R help - Dec 2012 - points3d and ordirgl

Hello all, I have been using the function ordirgl to plot 3D dynamic
ordinations.  The ordirgl function works just fine. IN fact, I was even
able to write a function that allows me to identify points in the 3D plot:

identify.rgl<-function(env_var,ord,dim1,dim2,dim3)

{
        tmp<-select3d(button="left")
        tmp.keep<-tmp(ord[,dim1],ord[,dim2],ord[,dim3])
        env_var[tmp.keep=="TRUE"]
}

where
env_var = a variable to be identified (e.g. plot IDs as in >
row.names(dataframe))
ord = ordination points or scores created using a function such as metaMDS
or nmds) that is recognized by points or scores
dim1 = dimension 1 (e.g., 1)
dim2 = dimension 2 (e.g., 2)
dim 3 = dimension 3 (e.g, 3

e.g.,  > identify.rgl(row.names(vegmat),veg_nmds$points,1,2,3)

My issue is that I would like to use the points3d function to add points of
different colors and sizes to the dynamic 3D plot created by using ordirgl.
In my case the different colored and sized points represent different
clusters from the results of the Partitioning Around Mediods (pam)
clustering function (from library cluster).  I have used this with success
in the past (two years back), but can't get it to work properly  now. An
example of the code I have used in the past is:
>
points3d(veg_nmds$points[,1],veg_nmds$points[,2],veg_nmds$points[,3],display
= "sites",veg_pam12$clustering=="1",col=2,size=3)

The code above is intended to add the points from cluster 1 to the nmds
plot in the color red and size 3.

Anyone have an ideas?

Thanks,
       Aaron

	[[alternative HTML version deleted]]

On 12-12-06 7:20 PM, Aaron Wells wrote:
> Hello all, I have been using the function ordirgl to plot 3D dynamic
> ordinations.  The ordirgl function works just fine. IN fact, I was even
> able to write a function that allows me to identify points in the 3D plot:
>
> identify.rgl<-function(env_var,ord,dim1,dim2,dim3)
>
> {
>          tmp<-select3d(button="left")
>          tmp.keep<-tmp(ord[,dim1],ord[,dim2],ord[,dim3])
>          env_var[tmp.keep=="TRUE"]
> }
>
> where
> env_var = a variable to be identified (e.g. plot IDs as in >
> row.names(dataframe))
> ord = ordination points or scores created using a function such as metaMDS
> or nmds) that is recognized by points or scores
> dim1 = dimension 1 (e.g., 1)
> dim2 = dimension 2 (e.g., 2)
> dim 3 = dimension 3 (e.g, 3
>
> e.g.,  > identify.rgl(row.names(vegmat),veg_nmds$points,1,2,3)
>
> My issue is that I would like to use the points3d function to add points of
> different colors and sizes to the dynamic 3D plot created by using ordirgl.
> In my case the different colored and sized points represent different
> clusters from the results of the Partitioning Around Mediods (pam)
> clustering function (from library cluster).  I have used this with success
> in the past (two years back), but can't get it to work properly  now.
An
> example of the code I have used in the past is:
>
>>
>
points3d(veg_nmds$points[,1],veg_nmds$points[,2],veg_nmds$points[,3],display
> = "sites",veg_pam12$clustering=="1",col=2,size=3)
Where are you finding the points3d function?  The one in rgl doesn't 
have a "display" argument.  The logical argument that follows it
doesn't
seem to make sense either.
>
> The code above is intended to add the points from cluster 1 to the nmds
> plot in the color red and size 3.
If you want red, it's slightly safer to use "red" instead of 2,
because
someone might have changed the palette.

Duncan Murdoch
>
> Anyone have an ideas?
>
> Thanks,
>         Aaron
>
> 	[[alternative HTML version deleted]]
>
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