R help - Feb 2015 - 2d rotation: vegan?

I've been working at interpreting the results of a non-metric
multidimensional scaling analysis. I have been using metaMDS in the vegan
package because one of the benefits is that it also rotates to solution to its
principal components. (Eventually I realized that there is no reason why my
results would be most interpretable when aligned along the PC, but it was a nice
starting point.)

I have been trying to find ways to rotate the resulting plot so I can visualize
it differently and look at actual plot positions (as opposed to just rotating
the print outs I have been looking at.) I'm able to find lots of suggestions
for how to rotate3d plots, but almost nothing for 2d. I have tried using the
MDSrotate function in vegan, but really it comes down to the fact that I'm
clueless when I try to make sense of the documentation. *somewhat embarrassed* 
My goal is basically to rotate the plot and exam the structure as a tool to
generate theories about the meaning of the different dimensions (the
interpretation of the clusters in my research are crystal clear.)

I generated a little fake data, just so there would be a plot. I've been
trying to figure out how to do this as either just a simple scatterplot or using
the vegan package.

Thank you for your time,
Randy

Randall Morris-Ostrom J.D., M.S.
Doctoral Candidate in Psychology,
University of St. Thomas
randall.morrisostrom at icloud.com


Sample Code

library(vegan)
set.seed(12345)
x <- rnorm(1:10)
y <- rnorm(1:10)
df <- data.frame(x,y)
d <- dist(df, method = "euclidean")
nmds <- metaMDS(df, distance = "euclidean", k = 2)
plot(nmds)
# or
nmdp <- as.data.frame(nmds$points)
plot(nmdp$MDS1, nmdp$MDS2)
	[[alternative HTML version deleted]]

Randall,
  You might try the factor.rotate function in the psych package.  That will
allow you to ?hand rotate? any solution where (in your example) nmdp is a
matrix.

You also could look at the the various rotations available in the GPArotation
package.

Bill
> On Feb 13, 2015, at 9:08 AM, Randall Morris-Ostrom <randall.morrisostrom
at icloud.com> wrote:
> 
> I've been working at interpreting the results of a non-metric
multidimensional scaling analysis. I have been using metaMDS in the vegan
package because one of the benefits is that it also rotates to solution to its
principal components. (Eventually I realized that there is no reason why my
results would be most interpretable when aligned along the PC, but it was a nice
starting point.)
> 
> I have been trying to find ways to rotate the resulting plot so I can
visualize it differently and look at actual plot positions (as opposed to just
rotating the print outs I have been looking at.) I'm able to find lots of
suggestions for how to rotate3d plots, but almost nothing for 2d. I have tried
using the MDSrotate function in vegan, but really it comes down to the fact that
I'm clueless when I try to make sense of the documentation. *somewhat
embarrassed*  My goal is basically to rotate the plot and exam the structure as
a tool to generate theories about the meaning of the different dimensions (the
interpretation of the clusters in my research are crystal clear.)
> 
> I generated a little fake data, just so there would be a plot. I've
been trying to figure out how to do this as either just a simple scatterplot or
using the vegan package.
> 
> Thank you for your time,
> Randy
> 
> Randall Morris-Ostrom J.D., M.S.
> Doctoral Candidate in Psychology,
> University of St. Thomas
> randall.morrisostrom at icloud.com
> 
> 
> Sample Code
> 
> library(vegan)
> set.seed(12345)
> x <- rnorm(1:10)
> y <- rnorm(1:10)
> df <- data.frame(x,y)
> d <- dist(df, method = "euclidean")
> nmds <- metaMDS(df, distance = "euclidean", k = 2)
> plot(nmds)
> # or
> nmdp <- as.data.frame(nmds$points)
> plot(nmdp$MDS1, nmdp$MDS2)
> 	[[alternative HTML version deleted]]
> 
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