[Vegan-commits] r2210 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2012-06-02 18:48:32 +0200 (Sat, 02 Jun 2012)
New Revision: 2210

Modified:
   branches/2.0/R/ordiplot3d.R
   branches/2.0/inst/ChangeLog
   branches/2.0/inst/NEWS.Rd
   branches/2.0/man/ordiplot3d.Rd
Log:
merge: ordiplot3d returns envfit.convert() -- relevant fixes r2157 thru 2168, 2208

Modified: branches/2.0/R/ordiplot3d.R
===================================================================
--- branches/2.0/R/ordiplot3d.R	2012-06-02 10:47:59 UTC (rev 2209)
+++ branches/2.0/R/ordiplot3d.R	2012-06-02 16:48:32 UTC (rev 2210)
@@ -45,6 +45,37 @@
                    col = arr.col)
         }
     }
+    ## save the location of the origin
+    pl$origin <- matrix(unlist(pl$xyz.convert(0, 0, 0)), nrow=1)
+    ## 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)
+            arr <- object$vectors$arrows[, choices, drop = FALSE]
+            arr <- sapply(xyz2xy(arr), cbind)
+            if (!is.matrix(arr))
+                arr <- matrix(arr, ncol = 2)
+            arr <- sweep(arr, 2, pl$origin)
+            rownames(arr) <- rn
+            object$vectors$arrows <- arr
+        }
+        if (!is.null(object$factors)) {
+            rn <- rownames(object$factors$centroids)
+            object$factors$centroids <-
+                object$factors$centroids[ ,choices, drop = FALSE]
+            object$factors$centroids <-
+                sapply(xyz2xy(object$factors$centroids), cbind)
+            if (!is.matrix(object$factors$centroids))
+                object$factors$centroids <-
+                    matrix(object$factors$centroids, ncol = 2)
+            rownames(object$factors$centroids) <- rn
+        }
+        object
+    }
+    pl$envfit.convert <- envfit.convert
+    ## save projected coordinates of points
     tmp <- pl$xyz.convert(x)
     pl$points <- cbind(tmp$x, tmp$y)
     rownames(pl$points) <- rownames(x)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-06-02 10:47:59 UTC (rev 2209)
+++ branches/2.0/inst/ChangeLog	2012-06-02 16:48:32 UTC (rev 2210)
@@ -17,6 +17,8 @@
 	* merge r2170: bioenv accepts dissimilarities as input.
 	* merge r2167: warn about unequal aspect ratio in ordiplot3d.
 	* merge r2162: set equal axis scales for ordiplot3d.
+	* merge r2157:2160,2167,2168,2208: ordiplot3d returns
+	envfit.convert().
 	* merge r2156: betadisper example adapted for default spatial
 	median.
 	* merge r2150: monoMDS checks that the number of dissimilarities

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2012-06-02 10:47:59 UTC (rev 2209)
+++ branches/2.0/inst/NEWS.Rd	2012-06-02 16:48:32 UTC (rev 2210)
@@ -60,6 +60,11 @@
         \code{ordihull} puts labels (with argument \code{label = TRUE})
         now in the real polygon centre.
 
+      \item \code{ordiplot3d} returns function \code{envfit.convert}
+        and the projected location of the \code{origin}.  Together
+        these functions can be used to add \code{envfit} results to
+        existint \code{ordiplot3d} plots.
+
       \item Function \code{ordipointlabel} gained argument to
         \code{select} only some of the items for plotting. The
         argument can be used only with one set of points.

Modified: branches/2.0/man/ordiplot3d.Rd
===================================================================
--- branches/2.0/man/ordiplot3d.Rd	2012-06-02 10:47:59 UTC (rev 2209)
+++ branches/2.0/man/ordiplot3d.Rd	2012-06-02 16:48:32 UTC (rev 2210)
@@ -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.
 
@@ -205,6 +208,17 @@
 ### Add species using xyz.convert function returned by ordiplot3d
 sp <- scores(ord, choices=1:3, display="species", scaling=3)
 text(pl$xyz.convert(sp), rownames(sp), cex=0.7, xpd=TRUE)
+### Two ways of adding fitted variables to ordination plots
+ord <- cca(dune)
+ef <- envfit(ord ~ Moisture + A1, dune.env, choices = 1:3)
+### 1. use argument 'envfit'
+ordiplot3d(ord, envfit = ef)
+### 2. use returned envfit.convert function for better user control
+pl3 <- ordiplot3d(ord)
+plot(pl3$envfit.convert(ef), at = pl3$origin)
+### envfit.convert() also handles different 'choices' of axes
+pl3 <- ordiplot3d(ord, choices = c(1,3,2))
+plot(pl3$envfit.convert(ef), at = pl3$origin)
 ### ordirgl
 ordirgl(ord, size=2)
 ordirgl(ord, display = "species", type = "t")