plot.pcmap3d: Diagnostic plots for the map estimation using calc.maps.pc with 3 dimensions.

Description

Diagnostic plots for the map estimation using calc.maps.pc with 3 dimensions.

Usage

# S3 method for pcmap3d
plot(
  x,
  D1lim = NULL,
  D2lim = NULL,
  D3lim = NULL,
  displaytext = TRUE,
  as2d = FALSE,
  ...
)

Arguments

x: Map object from calc.maps.pc() with 3 dimensions.
D1lim: Numeric vector specifying the limits of the axis relating to dimension 1 of the wMDS used to obtain pcmap3d.
D2lim: Numeric vector specifying the limits of the axis relating to dimension 2 of the wMDS used to obtain pcmap3d.
D3lim: Numeric vector specifying the limits of the axis relating to dimension 3 of the wMDS used to obtain pcmap3d.
displaytext: Logical argument determining how markers should be labelled in the wMDS configuration plot. If TRUE then marker names are used. If FALSE then numbers are used.
as2d: If TRUE: plot this pcmap3d as if it were a pcmap (2d).
...: Further arguments are ignored. (accepted for compatibility with generic plot)

Details

Plots 4 panels

Panels 1-3 show the final MDS configuration and the fitted principal curve from the calc.maps.pc() in 3 dimensions. plots D1 vs D2, D1 vs D3 and D2 vs D3. If D1lim, D2lim or D3lim is not specified, then limits are defined by plot.smacof.

Panel 4 shows the pointwise nearest neighbour fits in order of the position in the estimated map.

Also plots a 3 dimensional scatterplot of the final MDS configuration and the fitted principal curve in a new window using plot3d from the rgl package.

Markers are assigned numbers according to the order in which they occur in the input file. The locikey output of the map object is a data frame associating marker names with their numbers. This can be accessed using pcmap3d$locikey. If displaytext=FALSE then markers will be labelled by these numbers. By default displaytext=TRUE and markers are labelled by marker name.

References

de Leeuw J, Mair P (2009) Multidimensional scaling using majorization: SMACOF in R. J Stat Softw 31: 1-30 https://www.jstatsoft.org/v31/i03/

Examples

Run this code

map<-calc.maps.pc(system.file("extdata", "lgI.txt", package="MDSMap"),
ndim=3,weightfn='lod',mapfn='haldane')
plot(map)