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]