plotMeanSD: Plot Row Standard Deviations vs. Row Means

Description Usage Arguments Value Author(s) See Also Examples

Description

vsn::meanSdPlot() wrapper that plots log2(), rlog(), and varianceStabilizingTransformation() normalized counts.

Usage

1
2
3
4
5
6
7
8
9
plotMeanSD(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotMeanSD(object, orientation = c("vertical",
  "horizontal"), legend = FALSE)

## S4 method for signature 'DESeqDataSet'
plotMeanSD(object, orientation = c("vertical",
  "horizontal"), legend = FALSE)

Arguments

object

Object.

...

Additional arguments.

orientation

Orientation to use for plot grid, either horizontal or vertical.

legend

Include the color bar legend. This is typically not that informative and is disabled by default, to improve the plot appearance.

Value

ggplot grid.

Author(s)

Michael Steinbaugh, Lorena Patano

See Also

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

Examples

1
2
3
4
5
# bcbioRNASeq ====
plotMeanSD(bcb_small)

# DESeqDataSet ====
plotMeanSD(dds_small)

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