mds-class {chroGPS} | R Documentation

## Class `"mds"`

### Description

Multidimensional Scaling. Function `mds` creates object of this class.

### Details

Parameters for the S4 plot method for `mds` objects.

`x`:

  Object of class `"mds"` with a 2D or 3D Multidimensional Scaling to be plotted.

`drawlabels`:

  TRUE to use rownames of the MDS points as text labels.

`labels`:

  Alternative character vector giving the text labels for the MDS points.

`plantar`:

  If a 3D MDS is used, set plantar to TRUE to plot projected views of the MDS using XY, YZ and XZ axis decomposition.

`point.cex`:

  Size of the points / spheres for the MDS plot.

`text.cex`:

  Size of text labels for the MDS points.

`text.pos`:

  Alignment position of the text labels respective to its points (1,2,3,4).

`point.col`:

  Color for the MDS points / spheres.

`text.col`:

  Color for the MDS text labels.

`point.pch`:

  PCH type for the MDS points.

`type.3d`:

  Use 'p' for points, 's' for spheres.

`radius`:

  Radius for the spheres on a 3D MDS plot. Automatically generated from point.cex and the number of points in the MDS.

`app`:

  Appearance of the 3D spheres on a 3D MDS plot, can be 'fill', 'lines', 'grid'.

`alpha`:

  Number between 0 and 1 with the level of transparency to be used on spheres on a 3D MDS.

`scalecol`:

  Set to TRUE to use a color scale for points, for instance to color points (genes) according to their expression level on a chroGPS-genes MDS plot.

`scale`:

  Scale to use to generate scale colors (for instance normalized gene expression for each element (gene) on chroGPS-genes MDS).

`palette`:

  Color palette to be used for scale colors.

`xlim`:

  Graphical limit for the X axis.

`ylim`:

  Graphical limit for the Y axis.

`zlim`:

  Graphical limit for the Z axis for 3D plots.

### Objects from the Class

Objects can be created by calls of the form `new("mds", ...)`.

### Slots

`points`:

  Object of class `"matrix"` with coordinates in the approximated space.

`Type`:

  Object of class `"character"` with the type of MDS (classicMDS, isoMDS).

`Adj`:

  Object of class `"logical"` indicating if the MDS object has been adjusted by Procrustes or not.

`R.square`:

  Object of class `"numeric"` with the percentage of variability from the original dissimilarities captured in the approximated distances.

`stress`:

  Object of class `"numeric"` with the stress for the returned MDS configuration.

### Author(s)

Oscar Reina

### See Also

`cmdscale` from package base. `isoMDS` from package MASS.

### Examples

    showClass("mds")

[Package chroGPS version 1.27.3 Index]