mmds.3D.plot: Display the mmds coordinates onto a 3D space
In bios2mds: From Biological Sequences to Multidimensional Scaling

Description Usage Arguments Details Value Note Author(s) Examples

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

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, ...)

`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.

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.

Produces a 3D plot on graphical device.

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

Jean-Michel Becu

# 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)