plotGenesDetected: Plot Genes Detected

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot Genes Detected

Usage

1
2
3
4
5
6
plotGenesDetected(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotGenesDetected(object, interestingGroups,
  limit = 0L, minCounts = 1L, fill = scale_fill_hue(), flip = TRUE,
  title = "genes detected")

Arguments

object

Object.

...

Additional arguments.

interestingGroups

Character vector denoting groups of interest that define the samples. If left unset, defaults to sampleName.

limit

Threshold to denote on the plot, using a dashed line.

minCounts

Minimum number of counts per gene in the counts matrix.

fill

Desired ggplot 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().

flip

Flip x and y axes.

title

Title of plot.

Value

ggplot.

Author(s)

Michael Steinbaugh, Rory Kirchner, Victor Barrera

See Also

Other Quality Control Functions: plot5Prime3PrimeBias, plotCorrelationHeatmap, plotCountDensity, plotCountsPerGene, plotDispEsts, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotMeanSD, plotPCACovariates, plotPCA, plotRRNAMappingRate, plotTotalReads

Examples

1

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.