[Vegan-commits] r2178 - in pkg/vegan: R inst man

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

Author: gsimpson
Date: 2012-05-23 17:24:31 +0200 (Wed, 23 May 2012)
New Revision: 2178

Modified:
   pkg/vegan/R/ordipointlabel.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/ordipointlabel.Rd
Log:
add select argument to ordipointlabel

Modified: pkg/vegan/R/ordipointlabel.R
===================================================================
--- pkg/vegan/R/ordipointlabel.R	2012-05-23 07:07:44 UTC (rev 2177)
+++ pkg/vegan/R/ordipointlabel.R	2012-05-23 15:24:31 UTC (rev 2178)
@@ -1,13 +1,28 @@
 ### Modelled after maptools:::pointLabel.
 `ordipointlabel` <-
     function(x, display = c("sites", "species"), choices = c(1,2), col=c(1,2),
-             pch=c("o","+"), font = c(1,1), cex=c(0.8, 0.8), add = FALSE, ...)
+             pch=c("o","+"), font = c(1,1), cex=c(0.8, 0.8), add = FALSE,
+             select, ...)
 {
     xy <- list()
     ## Some 'scores' accept only one 'display': a workaround
     for (nm in display)
         xy[[nm]] <- scores(x, display = nm, choices = choices, ...)
     ##xy <- scores(x, display = display, choices = choices, ...)
+    ## remove `select`ed observations from scores as per text.cca
+    ## only useful if we are displaying only one set of scores
+    if(!missing(select)) {
+        if(isTRUE(all.equal(length(display), 1L))) {
+            ## check `select` and length of scores match
+            if(isTRUE(all.equal(length(select), NROW(xy[[1]])))) {
+                xy[[1]] <- xy[[1]][select, , drop = FALSE]
+            } else {
+                warning("Length of 'select' does not match the number of scores.\nIgnoring 'select'.")
+            }
+        } else {
+            warning("'select' does not apply when plotting more than one set of scores.\n'select' was ignored.")
+        }
+    }
     if (length(display) > 1) {
         col <- rep(col, sapply(xy, nrow))
         pch <- rep(pch, sapply(xy, nrow))

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-05-23 07:07:44 UTC (rev 2177)
+++ pkg/vegan/inst/ChangeLog	2012-05-23 15:24:31 UTC (rev 2178)
@@ -4,6 +4,11 @@
 
 Version 2.1-16 (opened May 11, 2012)
 
+	* ordipointlabel: gains argument 'select' which allows some rows
+	of the plotted scores to be skipped in the same manner as for
+	text.cca(). This only applies when a single set of scores is
+	plotted. Otherwise it is ignored and a warning issued.
+
 	* ordihull, ordiellipse: defaults to use semitransparent fill
 	colour with 'draw = "polygon"', and gain argument 'alpha' to set
 	the transparency. 

Modified: pkg/vegan/man/ordipointlabel.Rd
===================================================================
--- pkg/vegan/man/ordipointlabel.Rd	2012-05-23 07:07:44 UTC (rev 2177)
+++ pkg/vegan/man/ordipointlabel.Rd	2012-05-23 15:24:31 UTC (rev 2178)
@@ -12,7 +12,7 @@
 \usage{
 ordipointlabel(x, display = c("sites", "species"), choices = c(1, 2),
    col = c(1, 2),  pch = c("o", "+"), font = c(1, 1), 
-   cex = c(0.8, 0.8), add = FALSE, ...)
+   cex = c(0.8, 0.8), add = FALSE, select, ...)
 }
 
 \arguments{
@@ -24,6 +24,11 @@
      plot. These should be vectors of the same length as the number of
      items in \code{display}.}
   \item{add}{ Add to an existing plot. }
+  \item{select}{Items to be displayed.  This can either be a logical
+    vector which is \code{TRUE} for displayed items or a vector of indices
+    of displayed items. \code{select} is only used if a single set of
+    scores is being plotted (i.e. \code{length(display) == 1}),
+    otherwise it is ignored.}
   \item{\dots}{Other arguments passed to \code{\link{points}} and
   \code{\link{text}}.}
 }