mmds.plot {bios2mds}

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 mmds.

project

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

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 new.plot is inactivated.

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)