metaseqR (version 1.12.2)

diagplot.boxplot: 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.

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)