plotGenesDetected: Plot Genes Detected

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Plot Genes Detected

Usage

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

plotGenesDetected(bcb_small)

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