Re: [R-sig-eco] plotting capscale results using ordiplot in Vegan
Hi Colleen, Using capscale you can use the function plot.cca (use ?plot.cca to see all options) to make plots. If you use this: plot ( yourcapscaleresult, display=c(wa,bp)) you get the site scores (wa) and the constraining variables arrows (bp) biplot , but if you want the triplot, species scores are in a bigger scale and your sites collapse in the middle, so I would try to make the 2 biplots, plot ( yourcapscaleresult, display=c(wa,bp)) plot ( yourcapscaleresult, display=c(sp,bp)) hope this helps, Andrés ckellogg ctekell...@gmail.com escribió: Hi, I used capscale to examine relationships between relative species abundances at different sites with environmental variables. When I attempt to plot the results using ordiplot all of my site points are squished to the center of the biplot. I have tried changing the scaling and that only makes things worse. Is there anyway I can get the sites to spread out a bit in the ordination? Thanks so much! Colleen -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/plotting-capscale-results-using-ordiplot-in-Vegan-tp6288126p6288126.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Andrés Mellado Díaz Centre for Hydrological Studies CEH-CEDEX Water Quality Department Pº bajo de la Virgen del Puerto, 3 28005, Madrid SPAIN [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] plotting capscale results using ordiplot in Vegan
On Tue, 2011-04-19 at 10:47 -0700, ckellogg wrote: Hi, I used capscale to examine relationships between relative species abundances at different sites with environmental variables. When I attempt to plot the results using ordiplot all of my site points are squished to the center of the biplot. I have tried changing the scaling and that only makes things worse. Is there anyway I can get the sites to spread out a bit in the ordination? Thanks so much! Colleen Some code would be nice, otherwise how on earth can we know what you did to plot the data? Does: plot(, scaling = 3) where represents what ever you were including to plot the ordination in the first place help? Or is the problem that you have one (a few) rogue sample(s) and/or species? G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] plotting capscale results using ordiplot in Vegan
Right. The code. Sorry about that. This is what I used: plot(ANareabac_red.cap,choices=c(1,2),type='n',scaling=2) points(ANareabac_red.cap,choices=c(1,2),display='wa',pch=AN_info[,9],col=AN_info[,6],cex=1.5,scaling=2) I don't really have any outliers so I don't think that is the problem. I will give what Andres suggested (thanks!) a shot. Colleen -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/plotting-capscale-results-using-ordiplot-in-Vegan-tp6288126p6290975.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] plotting capscale results using ordiplot in Vegan
Hi, I used capscale to examine relationships between relative species abundances at different sites with environmental variables. When I attempt to plot the results using ordiplot all of my site points are squished to the center of the biplot. I have tried changing the scaling and that only makes things worse. Is there anyway I can get the sites to spread out a bit in the ordination? Thanks so much! Colleen -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/plotting-capscale-results-using-ordiplot-in-Vegan-tp6288126p6288126.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
