[R-sig-eco] nMDS plot with points of different size

[Gavin Simpson]

On Thu, 2013-03-07 at 15:37 +0000, Mark Fulton wrote:
> There's probably something "off the shelf", but
> I use a little function written in R:
> 
> #A function for doing an xyz bubbleplot.
> bubbleplot <- function(x, y, z, bmax=4, bmin=.5) {
>   plot(x,y, type="n")
>   z <- z-min(z); z <- z/max(z)
>   for (i in 1:length(x)) {
>     points(x[i],y[i],cex=bmin+(bmax-bmin)*z[i])
>   }
> }

`points()` is vectorised and can take numeric vectors for relevant
arguments. Hence you don't need the `for()` loop here. Just generate the
vector of cex values you want and pass the whole thing plus all
coordinates to `points()`:

cex <- bmin+(bmax-bmin)*z
points(x, y, cex = cex)

should be sufficient.

HTH

G

> This just makes an empty plot, and draws circles in it
> scaled to values in "z".  You'll need to extract the axis 
> scores from the NMDS output to use this.  Tweak
> other graphics parameters as needed to get what you
> want.
> 
> Dr. Mark Fulton
> Professor of Biology
> Bemidji State University
> Bemidji, MN   56601
> http://faculty.bemidjistate.edu/mfulton/
> 
> 
> -----Original Message-----
> From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Stas Malavin
> Sent: Thursday, March 07, 2013 12:07 AM
> To: r-sig-ecology at r-project.org
> Subject: [R-sig-eco] nMDS plot with points of different size
> 
> Dear list members,
> 
> I want to plot an nMDS diagram with points' area proportional to the abundance of particular species. I could imagine just plotting with type = "n" and then using points() with different cex, but may be some special functions/packages exist for that which you can point me to?
> 
> Thank you,
> Stas
> 
> 
> --------------------------------------------
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