diagplot.mds {metaseqR} | R Documentation

## 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.

### Author(s)

Panagiotis Moulos

### 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)

[Package metaseqR version 1.28.0 Index]