plot.cca with optimize=TRUE and ordipointlabel in pipe

NAMESPACE

@@ -100,8 +100,8 @@ importFrom(graphics, abline, arrows, axis, barplot, box, contour,
 import(permute) ## vegan depends on permute: import everything
 importFrom(utils, news, vignette, combn, flush.console, modifyList,
            object.size, read.fortran, read.fwf, str)
-importFrom(grDevices, bmp, check.options, chull, col2rgb, dev.off,
-           heat.colors, jpeg, palette, pdf, png, postscript, rainbow,
+importFrom(grDevices, bmp, check.options, chull, col2rgb, dev.hold, dev.flush,
+           dev.off, heat.colors, jpeg, palette, pdf, png, postscript, rainbow,
            rgb, svg, tiff, xfig, xy.coords)
 ## import(grDevices) ## too many functions to be listed separately
 ## import(lattice) # vegan depends on lattice: import all
@@ -249,6 +249,7 @@ S3method(identify, ordiplot)
 # labels: base
 S3method(labels, cca)
 S3method(labels, envfit)
+S3method(labels, ordipointlabel)
 # lines: graphics
 S3method(lines, fitspecaccum)
 S3method(lines, permat)

R/ordiArgAbsorber.R

@@ -1,3 +1,4 @@
+### List non-graphical arguments used in vegan plot commands
 `ordiArgAbsorber` <- function(..., shrink, origin, scaling, triangular,
-                              display, choices, const, truemean, FUN)
+                              display, choices, const, truemean, optimize, FUN)
     match.fun(FUN)(...)

R/ordilabel.R

@@ -26,14 +26,13 @@
     w <- (strwidth(labels, cex=cex,...) + em/1.5)/2
     h <- (strheight(labels, cex = cex, ...) + ex/1.5)/2
     if (is.null(col))
-        if (!is.null(border))
-            col <- border
-        else
-            col <- par("fg")
+        col <- par("fg")
     col <- rep(col, length=nrow(sco))[ord]
-    if(!is.null(border))
-        border <- rep(border, length=nrow(sco))[ord]
+    if (is.null(border))
+        border <- col
+    border <- rep(border, length=nrow(sco))[ord]
     fill <- rep(fill, length=nrow(sco))[ord]
+    dev.hold()
     for (i in 1:nrow(sco)) {
         ordiArgAbsorber(sco[i,1] + c(-1,1,1,-1)*w[i],
                         sco[i,2] + c(-1,-1,1,1)*h[i],
@@ -42,6 +41,7 @@
         ordiArgAbsorber(sco[i,1], sco[i,2], labels = labels[i], cex = cex,
                         col = col[i], xpd = xpd, FUN = text, ...)
     }
+    dev.flush()
     invisible(x)
 }
 

