ordihull: 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

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, 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, col = 1, show.groups, label = FALSE, lwd = NULL, length = 0,  ...)
ordispider(ord, groups, display="sites", w, spiders = c("centroid", "median"),
         show.groups, label = FALSE, col = NULL, lty = NULL, lwd = NULL, ...)
ordicluster(ord, cluster, prune = 0, display = "sites",
            w, col = 1, draw = c("segments", "none"), ...)
# S3 method for ordihull
summary(object, ...)
# S3 method for ordiellipse
summary(object, ...)
ordiareatest(ord, groups, area = c("hull", "ellipse"), kind = "sd",
         permutations = 999, parallel = getOption("mc.cores"), ...)

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 one-sided hypothesis that these areas are smaller than with randomized groups.

Arguments

ord: An ordination object or an ordiplot object.
groups: Factor giving the groups for which the graphical item is drawn.
display: Item to displayed.
draw: character; how should objects be represented on the plot? For ordihull and ordiellipse use either lines or polygon to draw the lines. For ordicluster, line segments are drawn using segments. To suppress plotting, use "none". Graphical parameters are passed to both. The main difference is that polygons may be filled and non-transparent. With none nothing is drawn, but the function returns the invisible plotting.
col: Colour of hull or ellipse lines (if draw = "lines") or their fills (if draw = "polygon") in ordihull and ordiellipse. When draw = "polygon", the colour of bordering lines can be set with argument border of the polygon function. For other functions the effect depends on the underlining functions this argument is passed to. When multiple values of col are specified these are used for each element of names(table(groups)) (in that order), shorter vectors are recycled. Function ordicluster has no groups, and there the argument will be recycled for points, and the colour of connecting lines is a mixture of point s in the cluster.
alpha: Transparency of the fill colour with draw = "polygon" in ordihull and ordiellipse. The argument takes precedence over possible transparency definitions of the colour. The value must be in range $0. . .255$ , and low values are more transparent. Transparency is not available in all graphics devices or file formats.
show.groups: Show only given groups. This can be a vector, or TRUE if you want to show items for which condition is TRUE. This argument makes it possible to use different colours and line types for groups. The default is to show all groups.
label: Label the groups by their names in the centroid of the object. ordiellipse and ordihull use standard text, and others use ordilabel.
w: Weights used to find the average within group. Weights are used automatically for cca and decorana results, unless undone by the user. w=NULL sets equal weights to all points.
kind: Draw standard deviations of points (sd), standard errors (se) or ellipsoid hulls that enclose all points in the group (ehull).
conf: Confidence limit for ellipses, e.g. 0.95. If given, the corresponding sd or se is multiplied with the corresponding value found from the Chi-squared distribution with 2df.
spiders: Are centres or spider bodies calculated either as centroids (averages) or spatial medians.
cluster: Result of hierarchic cluster analysis, such as hclust or agnes.
prune: Number of upper level hierarchies removed from the dendrogram. If prune $> 0$ , dendrogram will be disconnected.
object: A result object from ordihull or ordiellipse. The result is invisible, but it can be saved, and used for summaries (areas etc. of hulls and ellipses).
area: Evaluate the area of convex hulls of ordihull, or of ellipses of ordiellipse.
permutations: a list of control values for the permutations as returned by the function how, or the number of permutations required, or a permutation matrix where each row gives the permuted indices.
parallel: Number of parallel processes or a predefined socket cluster. With parallel = 1 uses ordinary, non-parallel processing. The parallel processing is done with parallel package.
lty, lwd, border: Vectors of these parameters can be supplied and will be applied (if appropriate) for each element of names(table(groups)) (in that order). Shorter vectors will be recycled.
length: Width (in inches) of the small (“caps”) at the ends of the bar segment (passed to arrows).
...: Parameters passed to graphical functions or to scores to select axes and scaling etc.

Author

Jari Oksanen

Details

Function ordihull draws lines or polygons for the convex hulls found by function chull encircling the items in the groups.

Function ordiellipse draws lines or polygons for ellipses by groups. The function can either draw standard deviation of points (kind="sd") or standard error of the (weighted) centroids (kind="se"), and the (weighted) correlation defines the direction of the principal axis of the ellipse. When kind = "se" is used together with argument conf, the ellipses will show the confidence regions for the locations of group centroids. 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 corresponding 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 one-sided 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.

Examples

Run this code

data(dune)
data(dune.env)
mod <- cca(dune ~ Management, dune.env)
plot(mod, type="n", scaling = "symmetric")
## Catch the invisible result of ordihull...
pl <- with(dune.env, 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 <- with(dune.env, ordihull(mod, Management,
                              scaling = "symmetric", col = 1:4,
                              draw="polygon", label =TRUE))
with(dune.env, 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")
with(dune.env, text(mod, display="sites", labels = as.character(Management),
                    col=as.numeric(Management)))
pl <- with(dune.env, 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
with(dune.env, ordibar(mod, Management, kind="se", conf=0.95, lwd=2, col=1:4,
                       label=TRUE))

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