diagplotEdaseq: Diagnostic plots based on the EDASeq package

In pmoulos/metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Diagnostic plots based on the EDASeq package

Description

A wrapper around the plotting functions availale in the EDASeq normalization Bioconductor package. For analytical explanation of each plot please see the vignette of the EDASeq package. It is best to use this function through the main plotting function metaseqrPlot.

Usage

    diagplotEdaseq(x, sampleList, covar = NULL,
        isNorm = FALSE,
        whichPlot = c("meanvar", "meandiff", "gcbias", "lengthbias"),
        output = "x11", altNames = NULL, path = NULL, ...)

Arguments

x	the count data matrix.
sampleList	the list containing condition names and the samples under each condition.
covar	The covariate to plot counts against. Usually "gc" or "length".
isNorm	a logical indicating whether object contains raw or normalized data. It is not essential and it serves only plot annotation purposes.
whichPlot	the EDASeq package plot to generate. See Details.
output	one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf" or "ps".
altNames	optional names, alternative or complementary to the rownames of x. It is used only in JSON output.
path	the path to create output files.
...	further arguments to be passed to plot devices, such as parameter from par.

Details

Regarding whichPlot, it can be one or more of "meanvar", "meandiff", "gcbias" or "lengthbias". Please refer to the documentation of the EDASeq package for details on the use of these plots. The whichPlot="lengthbias" case is not covered by EDASeq documentation, however it is similar to the GC-bias plot when the covariate is the gene length instead of the GC content.

Value

The filenames of the plot produced in a named list with names the which.plot argument. If output="x11", no output filenames are produced.

Author(s)

Panagiotis Moulos

Examples

dataMatrix <- metaseqR2:::exampleCountData(2000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
diagplotEdaseq(dataMatrix,sampleList,whichPlot="meandiff")

pmoulos/metaseqR2 documentation built on May 20, 2024, 5:48 a.m.