Description Usage Arguments Details Value Author(s) See Also Examples
Function draws a 3D plot where ordination result is at the bottom
plane and a hclust
dendrogram is drawn above the
plane.
1 2 3 4 |
ord |
An ordination object or an |
cluster |
Result of hierarchic cluster analysis, such as
|
prune |
Number of upper levels hierarchies removed from the
tree. If |
choices |
Choice of ordination axes. |
display |
Ordination scores displayed. |
col |
Colour of tree. The colour can be a vector and it is used for the points, text and terminal branches. The colour of internal branches is a mixture of connected leaves. |
text |
Text to replace the default of item labels when
|
type |
Display of leaves: |
... |
Arguments passed to |
orditree3d
uses scatterplot3d package to draw a static
3D plot of the dendrogram over the ordination, and
ordirgltree
uses rgl to make a dynamic, spinnable plot.
The functions were developed to plot a cluster dendrogram over a 2D
ordination plane, but any other plane can be used, for instance, a
map.
Function orditree3d
returns invisibly a
scatterplot3d
result object amended
with items points
and internal
that give the projected
coordinates of ordination scores and internal nodes, and
col.points
and col.internal
that give their
colours. All matrix-like objects can be accessed with
scores
.
Function ordirgltree
returns nothing.
Jari Oksanen.
orglcluster
and ordicluster
(in
vegan).
1 2 3 4 5 6 7 8 9 10 11 12 | data(dune, dune.env)
d <- vegdist(dune)
m <- metaMDS(d)
cl <- hclust(d, "aver")
orditree3d(m, cl, pch=16, col=cutree(cl, 3))
## ordirgltree makes ordinary rgl graphics. It accepts
## rgl.material() settings, and you can add elements to the
## open graph (for instance, bbox3d()).
if (interactive() && require(rgl, quietly = TRUE)) {
with(dune.env, ordirgltree(m, cl, col = as.numeric(Management), size = 6,
lwd = 2, alpha = 0.6))
}
|
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
Run 0 stress 0.1192678
Run 1 stress 0.1183186
... New best solution
... Procrustes: rmse 0.02027025 max resid 0.06495698
Run 2 stress 0.1183186
... Procrustes: rmse 1.68137e-05 max resid 5.417277e-05
... Similar to previous best
Run 3 stress 0.1192679
Run 4 stress 0.119268
Run 5 stress 0.1192686
Run 6 stress 0.119268
Run 7 stress 0.1192678
Run 8 stress 0.1192679
Run 9 stress 0.1183186
... New best solution
... Procrustes: rmse 9.014841e-06 max resid 2.822794e-05
... Similar to previous best
Run 10 stress 0.1192679
Run 11 stress 0.1192692
Run 12 stress 0.1808915
Run 13 stress 0.1183186
... Procrustes: rmse 9.458469e-06 max resid 3.07752e-05
... Similar to previous best
Run 14 stress 0.1192679
Run 15 stress 0.1939208
Run 16 stress 0.1183186
... New best solution
... Procrustes: rmse 3.160666e-06 max resid 8.838868e-06
... Similar to previous best
Run 17 stress 0.1192679
Run 18 stress 0.1183186
... Procrustes: rmse 2.741707e-05 max resid 8.838782e-05
... Similar to previous best
Run 19 stress 0.2034383
Run 20 stress 0.1183186
... Procrustes: rmse 8.220709e-05 max resid 0.0002677182
... Similar to previous best
*** Solution reached
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