R/ordipointlabel.R

@@ -1,8 +1,8 @@
 ### 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,
-             select, ...)
+             pch=c("o","+"), font = c(1,1), cex=c(0.7, 0.7),
+             add = inherits(x, "ordiplot"), labels, bg, select, ...)
 {
     xy <- list()
     ## Some 'scores' accept only one 'display': a workaround
@@ -19,33 +19,50 @@
         }
     }
     if (length(display) > 1) {
-        col <- rep(col, sapply(xy, nrow))
-        pch <- rep(pch, sapply(xy, nrow))
-        font <- rep(font, sapply(xy, nrow))
-        cex <- rep(cex, sapply(xy, nrow))
-        tmp <- xy[[1]]
-        for (i in 2:length(display))
-            tmp <- rbind(tmp, xy[[i]])
-        xy <- tmp
+        ld <- length(display)
+        col <- rep(rep(col, length=ld), sapply(xy, nrow))
+        pch <- rep(rep(pch, length=ld), sapply(xy, nrow))
+        font <- rep(rep(font, length=ld), sapply(xy, nrow))
+        cex <- rep(rep(cex, length=ld), sapply(xy, nrow))
+        if (!missing(bg))
+            fill <- rep(rep(bg, length=ld), sapply(xy, nrow))
+        xy <- do.call(rbind, xy)
     }
     else {
         xy <- xy[[1]]
         if (length(col) < nrow(xy))
-            col <- col[1]
+            col <- rep(col[1], nrow(xy))
         if (length(pch) < nrow(xy))
-            pch <- pch[1]
+            pch <- rep(pch[1], nrow(xy))
+        if (length(cex) < nrow(xy))
+            cex <- rep(cex[1], length = nrow(xy))
         if (length(font) < nrow(xy))
-            font <- font[1]
+            font <- rep(font[1], length = nrow(xy))
+        if (!missing(bg) && length(bg)  < nrow(xy))
+            fill <- rep(bg[1], length = nrow(xy))
     }
     if (!add)
-        pl <- ordiplot(x, display = display, choices = choices, type="n", ...)
-    labels <- rownames(xy)
+        pl <- ordiplot(xy, display = "sites", type="n")
+    if (!missing(labels)) {
+        if (length(labels) != nrow(xy))
+            stop(gettextf(
+                "you need  %d labels but arg 'labels' only had %d: arg ignored",
+                nrow(xy), length(labels)))
+    } else {
+        labels <- rownames(xy)
+    }
     em <- strwidth("m", cex = min(cex), font = min(font))
     ex <- strheight("x", cex = min(cex), font = min(font))
     ltr <- em*ex
-    w <- strwidth(labels, cex = cex, font = font) + em
-    h <- strheight(labels, cex = cex, font = font) + ex
-    box <- cbind(w, h)
+    ## bounding box: strwidth/height do not accept vector cex and font
+    ## and we loop
+    box <- matrix(0, nrow(xy), 2)
+    for (i in seq_len(nrow(xy))) {
+        box[i,1] <- strwidth(labels[i], cex = cex[i], font = font[i]) +
+            strwidth("m", cex = cex[i], font = font[i])
+        box[i,2] <- strheight(labels[i], cex = cex[i], font = font[i]) +
+            strheight("x", cex = cex[i], font = font[i])
+    }
     ## offset: 1 up, 2..4 sides, 5..8 corners
     makeoff <- function(pos, lab) {
         cbind(c(0,1,0,-1,0.9,0.9,-0.9,-0.9)[pos] * lab[,1]/2,
@@ -69,14 +86,21 @@
     k <- k[maylap]
     jk <- sort(unique(c(j,k)))
     ## SANN: no. of iterations & starting positions
-    nit <- min(48 * length(jk), 10000)
-    pos <- rep(1, n)
-    ## Criterion: overlap + penalty for positions other than directly
-    ## above and especially for corners
+    nit <- min(64 * length(jk), 10000)
+    pos <- ifelse(xy[,2] > 0, 1, 3)
+    ## Criterion: overlap + penalty for moving towards origin and also
+    ## for corners. Penalty is mild: max 1 ltr and one-character
+    ## string > 3*ltr due to padding (em, ex) of the bounding box.
     fn <- function(pos) {
+        move <- makeoff(pos, matrix(1, 1, 2))
         off <- makeoff(pos, box)
-        val <- sum(overlap(xy[j,]+off[j,], box[j,], xy[k,]+off[k,], box[k,]))
-        val <- val/ltr + sum(pos>1)*0.1 + sum(pos>4)*0.1
+        val <- sum(overlap(xy[j,,drop=FALSE]+off[j,,drop=FALSE],
+                           box[j,,drop=FALSE],
+                           xy[k,,drop=FALSE]+off[k,,drop=FALSE],
+                           box[k,,drop=FALSE]))
+        val <- val/ltr + sum(move[,1] * xy[,1] < 0) * 0.4 +
+            sum(move[,2] * xy[,2] < 0) * 0.4 +
+            sum(pos > 4) * 0.2
     }
     ## Move a label of one point
     gr <- function(pos) {
@@ -87,15 +111,32 @@
     ## Simulated annealing
     sol <- optim(par = pos, fn = fn, gr = gr, method="SANN",
                  control=list(maxit=nit))
-    if (!add)
-        ##points(xy, pch = pch, col = col, cex=cex, ...)
-        ordiArgAbsorber(xy, pch = pch, col = col, cex = cex, FUN = points,
-                        ...)
     lab <- xy + makeoff(sol$par, box)
+    dev.hold()
+    ## draw optional lab background first so it does not cover points
+    if (!missing(bg)) {
+        for(i in seq_len(nrow(lab))) {
+            polygon(lab[i,1] + c(-1,1,1,-1)*box[i,1]/2.2,
+                    lab[i,2] + c(-1,-1,1,1)*box[i,2]/2.2,
+                    col = fill[i], border = col[i], xpd = TRUE)
+            ordiArgAbsorber(lab[i,1], lab[i,2], labels = labels[i],
+                            col = col[i], cex = cex[i], font = font[i],
+                            FUN = text, ...)
+        }
+    } else {
+        ordiArgAbsorber(lab, labels=labels, col = col, cex = cex,
+                        font = font, FUN = text, ...)
+    }
+
+    ## always plot points (heck, the function is ordi*point*label)
+    ordiArgAbsorber(xy, pch = pch, col = col, cex = cex, FUN = points,
+                        ...)
     ##text(lab, labels=labels, col = col, cex = cex, font = font,  ...)
-    ordiArgAbsorber(lab, labels=labels, col = col, cex = cex, font = font,
-                    FUN = text, ...)
-    pl <- list(points = xy)
+    dev.flush()
+    if (!inherits(x, "ordiplot"))
+        pl <- list(points = xy)
+    else
+        pl <- x
     pl$labels <- lab
     attr(pl$labels, "font") <- font
     args <- list(tcex = cex, tcol = col, pch = pch, pcol = col,
@@ -107,3 +148,11 @@
     class(pl) <- c("ordipointlabel", "orditkplot", class(pl))
     invisible(pl)
 }
+
+### Extract labels: useful if arg labels= is given in ordipointlabel call
+
+`labels.ordipointlabel` <-
+    function(object, ...)
+{
+    rownames(object$labels)
+}

