Plot mapped reads

The number of mapped reads should correspond to the number of total reads.

plotMappedReads(object, ...)

# S4 method for bcbioRNASeq
plotMappedReads(object, interestingGroups = NULL,
  limit = 10000000L, perMillion = TRUE, fill = getOption(x =
  "acid.fill.discrete", default = acidplots::scale_fill_synesthesia_d()),
  labels = list(title = "Mapped reads", subtitle = NULL, sampleAxis =
  NULL, metricAxis = "reads"), 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.
perMillion	logical(1). Display as counts per million.
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)
plotMappedReads(bcb)