list(title = "rRNA mapping rate", subtitle = NULL, sampleAxis = NULL,
    metricAxis = "rRNA 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 ====
plotRrnaMappingRate(bcb)