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

[Mark Fulton]

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])
  }
}

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


--------------------------------------------
Junior Res Asst
Hydrobiology Lab
Institute of Limnology
Russian Academy of Sciences

Sevastyanova 9
196105 Russia, St Petersburg
http://www.limno.org.ru
Phone: +7 (812) 387-80-60
Fax: +7 (812) 388-73-27

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