Merge branch 'ordiplot-use-ordiplot'

vegandevs · Aug 7, 2024 · 8a1e228 · 8a1e228
2 parents 2a37aa8 + 412eacc
commit 8a1e228
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Showing 6 changed files with 18 additions and 12 deletions.
diff --git a/R/identify.ordiplot.R b/R/identify.ordiplot.R
@@ -1,7 +1,7 @@
 `identify.ordiplot` <-
     function (x, what, labels, ...)
 {
-    x <- scores(x, what)
+    x <- scores(x, display = what)
     if (missing(labels))
         labels <- rownames(x)
     identify(x, labels = labels, ...)

diff --git a/R/ordiplot.R b/R/ordiplot.R
@@ -1,12 +1,13 @@
 `ordiplot` <-
-    function (ord, choices = c(1, 2), type = "points", display, xlim,
-              ylim, ...)
+    function (ord, choices = c(1, 2), type = "points", display,
+              optimize = FALSE, arrows = FALSE, length = 0.05, arr.mul,
+              xlim, ylim, ...)
 {
     ## local functions to absorb non-par arguments of plot.default
     localPoints <- function(..., log, frame.plot, panel.first,
-                            panel.last, axes) points(...)
+                            panel.last, axes) points.ordiplot(...)
     localText <- function(..., log, frame.plot, panel.first,
-                          panel.last, axes) text(...)
+                          panel.last, axes) text.ordiplot(...)
     if (inherits(ord, "decorana") || inherits(ord, "cca")) {
         if (missing(display))
             out <- plot(ord, choices = choices, type = type, xlim = xlim,
@@ -75,15 +76,19 @@
                     warning("type='t', but no names available: using x1...")
                     labs <- paste0("x", as.character(seq_len(nrow(X))))
                 }
-                localText(X, labels = labs, col = 1,  ...)
+                localText(X, what = "sites", labels = labs, col = 1,
+                          optimize = optimize, arrows = arrows, length = length,
+                          arr.mul = arr.mul, ...)
             }
             if (!is.null(Y)) {
                 labs <- rownames(Y)
                 if (is.null(labs)) {
                     warning("type='t', but no names available: using y1...")
                     labs <- paste0("y", as.character(seq_len(nrow(Y))))
                 }
-                localText(Y, labels = labs, col = "red", ...)
+                localText(Y, what = "species", labels = labs, col = "red",
+                          optimize = optimize, arrows = arrows, length = length,
+                          arr.mul = arr.mul, ...)
             }
         }
         out <- list(sites = X, species = Y)

diff --git a/R/plot.isomap.R b/R/plot.isomap.R
@@ -1,12 +1,12 @@
 `plot.isomap` <-
-    function (x, net = TRUE, n.col = "gray", type = "points", ...) 
+    function (x, net = TRUE, n.col = "gray", type = "points", ...)
 {
     type <- match.arg(type, c("points", "text", "none"))
     if (!net) {
         pl <- ordiplot(x, display="sites", type = type, ...)
     } else {
         pl <- ordiplot(x, display = "sites", type = "none", ...)
-        z <- scores(pl, "sites")
+        z <- scores(pl, display = "sites")
         k <- x$net
         ## recycle colour for points
         n.col <- rep(n.col, length = nrow(z))

diff --git a/R/points.ordiplot.R b/R/points.ordiplot.R
@@ -2,7 +2,7 @@
     function (x, what, select, arrows = FALSE, length = 0.05,
               arr.mul, ...)
 {
-    sco <- scores(x, what)
+    sco <- scores(x, display = what)
     if (!missing(select))
         sco <- .checkSelect(select, sco)
     if (!missing(arr.mul)) {

diff --git a/R/text.ordiplot.R b/R/text.ordiplot.R
@@ -2,7 +2,7 @@
     function (x, what, labels, select, optimize = FALSE, arrows = FALSE,
               length = 0.05, arr.mul, bg, ...)
 {
-    sco <- scores(x, what)
+    sco <- scores(x, display = what)
     if (!missing(labels))
         rownames(sco) <- labels
     if (!missing(select))

diff --git a/man/ordiplot.Rd b/man/ordiplot.Rd
@@ -18,7 +18,8 @@
   by layers.  }
 
 \usage{
-ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim, ...)
+ordiplot(ord, choices = c(1, 2), type="points", display, optimize = FALSE,
+    arrows = FALSE, length = 0.05, arr.mul, xlim, ylim, ...)
 \method{points}{ordiplot}(x, what, select, arrows = FALSE,
     length = 0.05, arr.mul, ...)
 \method{text}{ordiplot}(x, what, labels, select, optimize = FALSE,