plotCountDensity: Plot Count Density

In roryk/bcbioRnaseq: RNA-Seq Utilities

Description

Plot Count Density

Usage

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

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

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