mds-class: Class '"mds"'

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

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")

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.