metaseqR (version 1.12.2)

diagplot.noiseq: Diagnostic plots based on the NOISeq package

Description

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

Usage

diagplot.noiseq(x, sample.list, covars,
        which.plot = c("biodetection", "countsbio", "saturation", "rnacomp", 
               "readnoise", "biodist"),
        output = "x11",
        biodist.opts = list(p = NULL, pcut = NULL, name = NULL),
        path = NULL, is.norm = FALSE, ...)

Arguments

x

the count data matrix.

sample.list

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

covars

a list (whose annotation elements are ideally a subset of an annotation data frame produced by get.annotation) with the following members: data (the data matrix), length (gene length), gc (the gene gc_content), chromosome (a data frame with chromosome name and co-ordinates), factors (a factor with the experimental condition names replicated by the number of samples in each experimental condition) and biotype (each gene's biotype as depicted in Ensembl-like annotations).

which.plot

the NOISeq package plot to generate. It can be one or more of "biodetection", "countsbio", "saturation", "rnacomp", "readnoise" or "biodist". Please refer to the documentation of the EDASeq package for details on the use of these plots. The which.plot="saturation" case is modified to be more informative by producing two kinds of plots. See diagplot.noiseq.saturation.

biodist.opts

a list with the following members: p (a vector of p-values, e.g. the p-values of a contrast), pcut (a unique number depicting a p-value cutoff, required for the "biodist" case), name (a name for the "biodist" plot, e.g. the name of the contrast.

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.

is.norm

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

...

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

Value

• The filenames of the plots 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"))
lengths <- round(1000*runif(nrow(data.matrix)))
starts <- round(1000*runif(nrow(data.matrix)))
ends <- starts + lengths
covars <- list(
    data=data.matrix,
    length=lengths,
    gc=runif(nrow(data.matrix)),
    chromosome=data.frame(
        chromosome=c(rep("chr1",nrow(data.matrix)/2),
            rep("chr2",nrow(data.matrix)/2)),
        start=starts,
        end=ends
    ),
    factors=data.frame(class=as.class.vector(sample.list)),
    biotype=c(rep("protein_coding",nrow(data.matrix)/2),rep("ncRNA",
            nrow(data.matrix)/2))
)
p <- runif(nrow(data.matrix))
diagplot.noiseq(data.matrix,sample.list,covars=covars,
        biodist.opts=list(p=p,pcut=0.1,name="A_vs_B"))