diagplot.boxplot {metaseqR} | R Documentation

## Boxplots wrapper for the metaseqR package

### Description

A wrapper over the general boxplot function, suitable for matrices produced and processed with the metaseqr package. Intended for internal use but can be easily used as stand-alone. It can colors boxes based on group depending on the name argument.

### Usage

        diagplot.boxplot(mat, name = NULL, log.it = "auto",
            y.lim = "default", is.norm = FALSE, output = "x11",
            path = NULL, alt.names = NULL, ...)

### Arguments

`mat` | the count data matrix.
`name` | the names of the samples plotted on the boxdiagplot. If `NULL`, the function check the column names of mat. If they are also `NULL`, sample names are autogenerated. If `name="none"`, no sample names are plotted. If name is a list, it should be the sample.list argument provided to the manin metaseqr function. In that case, the boxes are colored per group.
`log.it` | whether to log transform the values of mat or not. It can be `TRUE`, `FALSE` or `"auto"` for auto-detection. Auto-detection log transforms by default so that the boxplots are smooth and visible.
`y.lim` | custom y-axis limits. Leave the string `"default"` for default behavior.
`is.norm` | a logical indicating whether object contains raw or normalized data. It is not essential and it serves only plot annotation purposes.
`output` | one or more R plotting device to direct the plot result to. Supported mechanisms: `"x11"` (default), `"png"`, `"jpg"`, `"bmp"`, `"pdf"`, `"ps"` or `"json"`. The latter is currently available for the creation of interactive volcano plots only when reporting the output, through the highcharts javascript library (JSON for boxplots not yet available).
`path` | the path to create output files.
`alt.names` | an optional vector of names, e.g. HUGO gene symbols, alternative or complementary to the unique rownames of `mat` (which must exist!). It is used only in JSON output.
`...` | further arguments to be passed to plot devices, such as parameter from `par`.

### Value

The filename of the boxplot produced if it's a file.

### Author(s)

Panagiotis Moulos

### Examples

    # Non-normalized boxplot
    require(DESeq)
    data.matrix <- counts(makeExampleCountDataSet())
    sample.list <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
    diagplot.boxplot(data.matrix,sample.list)

    # Normalized boxplot
    norm.args <- get.defaults("normalization","deseq")
    object <- normalize.deseq(data.matrix,sample.list,norm.args)
    diagplot.boxplot(object,sample.list)

[Package metaseqR version 1.20.0 Index]