R/plot.cca.R

@@ -72,29 +72,34 @@
                       if (length(g$centroids) > 0 && all(is.na(g$centroids))) NA else g$centroids[, 2],
                       na.rm = TRUE)
     }
-    plot(g[[1]], xlim = xlim, ylim = ylim, type = "n", asp = 1,
-         ...)
+    ordiArgAbsorber(g[[1]], xlim = xlim, ylim = ylim, type = "n", asp = 1,
+         FUN = plot, ...)
     abline(h = 0, lty = 3)
     abline(v = 0, lty = 3)
     ## set up lists for graphical parameters
     GlobalPar <- list("type" = type)
     dots <- match.call(expand.dots = FALSE)$...
-    if (!is.null(dots))
+    if (!is.null(dots)) {
+        ## dots par optimize must be eval'ed to force it logical
+        if (!is.null(dots$optimize))
+            dots$optimize <- eval(dots$optimize)
         GlobalPar <- modifyList(GlobalPar, dots)
+    }
     ## Default graphical parameters
     defParText <- list("species" = list("col" = 2, "cex" = 0.7),
                        "sites" = list("cex" = 0.7),
                        "constraints" = list("col" = "darkgreen", "cex" = 0.7),
-                       "biplot" = list("col" = "blue"),
-                       "regression" = list("col" = "purple4"),
-                       "centroids" = list("col" = "blue"))
+                       "biplot" = list("col" = "blue", "cex" = 1.0),
+                       "regression" = list("col" = "purple4", "cex" = 1.0),
+                       "centroids" = list("col" = "blue", "cex" = 1.0))
     defParPoints <- list("species" = list("col" = 2, "cex" = 0.7, "pch" = "+"),
                          "sites" = list("cex" = 0.7, pch = 1),
                          "constraints" = list("col" = "darkgreen", "cex" = 0.7,
                                               "pch" = 2),
                          "biplot" = list("col" = "blue"),
                          "regression" = list("col" = "purple4"),
-                         "centroids" = list("col" = "blue", "pch" = "x"))
+                         "centroids" = list("col" = "blue", "pch" = "x",
+                                            "cex" = 1.0))
     UserPar <- list("species" = spe.par,
                     "sites" = sit.par,
                     "constraints" = con.par,
@@ -118,6 +123,17 @@
         par <- modifyList(par, GlobalPar)
         if (!is.null(UserPar[[kind]]))
             par <- modifyList(par, UserPar[[kind]])
+        ## sanitize par combinations
+        if (score == "points") # points cannot be optimized
+            par <- modifyList(par, list(optimize = NULL))
+        else if (score == "text") {
+            if (isTRUE(par$optimize)) {
+                if (isTRUE(par$arrows) || kind %in% c("biplot", "regression"))
+                    message("'optimize = TRUE' and arrows do not mix nicely")
+                if (is.null(par$pch)) # optimize=TRUE needs points
+                    par <- modifyList(par, list(pch = defParPoints[[kind]]$pch))
+            }
+        }
         ## add arguments for text/points.ordiplot, remove type
         par <- modifyList(par, list("x" = g, "what" = kind, "type" = NULL))
         do.call(score, par)

