[Vegan-commits] r2157 - in pkg/vegan: R inst man

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2012-05-10 08:39:47 +0200 (Thu, 10 May 2012)
New Revision: 2157

Modified:
   pkg/vegan/R/ordiplot3d.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordiplot3d.Rd
Log:
Squashed commit of the following:

commit ffa3ddf9d62bc8d7afd62abe60fce9960625f474
Merge: ddad83c 4ebe87b
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Wed May 9 23:10:15 2012 +0300

    Merge branch 'master' of https://github.com/jarioksa/vegan

commit ddad83cce47306420223502d69cacc7f15e9c912
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Wed May 9 23:04:57 2012 +0300

    ordiplot3d returns projected origin and function envfit.convert

    The envfit.convert function projects a 3-d envfit object to the
    the current 3d plot, and together with projected origin can be used
    to project the result to the plot:

    mod <- cca(varespec)
    ef <- envfit(mod ~ ., varechem, choices = 1:3)
    pl3 <- ordiplot3d(mod)
    plot(pl3$envfit.convert(ef), at = pl3$origin, p.max = 0.05)

Modified: pkg/vegan/R/ordiplot3d.R
===================================================================
--- pkg/vegan/R/ordiplot3d.R	2012-05-08 19:38:52 UTC (rev 2156)
+++ pkg/vegan/R/ordiplot3d.R	2012-05-10 06:39:47 UTC (rev 2157)
@@ -36,6 +36,28 @@
                    col = arr.col)
         }
     }
+    ## Add function that flattens 3d envfit object so that it can be
+    ## projected on the created 3d graph
+    xyz2xy <- pl$xyz.convert
+    envfit.convert <- function(object) {
+        if (!is.null(object$vectors)) {
+            rn <- rownames(object$vectors$arrows)
+            object$vectors$arrows <-
+                sapply(xyz2xy(object$vectors$arrows), cbind)
+            rownames(object$vectors$arrows) <- rn
+        }
+        if (!is.null(object$factors)) {
+            rn <- rownames(object$factors$centroids)
+            object$factors$centroids <-
+                sapply(xyz2xy(object$factors$centroids), cbind)
+            rownames(object$factors$centroids) <- rn
+        }
+        object
+    }
+    pl$envfit.convert <- envfit.convert
+    ## save the location of the origin
+    pl$origin <- matrix(unlist(pl$xyz.convert(0, 0, 0)), nrow=1)
+    ## save projected coordinates of points
     tmp <- pl$xyz.convert(x)
     pl$points <- cbind(tmp$x, tmp$y)
     rownames(pl$points) <- rownames(x)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-05-08 19:38:52 UTC (rev 2156)
+++ pkg/vegan/inst/ChangeLog	2012-05-10 06:39:47 UTC (rev 2157)
@@ -15,6 +15,10 @@
 	metaMDS. With over-defined models there is an infinite number of
 	different solutions with nearly zero stress, and no convergence is
 	found. 
+
+	* ordiplot3d: function returns the projected coordinates of the
+	origin, and function envfit.convert() that can project a
+	three-dimensional envfit() result to the current plot.
 	
 Version 2.1-14 (opened March 9, 2012)
 

Modified: pkg/vegan/man/ordiplot3d.Rd
===================================================================
--- pkg/vegan/man/ordiplot3d.Rd	2012-05-08 19:38:52 UTC (rev 2156)
+++ pkg/vegan/man/ordiplot3d.Rd	2012-05-10 06:39:47 UTC (rev 2157)
@@ -129,16 +129,19 @@
   Function \code{ordiplot3d} returns invisibly an object of class
   \code{"ordiplot3d"} inheriting from \code{\link{ordiplot}}. The
   return object will contain the coordinates projected onto two
-  dimensions for \code{"points"}, and possibly for the heads of
-  \code{"arrows"} and \code{"centroids"} of environmental
-  variables. Functions like \code{\link{identify.ordiplot}},
+  dimensions for \code{points}, and the projected coordinates of
+  \code{origin}, and possibly the projected coordinates of the heads
+  of \code{arrows} and \code{centroids} of environmental variables.
+  Functions like \code{\link{identify.ordiplot}},
   \code{\link{points.ordiplot}}, \code{\link{text.ordiplot}} can use
   this result, as well as \code{\link{ordihull}} and other functions
-  documented with the latter. In addition, the result will contain the
-  object returned by \code{\link[scatterplot3d]{scatterplot3d}},
-  including function \code{xyz.convert} which projects
-  three-dimensional coordinates onto the plane used in the current
-  plot (see Examples).
+  documented with the latter. The result will also contain the object
+  returned by \code{\link[scatterplot3d]{scatterplot3d}}, including
+  function \code{xyz.convert} which projects three-dimensional
+  coordinates onto the plane used in the current plot (see
+  Examples). In addition, there is a function \code{envfit.convert}
+  that projects a three-dimensional \code{\link{envfit}} object to the
+  current plot.
 
   Function \code{ordirgl} returns nothing.