diagplotBoxplot: Boxplots wrapper for the metaseqR2 package

In pmoulos/metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Boxplots wrapper for the metaseqR2 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

    diagplotBoxplot(mat, name = NULL, logIt = "auto",
        yLim = "default", isNorm = FALSE, output = "x11",
        path = NULL, altNames = NULL, ...)

Arguments

mat	the count data matrix.
name	the names of the samples plotted on the boxplot. See also Details.
logIt	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.
yLim	custom y-axis limits. Leave the string "default" for default behavior.
isNorm	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.
altNames	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.

Details

Regarding name, 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 sampleList argument provided to the manin metaseqr2 function. In that case, the boxes are colored per group.

Value

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

Author(s)

Panagiotis Moulos

Examples

# Non-normalized boxplot
require(DESeq2)
dataMatrix <- metaseqR2:::exampleCountData(2000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
diagplotBoxplot(dataMatrix,sampleList)

# Normalized boxplot
normArgs <- getDefaults("normalization","deseq2")
object <- normalizeDeseq2(dataMatrix,sampleList,normArgs)
diagplotBoxplot(object,sampleList)

pmoulos/metaseqR2 documentation built on May 20, 2024, 5:48 a.m.