[R] suggestions for plotting 5000 data points

[Tania Oh]

Dear all,

I have a collection of 5000 entries which represent the evolutionary  
rates of 3 animals.

I would like to show the differences between the rates of all 3  
animals and have tried using the function parallel (from the lattice  
package) and pairs() function.

The parallel function would have been perfect save for the large  
number of data (5000). The pairs() function doesn't show the  
difference explicitly. Does anyone have any suggestions on  
representing such data or have done similar plots?

I attach some simulated data:

mat3 <-matrix(sample(1:5000),nrow=5000,ncol=3, byrow=TRUE)
colnames(mat3) <- c("human","mouse", "chicken")
mat3 <-data.frame(mat3)
mat2$model <- factor( rep(  "Model 3"),  labels="model3")


## code I used for parallel

require(lattice)
parallel( ~ mat3[1:3]|model , mat3,varnames = c("human\ndnds", "mouse 
\ndnds", "chicken\ndnds") )


any suggestions or pointers would be greatly appreciated.

many thanks
tania

D.phil student
Department of Physiology, Anatomy and Genetics