| ordiplot {vegan} | R Documentation |
Ordination plot function especially for congested plots. Function
ordiplot always plots only unlabelled points, but
identify.ordiplot can be used to add labels to selected site,
species or constraint points. Function identify.ordiplot can
be used to identify points from plot.cca,
plot.decorana, plot.procrustes and
plot.rad as well.
ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim, ...) ## S3 method for class 'ordiplot': identify(x, what, labels, ...) ## S3 method for class 'ordiplot': points(x, what, select, ...) ## S3 method for class 'ordiplot': text(x, what, labels, select, ...)
ord |
A result from an ordination. |
choices |
Axes shown. |
type |
The type of graph which may be "points",
"text" or "none" for any ordination method. |
display |
Display only "sites" or "species". The default for most
methods is to display both, but for cca,
rda and capscale it is the same as in
plot.cca. |
xlim, ylim |
the x and y limits (min,max) of the plot. |
... |
Other graphical parameters. |
x |
A result object from ordiplot. |
what |
Items identified in the ordination plot. The types depend
on the kind of plot used. Most methods know sites and
species, functions cca and rda
know in addition
constraints (for `LC' scores), centroids and
biplot, and plot.procrustes ordination plot has
heads and points. |
labels |
Optional text used for labels. Row names will be used if this is missing. |
select |
Items to be displayed. This can either be a logical
vector which is TRUE for displayed items or a vector of indices
of displayed items. |
Function ordiplot draws an ordination diagram using black circles for
sites and red crosses for species. It returns invisibly an object of
class ordiplot which can be used by identify.ordiplot
to label selected sites or species, or constraints in
cca and rda.
The function can handle output from several alternative ordination
methods. For cca, rda and
decorana it uses their plot method with option
type = "points". In addition, the plot functions of
these methods return invisibly an ordiplot object which can
be used by identify.ordiplot to label points. For other
ordinations it relies on scores to extract the scores.
For full user control of plots, it is best to call ordiplot
with type = "none" and save the result, and then add sites and
species using points.ordiplot or text.ordiplot which
both pass all their arguments to the corresponding default graphical
functions.
Function ordiplot returns invisibly an object of class
ordiplot with items sites, species and
constraints (if these are available in the ordination
object). Function identify.ordiplot uses this object to label
the point.
The purpose of these functions is to provide similar functionality as
the plot, plotid and specid methods in library
labdsv. The functions are somewhat limited in parametrization,
but you can call directly the standard identify and
plot functions for a better user control.
Jari Oksanen
identify for basic operations, plot.cca,
plot.decorana, plot.procrustes which also
produce objects for
identify.ordiplot and scores for extracting
scores from non-vegan ordinations.
# Draw a cute NMDS plot from a non-vegan ordination (isoMDS). # Function metaMDS would be an easier alternative. data(dune) dune.dis <- vegdist(wisconsin(dune)) library(MASS) dune.mds <- isoMDS(dune.dis) dune.mds <- postMDS(dune.mds, dune.dis) dune.mds$species <- wascores(dune.mds$points, dune, expand = TRUE) fig <- ordiplot(dune.mds, type = "none") points(fig, "sites", pch=21, col="red", bg="yellow") text(fig, "species", col="blue", cex=0.9) # Default plot of the previous using identify to label selected points ## Not run: fig <- ordiplot(dune.mds) identify(fig, "spec") ## End(Not run)