plot_mds {NanoMethViz} | R Documentation

## Plot MDS

### Description

Plot multi-dimensional scaling plot using algorithm of limma::plotMDS(). It is recommended this be done with the log-methylation-ratio matrix generated by bsseq_to_log_methy_ratio().

### Usage

    plot_mds(
      x,
      top = 500,
      plot_dims = c(1, 2),
      labels = colnames(x),
      groups = NULL
    )

### Arguments

`x` | the log-methylation-ratio matrix.
`top` | the number of top genes used to calculate pairwise distances.
`plot_dims` | the numeric vector of the two dimensions to be plotted.
`labels` | the character vector of labels for data points. By default uses column names of x, set to NULL to plot points.
`groups` | the character vector of groups the data points will be coloured by.

### Value

ggplot object of the MDS plot.

### Examples

    nmr <- load_example_nanomethresult()
    bss <- methy_to_bsseq(nmr)
    lmr <- bsseq_to_log_methy_ratio(bss)
    plot_mds(lmr)

[Package NanoMethViz version 2.0.0 Index]