diagplot.noiseq {metaseqR} | R Documentation

## 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.

### Note

Please note that in case of `"biodist"` plots, the behavior of the function is unstable, mostly due to the very specific inputs this plotting function accepts in the NOISeq package. We have tried to predict unstable behavior and avoid exceptions through the use of tryCatch but it's still possible that you might run onto an error.

### Author(s)

Panagiotis Moulos

### 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"))

[Package metaseqR version 1.28.0 Index]