Plot Counts Per Gene

Plot Counts Per Gene

plotCountsPerGene(object, ...)

# S4 method for bcbioRNASeq
plotCountsPerGene(object, interestingGroups,
  normalized = "tmm", fill = scale_fill_viridis(discrete = TRUE),
  flip = TRUE)

# S4 method for data.frame
plotCountsPerGene(object,
  interestingGroups = "sampleName", 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.
normalized

Count normalization method. See counts() documentation for more information.
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, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotGene, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotRRNAMappingRate, plotTotalReads

Examples

plotCountsPerGene(bcb)


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

# data.frame

# NOT RUN {
meltLog10(bcb, normalized = "tmm") %>% plotCountsPerGene()
# }