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Last data update: 2014.03.03

R: Plots covariance matrices

plotsubspace

R Documentation

Plots covariance matrices

Description

Represents covariance matrices as 3-d ellipsoids using the rgl package. Covariance matrices of dimension greater than 3 are plotted on the subspace defined by the first three eigenvectors.

Usage

  plotsubspace(CA, CB=NULL, corr = FALSE, shadeCA = TRUE, 
      shadeCB = TRUE, axes.lab = FALSE, ...)

Arguments

`CA`	Matrix
`CB`	Optional second matrix
`corr`	If `TRUE` the covariance matrices are transformed into correlation matrices
`shadeCA`	If `TRUE` the ellipsoid is solid, if `FALSE` the ellipsoid is wireframe
`shadeCB`	If `TRUE` the ellipsoid is solid, if `FALSE` the ellipsoid is wireframe
`axes.lab`	If `TRUE` the axes are labelled with the eigenvectors
`...`	further arguments to be passed

Details

The matrix CA is always red, and the matrix CB if given is always blue. The subspace is defined by the first three eigenvectors of CA, and the percentage of variance for each matrix along these three dimensions is given in the plot title.

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk with code taken from the rgl package

Examples

 if(requireNamespace("rgl")!=FALSE){
   G1<-rIW(diag(4),10)
   G2<-G1*1.2
 #  plotsubspace(G1, G2, shadeCB=FALSE)
 # commented out because of problems with rgl 
 }

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(MCMCglmm)
Loading required package: Matrix
Loading required package: coda
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MCMCglmm/plotsubspace.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotsubspace
> ### Title: Plots covariance matrices
> ### Aliases: plotsubspace
> ### Keywords: hplot
> 
> ### ** Examples
> 
>  if(requireNamespace("rgl")!=FALSE){
+    G1<-rIW(diag(4),10)
+    G2<-G1*1.2
+  #  plotsubspace(G1, G2, shadeCB=FALSE)
+  # commented out because of problems with rgl 
+  } 
Loading required namespace: rgl
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>