Merge branch 'ordiplot-plot.cca-cex'

vegandevs · Jun 9, 2024 · 50154ab · 50154ab
2 parents f7f68a0 + e5b23a1
commit 50154ab
Show file tree

Hide file tree

Showing 4 changed files with 26 additions and 30 deletions.
diff --git a/R/ordiplot.R b/R/ordiplot.R
@@ -1,6 +1,6 @@
 `ordiplot` <-
     function (ord, choices = c(1, 2), type = "points", display, xlim,
-              ylim, cex = 0.7, ...)
+              ylim, ...)
 {
     ## local functions to absorb non-par arguments of plot.default
     localPoints <- function(..., log, frame.plot, panel.first,
@@ -10,9 +10,9 @@
     if (inherits(ord, "decorana") || inherits(ord, "cca")) {
         if (missing(display))
             out <- plot(ord, choices = choices, type = type, xlim = xlim,
-                        ylim = ylim, cex = cex, ...)
+                        ylim = ylim, ...)
         else out <- plot(ord, choices = choices, type = type, display = display,
-                         xlim = xlim, ylim = ylim, cex = cex, ...)
+                         xlim = xlim, ylim = ylim, ...)
     }
     else {
         type <- match.arg(type, c("points", "text", "none"))
@@ -45,9 +45,9 @@
             stop("no scores found: nothing to plot")
         ## Use linestack and exit if there is only one dimension
         if (NCOL(X) == 1 && NCOL(Y) == 1) {
-            pl <- linestack(X, ylim = range(c(X,Y), na.rm=TRUE), cex = cex, ...)
+            pl <- linestack(X, ylim = range(c(X,Y), na.rm=TRUE), ...)
             if (!is.null(Y))
-                linestack(Y, side = "left", add = TRUE, cex = cex, ...)
+                linestack(Y, side = "left", add = TRUE, ...)
             return(invisible(pl))
         }
         tmp <- apply(rbind(X, Y), 2, range, na.rm=TRUE)
@@ -57,11 +57,16 @@
             ylim <- tmp[, 2]
         plot(tmp, xlim = xlim, ylim = ylim, asp = 1, type = "n",
              ...)
+        ## default cex = 0.7 if not defined by the user
+        if (is.null(match.call(expand.dots = FALSE)$...$cex)) {
+            op <- par(cex = 0.7)
+            on.exit(par(op))
+        }
         if (type == "points") {
             if (!is.null(X))
-                localPoints(X, pch = 1, col = 1, cex = cex, ...)
+                localPoints(X, pch = 1, col = 1, ...)
             if (!is.null(Y))
-                localPoints(Y, pch = "+", col = "red", cex = cex, ...)
+                localPoints(Y, pch = "+", col = "red", ...)
         }
         if (type == "text") {
             if (!is.null(X)) {
@@ -70,15 +75,15 @@
                     warning("type='t', but no names available: using x1...")
                     labs <- paste0("x", as.character(seq_len(nrow(X))))
                 }
-                localText(X, labels = labs, col = 1, cex = cex, ...)
+                localText(X, labels = labs, col = 1,  ...)
             }
             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", cex = cex, ...)
+                localText(Y, labels = labs, col = "red", ...)
             }
         }
         out <- list(sites = X, species = Y)

diff --git a/R/plot.decorana.R b/R/plot.decorana.R
@@ -1,19 +1,19 @@
-"plot.decorana" <-
-    function (x, choices = c(1, 2), origin = TRUE, display = c("both", 
-                                                   "sites", "species", "none"), cex = 0.8, cols = c(1, 2), type, xlim, ylim, 
-              ...) 
+`plot.decorana` <-
+    function (x, choices = c(1, 2), origin = TRUE,
+              display = c("both", "sites", "species", "none"), cex = 0.7,
+              cols = c(1, 2), type, xlim, ylim, ...)
 {
     display <- match.arg(display)
     sites <- x$rproj
     specs <- x$cproj
     if (missing(type)) {
         nitlimit <- 120
         nit <- 0
-        if (display == "sites" || display == "both") 
+        if (display == "sites" || display == "both")
             nit <- nit + nrow(sites)
-        if (display == "species" || display == "both") 
+        if (display == "species" || display == "both")
             nit <- nit + nrow(specs)
-        if (nit > nitlimit) 
+        if (nit > nitlimit)
             type <- "points"
         else type <- "text"
     }
@@ -50,7 +50,7 @@
         if (missing(xlim)) xlim <- range(sp.x, st.x)
         if (missing(ylim)) ylim <- range(sp.y, st.y)
     })
-    plot(sites, type = "n", xlim = xlim, ylim = ylim, asp = 1, 
+    plot(sites, type = "n", xlim = xlim, ylim = ylim, asp = 1,
          ...)
     if (origin) {
         abline(h = 0, lty = 3)
@@ -61,12 +61,12 @@
         abline(v = x$origin[choices[1]], lty = 3)
     }
     if (type != "none" && (display == "both" || display == "sites")) {
-        if (type == "text" && !is.null(sitnam)) 
+        if (type == "text" && !is.null(sitnam))
             text(sites, sitnam, cex = cex, col = cols[1])
         else points(sites, cex = cex, col = cols[1])
     }
     if (type != "none" && (display == "both" || display == "species")) {
-        if (type == "text" && !is.null(spenam)) 
+        if (type == "text" && !is.null(spenam))
             text(specs, spenam, cex = cex, col = cols[2])
         else points(specs, pch = "+", cex = cex, col = cols[2])
     }

diff --git a/man/decorana.Rd b/man/decorana.Rd
@@ -18,7 +18,7 @@ decorana(veg, iweigh=0, iresc=4, ira=0, mk=26, short=0,
 
 \method{plot}{decorana}(x, choices=c(1,2), origin=TRUE,
      display=c("both","sites","species","none"),
-     cex = 0.8, cols = c(1,2), type, xlim, ylim, ...)
+     cex = 0.7, cols = c(1,2), type, xlim, ylim, ...)
 
 \method{text}{decorana}(x, display = c("sites", "species"), labels,
      choices = 1:2, origin = TRUE, select,  ...)

diff --git a/man/ordiplot.Rd b/man/ordiplot.Rd
@@ -19,8 +19,7 @@
 }
 
 \usage{
-ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim,
-     cex = 0.7, ...)
+ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim, ...)
 \method{points}{ordiplot}(x, what, select, arrows = FALSE,
     length = 0.05, arr.mul, ...)
 \method{text}{ordiplot}(x, what, labels, select, arrows = FALSE,
@@ -38,7 +37,6 @@ ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim,
     \code{\link{rda}}, \code{\link{dbrda}} and \code{\link{capscale}}
     it is the same as in \code{\link{plot.cca}}.  }
   \item{xlim, ylim}{the x and y limits (min,max) of the plot.}
-  \item{cex}{Character expansion factor for points and text.}
   \item{\dots}{Other graphical parameters. }
   \item{x}{A result object from \code{ordiplot}.}
   \item{what}{Items identified in the ordination plot. The types depend
@@ -107,13 +105,6 @@ ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim,
 \author{
   Jari Oksanen
 }
-\note{
-  The purpose of these functions is to provide similar functionality as
-  the \code{plot}, \code{plotid} and \code{specid} methods in library
-  \code{labdsv}. The functions are somewhat limited in parametrization,
-  but you can call directly the standard \code{\link{identify}} and
-  \code{\link{plot}} functions for a better user control.
-}
 
 \seealso{ \code{\link{identify}} for basic operations, \code{\link{plot.cca}},
   \code{\link{plot.decorana}}, \code{\link{plot.procrustes}} which also