Plot Gene Detection Saturation

Plot Gene Detection Saturation

plotGeneSaturation(object, counts, ...)

# S4 method for bcbioRNASeq,missing
plotGeneSaturation(object, interestingGroups,
  normalized = "tmm", minCounts = 0, color = scale_color_viridis(discrete
  = TRUE))

# S4 method for data.frame,matrix
plotGeneSaturation(object, counts,
  interestingGroups = "sampleName", minCounts = 0,
  color = scale_color_viridis(discrete = TRUE))

Arguments

object	Object.
counts	Object containing a count matrix.
...	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.
normalized	Count normalization method. See counts() documentation for more information.
minCounts	Numeric value for filtering the counts matrix before plotting.
color	Desired ggplot color scale. Defaults to viridis::scale_color_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_color_manual().

Value

ggplot.

See also

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

Examples

plotGeneSaturation(bcb)

# NOT RUN {
plotGeneSaturation(bcb, interestingGroups = "group")
# }

# data.frame, matrix
# NOT RUN {
plotGeneSaturation(metrics(bcb), assay(rld))
# }