mmds.3D.plot {bios2mds}

Display the mmds coordinates onto a 3D space

Description

Displays a 3D plot of the active elements and, if present, of supplementary elements, after a metric MDS analysis.

Usage

mmds.3D.plot(x, project = NULL, title = NULL, axis = c(1:3), 
active.type = "s", sup.type = "p", active.size = 2, radius = 0.005,
sup.size = 10, active.col = x$col[,3], sup.col = project$col[,3], 
box = TRUE, axes = TRUE, new.plot = TRUE, label = TRUE,
xlim = NULL, ylim = NULL, zlim = NULL, box.lwd = 2,
box.antialias = TRUE, ...)

Arguments

x

an object of class 'mmds', obtained from mmds function.

title

a string of characters representing the title of the plot. Default is "Metric MDS".

project

an object of class 'project', obtained from mmds.project function, or a list of object of class 'project'.

axis

a numeric vector of length three representing the principal components displayed on the plot. Default is c(1:3).

active.type

an character indicating the symbol of active elements. This should be one of "s" for spheres, "p" for points, "l" for lines, "h" for line segments from z=0 and "n" for none. Default is "s", corresponding to spheres.

sup.type

an character indicating the symbol of supplementary elements. This should be one of "s" for spheres, "p" for points, "l" for lines, "h" for line segments from z=0 and "n" for none. Default is "p", corresponding to points.

active.col

a string of characters or character vector representing the color(s) of the active elements. Default is x$col[,3]. It corresponds either to the user-provided colors if the col.group function has been used previously, or to black (filled automaticaly with the mmds function).

sup.col

a string or character vector representing the color(s) of supplementary elements. Default is project$col[,3]. It corresponds either to the user-provided colors if the col.group function has been used previously, or to magenta (filled automaticaly with the mmds function)

active.size

a numeric value indicating the size of active symbols. Default is 2.

sup.size

a numeric value indicating the size of supplementary symbols. Default is 20.

box

a boolean indicating whether the box should be displayed (TRUE) or not (FALSE). Default is TRUE.

axes

a boolean indicating whether axes should be displayed (TRUE) or not (FALSE). Default is TRUE.

radius

a numeric value indicating the radius of spheres symbols only. If x.type equal to "s" the x.size parameter was inactivated. Default is 0.01.

new.plot

a boolean indicating whether a new 3D plot create/replace active 3D device (TRUE) or not to insert in it (FALSE). Default is TRUE.

label

a boolean indicating whether the label axes should be displayed (TRUE) or not (FALSE). Default is TRUE.

xlim

a numeric vector representing the range for the x values. Default is full range.

ylim

a numeric vector representing the range for the y values. Default is full range.

zlim

a numeric vector representing the range for the z values. Default is full range.

box.lwd

a numeric value indicating the width of box and axes lines. Default is 2.

box.antialias

a boolean specifying if box and axes lines should be antiliased. Default is TRUE.

...

additional parameters which will be passed to par3d, material3d and decorate3d of rgl package.

Details

If mmds.3D.plot is used after the col.group function, the elements are colored by the color scheme provided in the .csv file (see col.group for details). If the col.group function has not been used, the default colors are black and magenta for active and supplementary elements.

mmds.3D.plot helps identify patterns in data and compare active and supplementary elements.

Value

Produces a 3D plot on graphical device.

Note

mmds.3D.plot requires plot3D function from rgl package. See rgl documentation to supplementary function like snapshot3D to save image file of 3D device.

Author(s)

Jean-Michel Becu

Examples

# 3D plot of human GPCRs onto the first three axes obained from MDS analysis
# with projection of GPCRs from D. melanogaster as supplementary elements:
data(gpcr)
mmds.3D.plot(gpcr$mmds$sapiens.active,active.type="p",label=FALSE,lit=FALSE,
point_antialias=TRUE,box.lwd=3,sup.size=4.3,active.size=4.3)
bbox3d(shininess=0.5)