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.

plotMappingRate(object, ...)

# S4 method for bcbioRNASeq
plotMappingRate(object, interestingGroups = NULL,
  limit = 0.7, fill = getOption(x = "acid.fill.discrete", default =
  acidplots::scale_fill_synesthesia_d()), 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.
fill	ggproto/ScaleDiscrete. Desired ggplot2 fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual(). To set the discrete fill palette globally, use: options(acid.fill.discrete = ggplot2::scale_fill_viridis_d())
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 2019-09-16.

Examples

data(bcb)
plotMappingRate(bcb)