metaseqR (version 1.12.2)

diagplot.edaseq: 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 diagplot.metaseqr.

Usage

diagplot.edaseq(x, sample.list, covar = NULL,
        is.norm = FALSE,
        which.plot = c("meanvar", "meandiff", "gcbias", "lengthbias"),
        output = "x11", path = NULL, ...)

Arguments

x

the count data matrix.

sample.list

the list containing condition names and the samples under each condition.

covar

The covariate to plot counts against. Usually "gc" or "length".

is.norm

a logical indicating whether object contains raw or normalized data. It is not essential and it serves only plot annotation purposes.

which.plot

the EDASeq package plot to generate. 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 which.plot="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.

output

one or more R plotting device to direct the plot result to. Supported mechanisms: "x11" (default), "png", "jpg", "bmp", "pdf" or "ps".

path

the path to create output files.

...

further arguments to be passed to plot devices, such as parameter from par.

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.

Examples

require(DESeq)
data.matrix <- counts(makeExampleCountDataSet())
sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
diagplot.edaseq(data.matrix,sample.list,which.plot="meandiff")