Plot Mapped Reads

Plot Mapped Reads

plotMappedReads(object, ...)

# S4 method for bcbioRNASeq
plotMappedReads(object, interestingGroups,
  passLimit = 20, warnLimit = 10, fill = scale_fill_viridis(discrete =
  TRUE), flip = TRUE)

# S4 method for data.frame
plotMappedReads(object,
  interestingGroups = "sampleName", passLimit = 20, warnLimit = 10,
  fill = scale_fill_viridis(discrete = TRUE), flip = TRUE)

Arguments

object	Object.
...	Additional arguments (for the S4 generic definition).
interestingGroups	Category to use to group samples. In the plotting functions, this will define color and shape, where applicable. If unset, this is automatically determined by the metadata set inside the bcbioRNASeq object. When set to NULL, this will default to sampleName.
passLimit	Threshold to plot pass color marker.
warnLimit	Threshold to plot warning color marker.
fill	Desired ggplot fill scale. Defaults to viridis::scale_fill_viridis(). 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().
flip	Flip x and y axes.

Value

ggplot.

See also

Other Quality Control Plots: plot53Bias, plotCountDensity, plotCountsPerGene, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotGene, plotIntronicMappingRate, plotMappingRate, plotRRNAMappingRate, plotTotalReads

Examples

plotMappedReads(bcb)

# NOT RUN {
plotMappedReads(
    bcb,
    interestingGroups = "group",
    fill = NULL)
# }

# data.frame
# NOT RUN {
metrics(bcb) %>% plotMappedReads()
# }