DaMiR.MDSplot {DaMiRseq} | R Documentation

## Plot multidimentional scaling (MDS)

### Description

A MDS plot is drawn in order to visualize class clustering.

### Usage

    DaMiR.MDSplot(data, df, type = c("spearman", "pearson"))

### Arguments

`data` | A SummarizedExperiment object or a matrix or a data.frame where rows and cols should be, respectively, observations and features
`df` | A data frame with class; it can be directly subset from data
`type` | A character string specifing the metric to be applied to correlation analysis. Either "spearman" or "pearson" is allowed; default is "spearman"

### Details

The MDS plot is drawn taking as input a dissimilarity matrix produced by either a sample-per-sample Pearson's or Spearman's correlation of normalized expression data.

### Value

A MDS plot, using only 'class' information

### Author(s)

Mattia Chiesa, Luca Piacentini

### Examples

    # use example data:
    data(data_reduced)
    data(df)
    # Draw MDS:
    DaMiR.MDSplot(data=data_reduced, df=df, type="pearson")

[Package DaMiRseq version 1.4.2 Index]