Merge branch 'issue-685': fixes #685

R/ordiplot.R

@@ -11,9 +11,10 @@
     if (inherits(ord, "decorana") || inherits(ord, "cca")) {
         if (missing(display))
             out <- plot(ord, choices = choices, type = type, xlim = xlim,
-                        ylim = ylim, ...)
+                        ylim = ylim, optimize = optimize, arrows = arrows, ...)
         else out <- plot(ord, choices = choices, type = type, display = display,
-                         xlim = xlim, ylim = ylim, ...)
+                         xlim = xlim, ylim = ylim, optimize = optimize,
+                         arrows = arrows, ...)
     }
     else {
         type <- match.arg(type, c("points", "text", "none"))

R/plot.cca.R

@@ -1,6 +1,7 @@
 `plot.cca` <- function (x, choices = c(1, 2), display = c("sp", "wa", "cn"),
                         scaling = "species", type, xlim, ylim, const,
                         correlation = FALSE, hill = FALSE,
+                        optimize = FALSE, arrows = FALSE,
                         spe.par = list(), sit.par = list(), con.par = list(),
                         bip.par = list(), cen.par = list(), reg.par = list(),
                         ...)
@@ -77,12 +78,9 @@
     abline(h = 0, lty = 3)
     abline(v = 0, lty = 3)
     ## set up lists for graphical parameters
-    GlobalPar <- list("type" = type)
+    GlobalPar <- list("type" = type, "optimize" = optimize, "arrows" = arrows)
     dots <- match.call(expand.dots = FALSE)$...
     if (!is.null(dots)) {
-        ## dots par optimize must be eval'ed to force it logical
-        if (!is.null(dots$optimize))
-            dots$optimize <- eval(dots$optimize)
         GlobalPar <- modifyList(GlobalPar, dots)
     }
     ## Default graphical parameters
@@ -152,5 +150,5 @@
     if (!("CA" %in% names(x)))
         stop(gettextf("%s is not a vegan rda object",
                       sQuote(deparse(substitute(x)))))
-    NextMethod("plot", x, ...)
+    NextMethod() # no need to pass ..., happens automagically
 }

man/plot.cca.Rd

@@ -20,9 +20,9 @@
 \usage{
 \method{plot}{cca}(x, choices = c(1, 2), display = c("sp", "wa", "cn"),
      scaling = "species", type, xlim, ylim, const,
-     correlation = FALSE, hill = FALSE, spe.par = list(), sit.par =
-     list(), con.par = list(), bip.par = list(), cen.par = list(),
-     reg.par = list(), ...)
+     correlation = FALSE, hill = FALSE, optimize = FALSE, arrows = FALSE,
+     spe.par = list(), sit.par = list(), con.par = list(), bip.par = list(),
+     cen.par = list(), reg.par = list(), ...)
 \method{text}{cca}(x, display = "sites", labels, choices = c(1, 2),
      scaling = "species", arrow.mul, head.arrow = 0.05, select, const,
      axis.bp = FALSE, correlation = FALSE, hill = FALSE, ...)
@@ -75,6 +75,17 @@
     are used to select the corresponding negative scaling type; either
     correlation-like scores or Hill's scaling for PCA/RDA and CA/CCA
     respectively. See argument \code{scaling} for details.}
+
+  \item{optimize}{Optimize locations of text to reduce overlap and plot
+    point in the actual locations of the scores. Uses
+    \code{\link{ordipointlabel}}. }
+
+  \item{arrows}{Draw arrows from the origin. This will always be
+    \code{TRUE} for biplot and regression scores in constrained
+    ordination (\code{\link{cca}} etc.). Setting this \code{TRUE} will
+    draw arrows for any type of scores. This allows, e.g, using biplot
+    arrows for species. The arrow head will be at the value of scores,
+    and possible text is moved outwards.}
 
   \item{spe.par, sit.par, con.par, bip.par, cen.par, reg.par}{
     Lists of graphical parameters for species, sites, constraints (lc