Display Groups or Factor Levels in Ordination Diagrams
Description
Functions to add convex hulls, ‘spider’ graphs, ellipses
or cluster dendrogram to ordination diagrams. The ordination
diagrams can be produced by vegan
plot.cca
,
plot.decorana
or ordiplot
.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21  ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"),
col = NULL, alpha = 127, show.groups, label = FALSE,
border = NULL, lty = NULL, lwd = NULL, ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se", "ehull"),
conf, draw = c("lines","polygon", "none"),
w = weights(ord, display), col = NULL, alpha = 127, show.groups,
label = FALSE, border = NULL, lty = NULL, lwd=NULL, ...)
ordibar(ord, groups, display = "sites", kind = c("sd", "se"), conf,
w = weights(ord, display), col = 1, show.groups, label = FALSE,
lwd = NULL, length = 0, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
spiders = c("centroid", "median"), show.groups,
label = FALSE, col = NULL, lty = NULL, lwd = NULL, ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
w = weights(ord, display), col = 1, ...)
## S3 method for class 'ordihull'
summary(object, ...)
## S3 method for class 'ordiellipse'
summary(object, ...)
ordiareatest(ord, groups, area = c("hull", "ellipse"), kind = "sd",
permutations = 999, parallel = getOption("mc.cores"), ...)

Arguments
ord 
An ordination object or an 
groups 
Factor giving the groups for which the graphical item is drawn. 
display 
Item to displayed. 
draw 
Use either 
col 
Colour of hull or ellipse lines (if 
alpha 
Transparency of the fill 
show.groups 
Show only given groups. This can be a vector, or

label 
Label the 
w 
Weights used to find the average within group. Weights are
used automatically for 
kind 
Draw standard deviations of points ( 
conf 
Confidence limit for ellipses, e.g. 0.95. If given, the
corresponding 
spiders 
Are centres or spider bodies calculated either as centroids (averages) or spatial medians. 
cluster 
Result of hierarchic cluster analysis, such as

prune 
Number of upper level hierarchies removed from the
dendrogram. If 
object 
A result object from 
area 
Evaluate the area of convex hulls of 
permutations 
a list of control values for the permutations
as returned by the function 
parallel 
Number of parallel processes or a predefined socket
cluster. With 
lty, lwd, border 
Vectors of these parameters can be supplied
and will be applied (if appropriate) for each element of

length 
Width (in inches) of the small (“caps”) at the
ends of the bar segment (passed to 
... 
Parameters passed to graphical functions or to

Details
Function ordihull
draws lines
or
polygon
s for the convex
hulls found by function chull
encircling
the items in the groups.
Function ordiellipse
draws lines
or
polygon
s for ellipses by groups
. The function
can either draw standard deviation of point scores
(kind="sd"
) or standard error of the (weighted) average of
scores (kind="sd"
), and the (weighted) correlation defines
the direction of the principal axis of the ellipse. With
kind="ehull"
the function draws an ellipse that encloses all
points of a group using ellipsoidhull
(cluster package).
Function ordibar
draws crossed “error bars” using
either either standard deviation of point scores or standard error
of the (weighted) average of scores. These are the principal axes of
the correspoding ordiellipse
, and are found by principal
component analysis of the (weighted) covariance matrix.
Functions ordihull
and ordiellipse
return invisibly an
object that has a summary
method that returns the coordinates
of centroids and areas of the hulls or ellipses. Function
ordiareatest
studies the onesided hypothesis that these
areas are smaller than with randomized groups
. Argument
kind
can be used to select the kind of ellipse, and has no
effect with convex hulls.
Function ordispider
draws a ‘spider’ diagram where
each point is connected to the group centroid with
segments
. Weighted centroids are used in the
correspondence analysis methods cca
and
decorana
or if the user gives the weights in the
call. If ordispider
is called with cca
or
rda
result without groups
argument, the
function connects each ‘WA’ scores to the corresponding
‘LC’ score. If the argument is a (invisible
)
ordihull
object, the function will connect the points of the
hull to their centroid.
Function ordicluster
overlays a cluster dendrogram onto
ordination. It needs the result from a hierarchic clustering such as
hclust
or agnes
, or other with
a similar structure. Function ordicluster
connects cluster
centroids to each other with line segments
. Function
uses centroids of all points in the clusters, and is therefore
similar to average linkage methods.
Value
Functions ordihull
, ordiellipse
and ordispider
return the invisible
plotting structure.
Function ordispider
return the coordinates to which each
point is connected (centroids or ‘LC’ scores).
Function ordihull
and ordiellipse
return invisibly an
object that has a summary
method that returns the coordinates
of centroids and areas of the hulls or ellipses. Function
ordiareatest
studies the onesided hypothesis that these
areas are smaller than with randomized groups
.
Note
These functions add graphical items to ordination graph: You
must draw a graph first. To draw line segments, grids or arrows, see
ordisegments
, ordigrid
andordiarrows
.
Author(s)
Jari Oksanen
See Also
The functions pass parameters to basic graphical functions,
and you may wish to change the default values in
lines
, segments
and
polygon
. You can pass parameters to
scores
as well. Underlying functions for
ordihull
is chull
. The underlying function for
ellipsoid hulls in ordiellipse
is
ellipsoidhull
.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31  data(dune)
data(dune.env)
mod < cca(dune ~ Management, dune.env)
attach(dune.env)
plot(mod, type="n", scaling = "symmetric")
## Catch the invisible result of ordihull...
pl < ordihull(mod, Management, scaling = "symmetric", label = TRUE)
## ... and find centres and areas of the hulls
summary(pl)
## use more colours and add ellipsoid hulls
plot(mod, type = "n")
pl < ordihull(mod, Management, scaling = "symmetric", col = 1:4,
draw="polygon", label =TRUE)
ordiellipse(mod, Management, scaling = "symmetric", kind = "ehull",
col = 1:4, lwd=3)
## ordispider to connect WA and LC scores
plot(mod, dis=c("wa","lc"), type="p")
ordispider(mod)
## Other types of plots
plot(mod, type = "p", display="sites")
cl < hclust(vegdist(dune))
ordicluster(mod, cl, prune=3, col = cutree(cl, 4))
## confidence ellipse: location of the class centroids
plot(mod, type="n", display = "sites")
text(mod, display="sites", labels = as.character(Management),
col=as.numeric(Management))
pl < ordiellipse(mod, Management, kind="se", conf=0.95, lwd=2,
draw = "polygon", col=1:4, border=1:4, alpha=63)
summary(pl)
## add confidence bars
ordibar(mod, Management, kind="se", conf=0.95, lwd=2, col=1:4, label=TRUE)
