plotGeneSaturation: Plot Gene Detection Saturation

In WeiSong-bio/roryk-bcbioRNASeq: RNA-Seq Utilities

Description

Plot Gene Detection Saturation

Usage

plotGeneSaturation(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotGeneSaturation(object, normalized = c("rlog",
  "vst", "tmm", "tpm"), interestingGroups, minCounts = 1L,
  trendline = FALSE, color = scale_color_hue(), title = "gene saturation")

Arguments

object	Object.
...	Additional arguments.
normalized	Character indicating which normalization method to apply: "tpm": Transcripts per million (tximport). "tmm": edgeR trimmed mean of M-values. Calculated on the fly. "rlog": DESeq2 log2 regularized log transformation. "vst": DESeq2 log2 variance stabilizing transformation.
interestingGroups	Character vector denoting groups of interest that define the samples. If left unset, defaults to sampleName.
minCounts	Minimum number of counts per gene in the counts matrix.
trendline	Include a trendline for each group.
color	Desired ggplot color 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_color_manual().
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, plotGenesDetected, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotMeanSD, plotPCACovariates, plotPCA, plotRRNAMappingRate, plotTotalReads

Examples

# Minimal example distorts the y-axis
plotGeneSaturation(bcb_small)

WeiSong-bio/roryk-bcbioRNASeq documentation built on July 6, 2019, 12:02 a.m.