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)
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