[Vegan-commits] r2239 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2012-07-31 13:43:17 +0200 (Tue, 31 Jul 2012)
New Revision: 2239

Modified:
   pkg/vegan/R/plot.envfit.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/envfit.Rd
Log:
plot.envfit() gained argument 'labels' to change the default labels.

Modified: pkg/vegan/R/plot.envfit.R
===================================================================
--- pkg/vegan/R/plot.envfit.R	2012-07-31 11:43:09 UTC (rev 2238)
+++ pkg/vegan/R/plot.envfit.R	2012-07-31 11:43:17 UTC (rev 2239)
@@ -1,11 +1,30 @@
 `plot.envfit` <-
-    function (x, choices = c(1, 2), arrow.mul, at = c(0, 0),
+    function (x, choices = c(1, 2), labels, arrow.mul, at = c(0, 0),
               axis = FALSE, p.max = NULL, col = "blue", bg, add = TRUE, ...)
 {
     formals(arrows) <- c(formals(arrows), alist(... = ))
     ## get labels
     labs <- list("v" = rownames(x$vectors$arrows),
                  "f" = rownames(x$factors$centroids))
+    ## Change labels if user so wishes
+    if (!missing(labels)) {
+        ## input list of "vectors" and/or "factors"
+        if (is.list(labels)) {
+            if (!is.null(labs$v) && !is.null(labels$vectors))
+                labs$v <- labels$vectors
+            if (!is.null(labs$f) && !is.null(labels$factors))
+                labs$f <- labels$factors
+        } else {
+            ## input vector: either vectors or factors must be NULL,
+            ## and the existing set of labels is replaced
+            if (!is.null(labs$v) && !is.null(labs$f))
+                stop("needs a list with both 'vectors' and 'factors' labels")
+            if (!is.null(labs$v))
+                labs$v <- labels
+            else
+                labs$f <- labels
+        }
+    }
     vect <- NULL
     if (!is.null(p.max)) {
         if (!is.null(x$vectors)) {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-07-31 11:43:09 UTC (rev 2238)
+++ pkg/vegan/inst/ChangeLog	2012-07-31 11:43:17 UTC (rev 2239)
@@ -4,8 +4,9 @@
 
 Version 2.1-18 (opened July 30, 2012)
 
-	* envift: got labels() method that returns the labels used in
-	plot().
+	* envift: the plot() method gained argument 'labels' to change the
+	default labels. The default labels are displayed with the new
+	labels() function.
 	
 Version 2.1-17 (closed July 30, 2012)
 

Modified: pkg/vegan/man/envfit.Rd
===================================================================
--- pkg/vegan/man/envfit.Rd	2012-07-31 11:43:09 UTC (rev 2238)
+++ pkg/vegan/man/envfit.Rd	2012-07-31 11:43:17 UTC (rev 2239)
@@ -19,8 +19,8 @@
 \method{envfit}{default}(ord, env, permutations = 999, strata, choices=c(1,2), 
    display = "sites", w  = weights(ord), na.rm = FALSE, ...)
 \method{envfit}{formula}(formula, data, ...)
-\method{plot}{envfit}(x, choices = c(1,2), arrow.mul, at = c(0,0), axis = FALSE, 
-    p.max = NULL, col = "blue", bg, add = TRUE, ...)
+\method{plot}{envfit}(x, choices = c(1,2), labels, arrow.mul, at = c(0,0), 
+   axis = FALSE, p.max = NULL, col = "blue", bg, add = TRUE, ...)
 \method{scores}{envfit}(x, display, choices, ...)
 vectorfit(X, P, permutations = 0, strata, w, ...)
 factorfit(X, P, permutations = 0, strata, w, ...)
@@ -47,6 +47,13 @@
     \code{na.rm = TRUE}.}
   \item{x}{A result object from \code{envfit}.}
   \item{choices}{Axes to plotted.}
+  \item{labels}{Change plotting labels. The argument should be a list
+    with elements \code{vectors} and \code{factors} which give the new
+    plotting labels. If either of these elements is omitted, the
+    default labels will be used. If there is only one type of elements
+    (only \code{vectors} or only \code{factors}), the labels can be
+    given as vector. The default labels can be displayed with
+    \code{labels} command.}
   \item{arrow.mul}{Multiplier for vector lengths. The arrows are
     automatically scaled similarly as in \code{\link{plot.cca}} if this
     is not given and \code{add = TRUE}.}
@@ -212,6 +219,10 @@
 ordispider(ord, Moisture, col="skyblue")
 points(ord, display = "sites", col = as.numeric(Moisture), pch=16)
 plot(fit, cex=1.2, axis=TRUE, bg = rgb(1, 1, 1, 0.5))
+## Use shorter labels for factor centroids
+labels(fit)
+plot(ord)
+plot(fit, labels=list(factors = paste0("M", c(1,2,4,5))), bg = rgb(1,1,0,0.5))
 }
 \keyword{multivariate }
 \keyword{aplot}