Merge branch 'issue-#656'

R/ordiArrowTextXY.R

@@ -3,7 +3,9 @@
 ### label these heads, '...' passes arguments (such as 'cex') to
 ### strwidth() and strheight().
 `ordiArrowTextXY` <- function (x, labels, display, choices = c(1,2),
-                               rescale = TRUE, fill = 0.75, at = c(0,0), ...) {
+                               rescale = TRUE, fill = 0.75, at = c(0,0),
+                               cex = NULL, ...)
+{
     ## handle x, which we try with scores, but also retain past usage of
     ## a two column matrix
     X <- if (is.matrix(x)) {
@@ -38,8 +40,8 @@
         }
     }
 
-    w <- strwidth(labels, ...)
-    h <- strheight(labels, ...)
+    w <- strwidth(labels, cex = cex, ...)
+    h <- strheight(labels, cex = cex, ...)
 
     ## slope of arrows
     b <- (X[,2] - at[2]) / (X[,1] - at[1])

R/plot.cca.R

@@ -1,6 +1,6 @@
 `plot.cca` <- function (x, choices = c(1, 2), display = c("sp", "wa", "cn"),
                         scaling = "species", type, xlim, ylim, const,
-                        correlation = FALSE, hill = FALSE, ...) {
+                        correlation = FALSE, hill = FALSE, cex = 0.7, ...) {
     TYPES <- c("text", "points", "none")
     ## take care that bp arrows are also returned if only cn given
     if (any(display %in% c("c","cn")))
@@ -77,22 +77,22 @@
     if (!is.null(g$species)) {
         if (type == "text")
             text(g$species, rownames(g$species), col = "red",
-                 cex = 0.7)
+                 cex = cex)
         else if (type == "points")
-            points(g$species, pch = "+", col = "red", cex = 0.7)
+            points(g$species, pch = "+", col = "red", cex = cex)
     }
     if (!is.null(g$sites)) {
         if (type == "text")
-            text(g$sites, rownames(g$sites), cex = 0.7)
+            text(g$sites, rownames(g$sites), cex = cex)
         else if (type == "points")
-            points(g$sites, pch = 1, cex = 0.7)
+            points(g$sites, pch = 1, cex = cex)
     }
     if (!is.null(g$constraints)) {
         if (type == "text")
-            text(g$constraints, rownames(g$constraints), cex = 0.7,
+            text(g$constraints, rownames(g$constraints), cex = cex,
                  col = "darkgreen")
         else if (type == "points")
-            points(g$constraints, pch = 2, cex = 0.7, col = "darkgreen")
+            points(g$constraints, pch = 2, cex = cex, col = "darkgreen")
     }
     if (!is.null(g$biplot) && nrow(g$biplot) > 0 && type != "none") {
         if (length(display) > 1) {
@@ -102,8 +102,9 @@
         attr(g$biplot, "arrow.mul") <- mul
         arrows(0, 0, mul * g$biplot[, 1], mul * g$biplot[, 2],
                length = 0.05, col = "blue")
-        biplabs <- ordiArrowTextXY(mul * g$biplot, rownames(g$biplot))
-        text(biplabs, rownames(g$biplot), col = "blue")
+        biplabs <- ordiArrowTextXY(mul * g$biplot, rownames(g$biplot),
+                                   cex = cex)
+        text(biplabs, rownames(g$biplot), col = "blue", cex = cex)
     }
     if (!is.null(g$regression) && nrow(g$regression > 0) && type != "none") {
         rcol <- "purple4"
@@ -114,21 +115,22 @@
         attr(g$regression, "arrow.mul") <- mul
         arrows(0, 0, mul * g$regression[, 1], mul * g$regression[, 2],
                length = 0.05, col = rcol)
-        biplabs <- ordiArrowTextXY(mul * g$regression, rownames(g$regression))
-        text(biplabs, rownames(g$regression), col = rcol)
+        biplabs <- ordiArrowTextXY(mul * g$regression, rownames(g$regression),
+                                   cex = cex)
+        text(biplabs, rownames(g$regression), col = rcol, cex = cex)
     }
     if (!is.null(g$centroids) && !anyNA(g$centroids) && type !=
         "none") {
         if (type == "text")
-            text(g$centroids, rownames(g$centroids), col = "blue")
+            text(g$centroids, rownames(g$centroids), col = "blue", cex = cex)
         else if (type == "points")
-            points(g$centroids, pch = "x", col = "blue")
+            points(g$centroids, pch = "x", col = "blue", cex = cex)
     }
     if (!is.null(g$default) && type != "none") {
         if (type == "text")
-            text(g$default, rownames(g$default), cex = 0.7)
+            text(g$default, rownames(g$default), cex = cex)
         else if (type == "points")
-            points(g$default, pch = 1, cex = 0.7)
+            points(g$default, pch = 1, cex = cex)
     }
     class(g) <- "ordiplot"
     invisible(g)

R/text.ordiplot.R

@@ -13,7 +13,7 @@
     }
     if (arrows) {
         arrows(0, 0, sco[,1], sco[,2], length = length, ...)
-        sco <- ordiArrowTextXY(sco, rownames(sco), rescale = FALSE)
+        sco <- ordiArrowTextXY(sco, rownames(sco), rescale = FALSE, ...)
     }
     text(sco, labels = rownames(sco), ...)
     invisible(x)

man/ordiArrowTextXY.Rd

@@ -13,9 +13,8 @@
 }
 \usage{
 ordiArrowTextXY(x, labels, display, choices = c(1,2),
-                rescale = TRUE, fill = 0.75, at = c(0,0), \ldots)
-ordiArrowMul(x, at = c(0,0), fill = 0.75,
-             display, choices = c(1,2), \ldots)
+    rescale = TRUE, fill = 0.75, at = c(0,0), cex = NULL, \ldots)
+ordiArrowMul(x, at = c(0,0), fill = 0.75, display, choices = c(1,2), \ldots)
 }
 