R/plot.ordipointlabel.R

@@ -7,5 +7,10 @@ plot.ordipointlabel <- function (x, ...)
         font <- par("font")
     text(x$labels, rownames(x$labels), cex = x$args$tcex, col = x$args$tcol,
          font = font, ...)
+    psize <- par("din")
+    if(any(abs(psize - x$dim)/x$dim > 0.1))
+        message(gettextf(
+            "original plot size was %.1f x %.1f, current is %.1f x %.1f",
+            x$dim[1], x$dim[2], psize[1], psize[2]))
     invisible(x)
 }

R/scores.default.R

@@ -1,12 +1,15 @@
-"scores.default" <-
+`scores.default` <-
     function (x, choices, display = c("sites", "species", "both"),
               tidy = FALSE, ...)
 {
-    display <- match.arg(display)
+    if (is.list(x)) {
+        ## why not display <- match.arg(display, names(x)) ?
+        display <- match.arg(display)
+        if (tidy)
+            display <- "both"
+        att <- names(x)
+    }
     X <- Y <- NULL
-    if (tidy)
-        display <- "both"
-    att <- names(x)
     if (is.data.frame(x) && all(sapply(x, is.numeric)))
         x <- as.matrix(x)
     if (is.list(x) && display %in% c("sites", "both")) {
@@ -44,7 +47,6 @@
         else { # "both" may be non-chalant: only warn
             warning("cannot find species scores")
         }
-
     }
     else if (is.numeric(x)) {
         X <- as.matrix(x)

R/text.ordiplot.R

@@ -1,6 +1,6 @@
 `text.ordiplot`  <-
-    function (x, what, labels, select, arrows = FALSE, length = 0.05,
-              arr.mul, bg, ...)
+    function (x, what, labels, select, optimize = FALSE, arrows = FALSE,
+              length = 0.05, arr.mul, bg, ...)
 {
     sco <- scores(x, what)
     if (!missing(labels))
@@ -21,7 +21,12 @@
         arrows(0, 0, sco[,1], sco[,2], length = length, ...)
         sco <- ordiArrowTextXY(sco, rownames(sco), rescale = FALSE, ...)
     }
-    if (missing(bg))
+    if (optimize) {
+        if (missing(bg))
+            ordipointlabel(sco, display = what, add = TRUE, ...)
+        else
+            ordipointlabel(sco, display = what, bg = bg, add = TRUE, ...)
+    } else if (missing(bg))
         text(sco, labels = rownames(sco), ...)
     else
         ordilabel(sco, labels = rownames(sco), fill = bg, ...)