nMDS: non-Metric Multi-Dimensional Scaling
In NeatMap: Non-clustered heatmap alternatives

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	nMDS(data, embed.dim = 2, n.iters = 300, metric = "pearson",random.seed=NULL)

`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 `data` and having `embed.data` columns

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.

prcomp

#Two dimensional embedding
mtcars.nMDS<-nMDS(as.matrix(mtcars),embed.dim=2,metric="euclidean")
plot(mtcars.nMDS$x,type='n')
text(mtcars.nMDS$x,labels=rownames(mtcars.nMDS$x))

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