 \arguments{
@@ -55,6 +54,8 @@ ordiArrowMul(x, at = c(0,0), fill = 0.75,
     in other places than origin, you probably have to specify
     \code{arrrow.mul}.}
 
+  \item{cex}{Character expansion for text.}
+
   \item{...}{Parameters passed to \code{\link{scores}}, and
     \code{\link{strwidth}} and \code{\link{strheight}}.}
 }

man/plot.cca.Rd

@@ -19,7 +19,7 @@
 \usage{
 \method{plot}{cca}(x, choices = c(1, 2), display = c("sp", "wa", "cn"),
      scaling = "species", type, xlim, ylim, const,
-     correlation = FALSE, hill = FALSE, ...)
+     correlation = FALSE, hill = FALSE, cex = 0.7, ...)
 \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, ...)
@@ -112,6 +112,7 @@
     kind of scores were requested.}
   \item{axis.bp}{Draw \code{\link{axis}} for biplot arrows.}
   \item{digits}{Number of digits in output.}
+  \item{cex}{Character expansion.}
   \item{...}{Parameters passed to other functions.}
 }
 
@@ -157,19 +158,21 @@
   standard and more easily interpreted, and regression arrows should be
   used only if you know that you need them.
 
-  If you want to have a better control of plots, it is best to
-  construct the plot \code{text} and \code{points} commands which
-  accept graphical parameters. It is important to remember to use the
-  same \code{scaling}, \code{correlation} and \code{hill} arguments
-  in all calls. The \code{plot.cca} command returns invisibly an
+  If you want to have a better control of plots, it is best to construct
+  the plot \code{text} and \code{points} commands which accept graphical
+  parameters. It is important to remember to use the same
+  \code{scaling}, \code{correlation} and \code{hill} arguments in all
+  calls. The \code{plot.cca} command returns invisibly an
   \code{\link{ordiplot}} result object, and this will have consistent
-  scaling for all its elements. The easiest way for full control of
-  graphics is to first set up the plot frame using \code{plot} with
-  \code{type = "n"} and all needed scores in \code{display} and save
-  this result. The \code{points} and \code{text} commands for
-  \code{\link{ordiplot}} will allow full graphical control (see
-  section Examples). Utility function \code{labels} returns the default
-  labels in the order they are applied in \code{text}.
+  scaling for all its elements. It is also possible to use \R{} pipes
+  (\code{|>}) which maintain consistent scaling and setting. The easiest
+  way for full control of graphics is to first set up the plot frame
+  using \code{plot} with \code{type = "n"} and all needed scores in
+  \code{display} and save this result or use it as a first command in a
+  pipe. The \code{points} and \code{text} commands for
+  \code{\link{ordiplot}} will allow full graphical control (see section
+  Examples). Utility function \code{labels} returns the default labels
+  in the order they are applied in \code{text}.
 
   Palmer (1993) suggested using linear constraints (\dQuote{LC scores})
   in ordination diagrams, because these gave better results in
@@ -208,7 +211,12 @@ pca <- rda(dune)
 pl <- plot(pca, type="n", scaling="sites", correlation=TRUE)
 with(dune.env, points(pl, "site", pch=21, col=1, bg=Management))
 text(pl, "sp", arrow=TRUE, length=0.05, col=4, cex=0.6, xpd=TRUE)
-with(dune.env, legend("bottomleft", levels(Management), pch=21, pt.bg=1:4, bty="n"))
+with(dune.env, legend("bottomleft", levels(Management), pch=21,
+   pt.bg=1:4, bty="n"))
+## Configuration with pipes: make an arrow biplot
+plot(pca, type="n", scaling="sites", correlation=TRUE) |>
+    points("sites", pch=21, col = 1, cex=1.5, bg = dune.env$Management) |>
+    text("species", col = "blue", arrow = TRUE, xpd = TRUE)
 ## Scaling can be numeric or more user-friendly names
 ## e.g. Hill's scaling for (C)CA
 scrs <- scores(mod, scaling = "sites", hill = TRUE)

tests/Examples/vegan-Ex.Rout.save

@@ -6111,7 +6111,12 @@ ungrazed-grazed -0.1219422 -0.2396552 -0.004229243 0.0429502
 > pl <- plot(pca, type="n", scaling="sites", correlation=TRUE)
 > with(dune.env, points(pl, "site", pch=21, col=1, bg=Management))
 > text(pl, "sp", arrow=TRUE, length=0.05, col=4, cex=0.6, xpd=TRUE)
-> with(dune.env, legend("bottomleft", levels(Management), pch=21, pt.bg=1:4, bty="n"))
+> with(dune.env, legend("bottomleft", levels(Management), pch=21,
++    pt.bg=1:4, bty="n"))
+> ## Configuration with pipes: make an arrow biplot
+> plot(pca, type="n", scaling="sites", correlation=TRUE) |>
++     points("sites", pch=21, col = 1, cex=1.5, bg = dune.env$Management) |>
++     text("species", col = "blue", arrow = TRUE, xpd = TRUE)
 > ## Scaling can be numeric or more user-friendly names
 > ## e.g. Hill's scaling for (C)CA
 > scrs <- scores(mod, scaling = "sites", hill = TRUE)
@@ -8948,7 +8953,7 @@ Procrustes sum of squares:
 > cleanEx()
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  8.559 0.295 8.885 0 0 
+Time elapsed:  8.568 0.288 8.883 0 0 
 > grDevices::dev.off()
 null device 
           1