clusGPS-class {chroGPS} | R Documentation

## Class `"clusGPS"`

### Description

Agglomerative Nesting for a distGPS object. Contains probability contours and bayesian posterior probability of mis-classification for the clusters evaluated.

### 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.

### Objects from the Class

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

### Slots

`h`:

  Object of class `"hclust"` with Agglomerative Nesting or user-provided cluster object.

`clus`:

  Object of class `"list"` with probability contour and bayesian posterior probability of mis-classification information for the clusters evaluated.

`adjusted`:

  Object of class `"logical"` indicating if bayesian posterior probabilities of mis-classification are adjusted for multiple testing.

### Author(s)

Oscar Reina

### Examples

    showClass("clusGPS")

[Package chroGPS version 1.27.3 Index]