Plot Genes Detected

Plot Genes Detected

plotGenesDetected(object, counts, ...)

# S4 method for bcbioRNASeq,missing
plotGenesDetected(object, interestingGroups,
  passLimit = 20000, warnLimit = 15000, minCounts = 0,
  fill = scale_fill_viridis(discrete = TRUE), flip = TRUE)

# S4 method for data.frame,DESeqDataSet
plotGenesDetected(object, counts,
  interestingGroups = "sampleName", passLimit = 20000, warnLimit = 15000,
  minCounts = 0, fill = scale_fill_viridis(discrete = TRUE), flip = TRUE)

# S4 method for data.frame,matrix
plotGenesDetected(object, counts,
  interestingGroups = "sampleName", passLimit = 20000, warnLimit = 15000,
  minCounts = 0, fill = scale_fill_viridis(discrete = TRUE), flip = 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.
passLimit

Threshold to plot pass color marker.
warnLimit

Threshold to plot warning color marker.
minCounts

Numeric value for filtering the counts matrix before plotting.
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, plotGene, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotRRNAMappingRate, plotTotalReads

Examples

plotGenesDetected(bcb, passLimit = NULL, warnLimit = NULL)


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

# data.frame, DESeqDataSet

# NOT RUN {
plotGenesDetected(metrics(bcb), counts = dds)
# }

# data.frame, matrix

# NOT RUN {
plotGenesDetected(metrics(bcb), counts = assay(dds))
# }