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 Rplot function to other graphical formats, or saved in the Rsession
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 class 'orditkplot':
plot(x, ...)
## S3 method for class 'orditkplot':
points(x, ...)
## S3 method for class 'orditkplot':
text(x, ...)
## S3 method for class 'orditkplot':
scores(x, display, ...)scores can handle, or for the plot function the
object dumped from the interactive orditkplot session.scores displayed. For ordination
scores this typically is either "species" or "sites",
and for orditkplot result it is either "points" or
pcol="black" and pbg="transparent".
Argument pbg has an effect
only in filled plotting characters pch = 21 to 25.orditkplot uses The function knows the following mouse operations:
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, png, jpeg or
bmp. The file type is deduced from the file suffix or the selection of
the file type in the dialogue box. Alternatively, the same dialogue can be
used to save the plot to an editable xfig file. Button
Dump to R writes the edited coordinates of labels and points
to the Rsession 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, and unaware of the
original Tcl/Tk plot settings (probably you must set cex at
least to get a decent plot). Finally, button Dismiss 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
Rplots, 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 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 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 Rplots and in
plot.orditkplot.
ordipointlabel is an automatic
procedure with similar goals of avoiding overplotting.
See ordiplot, plot.cca,
ordirgl 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.
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)Run the code above in your browser using DataLab