Color of points in a 3d plot of a PCA
On 4/17/2009 10:43 AM, Alejandro Gonz?lez wrote:
Dear all, I'm trying to perform a principal components analysis of a sample of individuals, and to plot it in 3D, assigning different colors according to the population each individual belongs to. Given that the matrix I have to use for the PCA cannot contain cualitative variables (here, the population of origin), I have no idea how can I do this in R. ANy help? Thanks in advance
As long as the order of rows in the matrix is unchanged when you calculate the pc scores, you should be able to use a separate dataframe or vector to give information about each row, and to work out a colour for plotting it. For example: X <- matrix(rnorm(1000), 100, 10) # Make up a fake population based on the first column popn <- round(X[,1]) colour <- popn - min(popn) + 1 pc <- princomp(X) library(rgl) plot3d(pc$scores[,1:3], col=colour) Duncan Murdoch
Alejandro Gonz?lez Departamento de Biodiversidad y Conservaci?n Real Jard?n Bot?nico Consejo Superior de Investigaciones Cient?ficas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034 914203017
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