metaseqR (version 1.12.2)

diagplot.mds: Multi-Dimensinal Scale plots or RNA-Seq samples

Description

Creates a Multi-Dimensional Scale plot for the given samples based on the count data matrix. MDS plots are very useful for quality control as you can easily see of samples of the same groups are clustered together based on the whole dataset.

Usage

diagplot.mds(x, sample.list, method = "spearman",
        log.it = TRUE, output = "x11", path = NULL, ...)

Arguments

x

the count data matrix.

sample.list

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

method

which correlation method to use. Same as the method parameter in cor function.

log.it

whether to log transform the values of x or not.

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.

path

the path to create output files.

...

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

Value

• The filename of the MDS plot produced if it's a file.

Examples

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