[Vegan-commits] r1313 - in pkg/vegan: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 23 12:47:20 CEST 2010
Author: jarioksa
Date: 2010-09-23 12:47:20 +0200 (Thu, 23 Sep 2010)
New Revision: 1313
Modified:
pkg/vegan/R/ordiellipse.R
pkg/vegan/R/ordilabel.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/ordihull.Rd
pkg/vegan/man/ordilabel.Rd
Log:
use border colour for labels in ordiellipse polygons
Modified: pkg/vegan/R/ordiellipse.R
===================================================================
--- pkg/vegan/R/ordiellipse.R 2010-09-23 10:29:25 UTC (rev 1312)
+++ pkg/vegan/R/ordiellipse.R 2010-09-23 10:47:20 UTC (rev 1313)
@@ -1,7 +1,7 @@
"ordiellipse" <-
function (ord, groups, display = "sites", kind = c("sd", "se"),
conf, draw = c("lines", "polygon", "none"),
- w = weights(ord, display),
+ w = weights(ord, display), col = NULL,
show.groups, label = FALSE, ...)
{
weights.default <- function(object, ...) NULL
@@ -43,9 +43,12 @@
else t <- sqrt(qchisq(conf, 2))
xy <- veganCovEllipse(mat$cov, mat$center, t)
if (draw == "lines")
- ordiArgAbsorber(xy, FUN = lines, ...)
+ ordiArgAbsorber(xy, FUN = lines,
+ col = if(is.null(col)) par("fg") else col,
+ ...)
else if (draw == "polygon")
- ordiArgAbsorber(xy[, 1], xy[, 2], FUN = polygon, ...)
+ ordiArgAbsorber(xy[, 1], xy[, 2], col = col, FUN = polygon,
+ ...)
if (label && draw != "none") {
cntrs <- rbind(cntrs, mat$center)
names <- c(names, is)
@@ -56,10 +59,11 @@
}
if (label && draw != "none") {
if (draw == "lines")
- ordiArgAbsorber(cntrs[,1], cntrs[,2], labels=names,
+ ordiArgAbsorber(cntrs[,1], cntrs[,2], labels=names, col = col,
FUN = text, ...)
- else
- ordiArgAbsorber(cntrs, labels = names, FUN = ordilabel, ...)
+ else
+ ordiArgAbsorber(cntrs, labels = names, col = NULL,
+ FUN = ordilabel, ...)
}
class(res) <- "ordiellipse"
invisible(res)
Modified: pkg/vegan/R/ordilabel.R
===================================================================
--- pkg/vegan/R/ordilabel.R 2010-09-23 10:29:25 UTC (rev 1312)
+++ pkg/vegan/R/ordilabel.R 2010-09-23 10:47:20 UTC (rev 1313)
@@ -1,6 +1,7 @@
`ordilabel` <-
function(x, display, labels, choices = c(1,2), priority,
- cex = 0.8, fill = "white", border = NULL, ...)
+ cex = 0.8, fill = "white", border = NULL, col = NULL,
+ ...)
{
if (missing(display))
display <- "sites"
@@ -16,10 +17,15 @@
ex <- strheight("x", cex = cex, ...)
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")
for (i in 1:nrow(x)) {
polygon(x[i,1] + c(-1,1,1,-1)*w[i], x[i,2] + c(-1,-1,1,1)*h[i],
col = fill, border = border)
- text(x[i,1], x[i,2], labels = labels[i], cex = cex, ...)
+ text(x[i,1], x[i,2], labels = labels[i], cex = cex, col = col, ...)
}
invisible(x)
}
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2010-09-23 10:29:25 UTC (rev 1312)
+++ pkg/vegan/inst/ChangeLog 2010-09-23 10:47:20 UTC (rev 1313)
@@ -4,6 +4,15 @@
Version 1.18-12 (opened September 17, 2010)
+ * ordilabel: gained argument 'col' to set the text colour of the
+ labels separately from 'border' (default action is to use 'border'
+ colour).
+
+ * ordiellipse: gained argument 'col'. For draw = "lines" this
+ works similarly as previously when 'col' was passed on. For draw =
+ "polygon" 'col' sets only the polygon fill, and the text of the
+ labels will use the colour of the border or of the foreground.
+
* ordiR2step: gained argument 'direction = c("both", "response")',
and iwth "both" gives also adjusted R2 when dropping terms. I have
not yet seen a case where a terms is dropped. Abandoned dangerous
Modified: pkg/vegan/man/ordihull.Rd
===================================================================
--- pkg/vegan/man/ordihull.Rd 2010-09-23 10:29:25 UTC (rev 1312)
+++ pkg/vegan/man/ordihull.Rd 2010-09-23 10:47:20 UTC (rev 1313)
@@ -27,7 +27,7 @@
show.groups, label = FALSE, ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se"), conf,
draw = c("lines","polygon", "none"), w = weights(ord, display),
- show.groups, label = FALSE, ...)
+ show.groups, col = NULL, label = FALSE, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
show.groups, label = FALSE, ...)
ordiarrows(ord, groups, levels, replicates, display = "sites",
@@ -83,7 +83,10 @@
2df. }
\item{cluster}{Result of hierarchic cluster analysis, such as
\code{\link{hclust}} or \code{\link[cluster]{agnes}}.}
- \item{lty, col, lwd}{Line type, line colour and line width used for
+ \item{col}{Colour of ellipses or ellipse fills in \code{ordiellipse}
+ or lines in \code{ordigrid}. For other functions the effect depends
+ on the underlining functions this argument is passed to.}
+ \item{lty, lwd}{Line type, line width used for
\code{level}s and \code{replicate}s in \code{ordigrid}.}
\item{prune}{Number of upper level hierarchies removed from the
dendrogram. If \code{prune} \eqn{>0}, dendrogram will be
Modified: pkg/vegan/man/ordilabel.Rd
===================================================================
--- pkg/vegan/man/ordilabel.Rd 2010-09-23 10:29:25 UTC (rev 1312)
+++ pkg/vegan/man/ordilabel.Rd 2010-09-23 10:47:20 UTC (rev 1313)
@@ -11,7 +11,7 @@
\usage{
ordilabel(x, display, labels, choices = c(1, 2), priority, cex = 0.8,
- fill = "white", border = NULL, ...)
+ fill = "white", border = NULL, col = NULL, ...)
}
\arguments{
@@ -30,6 +30,8 @@
of \code{\link{polygon}}).}
\item{border}{The colour and visibility of the border of the label as
defined in \code{\link{polygon}}).}
+ \item{col}{Text colour. Default \code{NULL} will give the value of
+ \code{border} or \code{par("fg")} if \code{border} is \code{NULL}.}
\item{\dots}{Other arguments (passed to \code{\link{text}}). }
}
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