Description Usage Arguments Details Value Author(s) References See Also Examples

Given a matrix, and a distance measure, an embedding of the rows into desired Euclidean space is performed using non-Metric Multi-Dimensional Scaling.

1 |

`data` |
matrix whose rows shall be embedded. |

`embed.dim` |
Dimensionality of Euclidean space into which embedding shall be performed. |

`n.iters` |
Number of iterations of the nMDS scheme |

`metric` |
The distance metric used to compare rows. Currently only "pearson" and "euclidean" ae supported. |

`random.seed` |
A random seed used by nMDS. Use of this option allows reproducability of nMDS results |

non-Metric Multi-Dimensional Scaling is performed using the scheme proposed by Taguchi and Oono.

If an element is missing (NA) in a particular row, all distance comparisons to that row shall ignore that particular element.

An object of class "nMDS" containing:

`x` |
matrix with the same number of rows and row names as |

Satwik Rajaram and Yoshi Oono

Relational patterns of gene expression via non-metric multidimensional scaling analysis: Y.-h. Taguchi and Y. Oono, Bioinformatics, 2005 21(6):730-740.

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```
Loading required package: ggplot2
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
```

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