Function orditkplot produces an editable ordination plot with
points and labels. The labels can be moved with mouse, and the edited
plot can be saved as an encapsulated postscript file or exported via R
plot function to other graphical formats, or saved in the R session
for further processing.
orditkplot(x, display = "species", choices = 1:2, width, xlim, ylim,
tcex = 0.8, tcol, pch = 1, pcol, pbg, pcex = 0.7, labels, ...)
# S3 method for orditkplot
plot(x, ...)
# S3 method for orditkplot
points(x, pch = x$args$pch, cex = x$args$pcex,
col = x$args$pcol, bg = x$args$pbg, ...)
# S3 method for orditkplot
text(x, cex = x$args$tcex, col = x$args$tcol,
font = attr(x$labels, "font"), ...)
# S3 method for orditkplot
scores(x, display, ...)Function returns nothing useful directly, but you can save the edited graph to a file or save the edited positions to an R session for further processing and plotting.
An ordination result or any other object that
scores can handle, or for the plot function the
object dumped from the interactive orditkplot session.
Type of scores displayed. For ordination
scores this typically is either "species" or "sites",
and for orditkplot result it is either "points" or
"labels".
Axes displayed.
Width of the plot in inches; defaults to the current width of the graphical device.
x and y limits for plots: points outside these limits will be completely removed.
Character expansion for text labels.
Colour of text labels.
Point type and outline and fill colours.
Defaults pcol="black" and pbg="transparent".
Argument pbg has an effect only in filled plotting characters
pch = 21 to 25.
Expansion factor for point size.
Labels used instead of row names.
graphical parameters used in the
points and text methods. See par.
Other arguments passed to the function. These can be
graphical parameters (see par) used in the plot, or
extra arguments to scores. These arguments are
ignored in plot, but honoured in text and points.
Jari Oksanen
Function orditkplot uses tcltk package to draw
Tcl/Tk based ordination graphics with points and labels. The function
opens an editable canvas with fixed points, but the labels can be
dragged with mouse to better positions or edited. In addition, it is
possible to zoom to a part of the graph.
The function knows the following mouse operations:
Left mouse button can be used to move labels to better positions. A line will connect a label to the corresponding point.
Double clicking left mouse button opens a window where the label can be edited. After editing the label, hit the Return key.
Right mouse button (or alternatively, Shift-Mouse button with one-button mouse) can be used for zooming to a part of the graph. Keeping the mouse button down and dragging will draw a box of the zoomed area, and after releasing the button, a new plot window will be created (this is still preliminary: all arguments are not passed to the new plot).
In addition there are buttons for the following tasks: Copy
to EPS copies the current plot to an encapsulated postscript (eps)
file using standard Tcl/Tk utilities. The faithfulness of this copy
is system dependent. Button Export plot uses
plot.orditkplot function to redraw the plot into graphical
file formats. Depending on the system, the following graphical
formats may be available: eps, pdf, svg, png, jpeg, tiff, bmp or
xfig. Some of the output formats may be edited with external
software: svg files with Illustrator or Inkscape, and xfig with the
legacy program XFig. Button Save to R writes the edited
coordinates of labels and points to the R session for further
processing, and the plot.orditkplot function can be used to
display the results. For faithful replication of the plot, the graph
must have similar dimensions as the orditkplot canvas had
originally. The plot function cannot be configured, but it
uses the same settings as the original Tcl/Tk plot. However,
points and text functions are fully configurable, but
use the stored defaults for consistency with plot.orditkplot
if none are supplied. Finally, button Close closes the
window.
The produced plot will have equal aspect ratio. The width of the
horizontal axis is fixed, but vertical axes will be scaled to needed
height, and you can use scrollbar to move vertically if the whole
canvas does not fit the window. If you use dumped labels in ordinary
R plots, your plot must have the same dimensions as the
orditkplot canvas to have identical location of the labels.
The function only displays one set of scores. However, you can use
ordipointlabel to produce a result object that has
different points and text types for several sets of scores and this
can be further edited with orditkplot. For a good starting
solution you need to scale the ordipointlabel result
so that the points span over the whole horizontal axis. The function
cannot show environmental variables or constraints, but it is
limited to unconstrained ordination.
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 par). Many of the graphical
parameters can be given on the command line, and they will be passed
to the function without influencing other graphical devices in R.
At the moment, the
following graphical parameters are honoured:
pch bg, cex,
cex.axis, cex.lab, col (for labels),
col.axis, col.lab, family (for font faces),
fg, font, font.axis, font.lab,
lheight, lwd (for the box), mar, mex,
mgp, ps, tcl. These can be set with
par, and they also will influence other plots similarly.
The tkcanvas text cannot be rotated, and
therefore vertical axis is not labelled, and las
parameter will not be honoured in the Tcl/Tk plot, but
it will be honoured in the exported R plots and in
plot.orditkplot.
Function ordipointlabel is an automatic
procedure with similar goals of avoiding overplotting, and its
output can be edited with orditkplot. See
ordiplot, plot.cca,
and orditorp for
alternative ordination plots, and scores for
extracting ordination scores.
## The example needs user interaction and is not executed directly.
## It should work when pasted to the window.
if (FALSE) {
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)
}
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