nMDS plot with points of different size
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 -------------------------------------------- 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 [[alternative HTML version deleted]]
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