On Wednesday 30 July 2008, Gavin Simpson wrote: > On Wed, 2008-07-30 at 04:59 -0700, Andrewjohnclose wrote: > > Hi, I have been trying to create a function to generate a Procrustes > > plot, generated from package "vegan" > > in lattice. > > > > standard vegan code as follows > > library(vegan) > > pro=protest(P1, P8, permutations=4999,choices=1:4) > > plot(pro) > > > > Now, here is the code for the function that I have failed to get to work > > properly. > > > > panel.procrustes=function(x,y) > > }Pro=protest(x,y,permutations=4999,choices=1:4) > > Proplot=plot(Pro) > > } > > xyplot(P1[1:4]~P8[1:4],panel=panel.procrustes) > > > > I can generate an empty plot, but not much else - hope someone can help > > and point out the obvious! > > > > Kind regards > > > > Andrew > > The obvious thing is that whole thing is wrong! ;-) > > What's wrong with the standard plot? > > You are trying to mix base (standard) graphics functions with > grid/lattice graphics and this is not possible (well Ok there is package > gridBase). > > You'll have to start doing the plotting from scratch in > panel.procrustes. You might get some ideas of how to do this by looking > at the ordixyplot functions and panel functions in current vegan that > implement lattice graphics plots for ordiplot objects. I'm not > sufficiently familiar with Lattice yet to advise how to go about > producing a panel function, but the basic elements are: > > * draw the points from x$Yrot[, 1:2] > * draw the arrows from x$Yrot[, 1:2] to x$X[, 1:2] > * draw the origin - equivalent of abline(h = 0) and abline(v = 0) > * draw the rotation involved in the Procrustes analysis: abline(0, > tan(acos(x$rotation[1, 1])) and abline(0, 1/tan(acos(-x > $rotation[1, 1])) > > So you'll need the Lattice equivalents of abline and then work out how > to pass the X, Yrot and rotation components to your panel function. This > is the bit I'm not clear on but look at ordixyplot and panel.ordi for > inspiration. >
Here is a relatively simple demonstration of creating a custom panel function: http://casoilresource.lawr.ucdavis.edu/drupal/node/630 Cheers, Dylan -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
