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

In MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling

Description

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

Usage

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

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 1 of the wMDS used to obtain pcmap3d.
D3lim	Numeric vector specifying the limits of the axis relating to dimension 1 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.
...	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 http://www.jstatsoft.org/v31/i03/

See Also

plot.pcmap, plot.spheremap,plot.smacof, calc.maps.pc, plot3d

Examples

map<-calc.maps.pc(system.file("extdata", "lgV.txt", package="MDSMap"),
ndim=3,weightfn='lod2',mapfn='haldane')
plot(map)

MDSMap documentation built on May 1, 2019, 6:51 p.m.