mmds.plot {bios2mds} | R Documentation |
Plots a summary of the mmds results
Description
Displays one scree plot and three scatter plots of mmds
results.
Usage
mmds.plot(x, project = NULL, new.plot = TRUE, pdf.file = NULL)
Arguments
x |
an object of class 'mmds', obtained from |
project |
an object of class 'project', obtained from |
new.plot |
a boolean indicating whether a new graphical device should be created (TRUE) or not (FALSE). Default is TRUE. |
pdf.file |
a string indicating the name and directory of the pdf graph outfile. Default is NULL. If this parameter is not
NULL, the parameter |
Details
mmds.plot
is a wrapper calling of both scree.plot
and mmds.2D.plot
.
It produces a 2x2 plot with one scree plot of the relative eigenvalues, in the upper left, and three scatter plots. The three scatter plots are generated as follows:
scatter plot of the elements on the first and second components in the upper right.
scatter plot of the elements on the first and third components in the lower left.
scatter plot of the elements on the second and third components in the lower right.
If object x
contains supplementary elements, they are also projected onto the three scatter plots.
The active and supplementary elements are represented by dots and crosses, respectively.
The color.group
function may be used before calling mmds.plot
to color elements by user-provided groups.
Value
Produces a summary plot of the MDS analysis on the same active graphical device.
Note
The scatter plots can display supplementary objects if their coordinates are present in x
input.
Author(s)
Julien Pele and Jean-Michel Becu
See Also
plot.pca
function in bio3d
package.
Examples
# summary plot of the MDS analysis of human GPCRs with projection of GPCRs
# from D. melanogaster as supplementary elements:
data(gpcr)
mmds.plot(gpcr$mmds$sapiens.active,gpcr$mmds$melanogaster.project)