[Vegan-commits] r504 - in pkg: R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 26 12:27:02 CEST 2008
Author: jarioksa
Date: 2008-09-26 12:27:02 +0200 (Fri, 26 Sep 2008)
New Revision: 504
Modified:
pkg/R/ordipointlabel.R
pkg/R/orditkplot.R
pkg/R/plot.orditkplot.R
pkg/inst/ChangeLog
pkg/inst/NEWS
pkg/man/ordipointlabel.Rd
pkg/man/orditkplot.Rd
Log:
improved graphics transport from ordipointlabel to orditkplot
Modified: pkg/R/ordipointlabel.R
===================================================================
--- pkg/R/ordipointlabel.R 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/R/ordipointlabel.R 2008-09-26 10:27:02 UTC (rev 504)
@@ -83,13 +83,13 @@
text(lab, labels=labels, col = col, cex = cex, font = font, ...)
pl <- list(points = xy)
pl$labels <- lab
+ attr(pl$labels, "font") <- font
args <- list(tcex = cex, tcol = col, pch = pch, pcol = col,
pbg = NA, pcex = cex)
pl$args <- args
pl$par <- par(no.readonly = TRUE)
- pl$font <- font
+ pl$dim <- par("din")
attr(pl, "optim") <- sol
class(pl) <- c("ordipointlabel", "orditkplot", class(pl))
invisible(pl)
}
-
Modified: pkg/R/orditkplot.R
===================================================================
--- pkg/R/orditkplot.R 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/R/orditkplot.R 2008-09-26 10:27:02 UTC (rev 504)
@@ -293,7 +293,10 @@
diam <- rep(diam, length=nr)
labfam <- rep(labfam, length=nr)
labsize <- rep(labsize, length=nr)
- labfnt <- rep(p$font, length=nr)
+ if (inherits(x, "ordipointlabel"))
+ labfnt <- attr(x$labels, "font")
+ else
+ labfnt <- rep(p$font, length=nr)
## Select only items within xlim, ylim
take <- rep(TRUE, nr)
if (!missing(xlim))
Modified: pkg/R/plot.orditkplot.R
===================================================================
--- pkg/R/plot.orditkplot.R 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/R/plot.orditkplot.R 2008-09-26 10:27:02 UTC (rev 504)
@@ -5,7 +5,10 @@
on.exit(par(op))
plot(x$points, pch = x$args$pch, cex = x$args$pcex, col = x$args$pcol,
bg = x$args$pbg, xlim = x$args$xlim, ylim = x$args$ylim, asp=1)
+ font <- attr(x$labels, "font")
+ if (is.null(font))
+ font <- par("font")
text(x$labels, rownames(x$labels), cex = x$args$tcex,
- col = x$args$tcol)
+ col = x$args$tcol, font = font)
invisible(x)
}
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/inst/ChangeLog 2008-09-26 10:27:02 UTC (rev 504)
@@ -26,6 +26,9 @@
* anova.cca(..., by = "margin") or function anova.ccabymargin
gained a 'scope' argument which is used in drop.scope().
+
+ * orditkplot & ordipointlabel: improved interface allows passing
+ font type from ordipointlabel to orditkplot.
Version 1.14-11 (closed September 10, 2008)
Modified: pkg/inst/NEWS
===================================================================
--- pkg/inst/NEWS 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/inst/NEWS 2008-09-26 10:27:02 UTC (rev 504)
@@ -27,8 +27,7 @@
relocated to avoid overplotting. The optimization uses simulated
annealing of 'optim' function. Returns an "orditkplot" object so
that the results can be edited with 'orditkplot'. Similar to
- 'pointLabel' function in maptools package. FIXME: INTERFACE
- WITH orditkplot NEEDS A FINISHING TOUCH.
+ 'pointLabel' function in maptools package.
- permatfull, permatswap: functions to permute quantitative count
data.
@@ -75,7 +74,6 @@
- orditkplot: Improved user interface. Improved zooming into
graphs. Imitates R plotting characters ('pch'). Label family,
size and font can be vectors.
- FIXME: SHOULD BE ABLE TO EDIT ALL ordipointlabel RESULTS.
- permuted.index2 and associated functions allow for restricted
permutations of strata (i.e., restricted shuffling of blocks).
Modified: pkg/man/ordipointlabel.Rd
===================================================================
--- pkg/man/ordipointlabel.Rd 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/man/ordipointlabel.Rd 2008-09-26 10:27:02 UTC (rev 504)
@@ -50,7 +50,12 @@
label. In addition, it returns the result of \code{\link{optim}} as
an attribute \code{"optim"}. The unit of overlap is the area
of character \code{"m"}, and with variable \code{cex} it is the
- smallest alternative.
+ smallest alternative. The result object inherits from
+ \code{\link{orditkplot}} result, and can be replotted with its
+ \code{plot} command. It may be possible to further edit the result
+ object with \code{\link{oridtkplot}}, but for good results it is
+ necessary that the points span the whole horizontal axis without empty
+ margins.
}
\references{ See \code{\link[maptools]{pointLabel}} for references. }
\author{ Jari Oksanen }
Modified: pkg/man/orditkplot.Rd
===================================================================
--- pkg/man/orditkplot.Rd 2008-09-26 09:09:01 UTC (rev 503)
+++ pkg/man/orditkplot.Rd 2008-09-26 10:27:02 UTC (rev 504)
@@ -98,6 +98,13 @@
\R plots, your plot must have the same dimensions as the
\code{orditkplot} canvas to have identical location of the labels.
+ The function only displays one set of scores. However, you can use
+ \code{\link{ordipointlabel}} to produce a result object that has
+ different points and text types for several sets of scores and this
+ can further edited fith \code{orditkplot}. For a good starting
+ solution you need to scale the \code{\link{ordipointlabel}} result so
+ that the points span over the whole horizontal axis.
+
The plot is a Tcl/Tk canvas, but the function tries to replicate
standard graphical device of the platform, and it honours several
graphical parameters (see \code{\link{par}}). Many of the graphical
@@ -146,7 +153,12 @@
\dontrun{
data(varespec)
ord <- cca(varespec)
+## Do something with the graph and end by clicking "Dismiss"
orditkplot(ord, mar = c(4,4,1,1)+.1, font=3)
+## Use ordipointlabel to produce a plot that has both species and site
+## scores in different colors and plotting symbols
+pl <- ordipointlabel(ord)
+orditkplot(pl)
}
}
\keyword{ iplot }
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