plotCountDensity: Plot Count Density

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot Count Density

Usage

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plotCountDensity(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotCountDensity(object, interestingGroups,
  normalized = c("tmm", "rlog", "vst", "tpm", "rle"), style = c("line",
  "solid"), color = scale_color_hue(), fill = scale_fill_hue(),
  title = "count density")

Arguments

object

Object.

...

Additional arguments.

interestingGroups

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

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.

style

Desired plot style ("line" or "solid").

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().

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().

title

Title of plot.

Value

ggplot.

Author(s)

Michael Steinbaugh, Rory Kirchner, Victor Barrera

See Also

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

Examples

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# bcbioRNASeq ====
plotCountDensity(bcb_small)
plotCountDensity(
    object = bcb_small,
    style = "line",
    interestingGroups = "sampleName"
)

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