diagplotEdaseq {metaseqR2} | R Documentation

## 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")

[Package metaseqR2 version 1.0.11 Index]