fortify.isomap | R Documentation |
Prepares fortified versions of results from isomap
objects.
## S3 method for class 'isomap'
fortify(model, data = NULL, axes = 1:6, what = c("sites", "network"), ...)
model |
an object of class |
data |
data.frame; additonal data to be added to the forified object. |
axes |
numeric; which axes to return. For |
what |
character; what aspect of the results should be fortified? |
... |
additional arguments for other methods. Currently ignored. |
Two different objects can be created from the results of an isomap
object. The first is the standard scores representation of fortified ordinations in vegan, which results in a wide data frame where rows cotain observations and columne the coordinates of observations on the MDS axes. Because ISOMAP also produces a network or sorts, the coordinates of the edges of the network can also be returned in a tidy format using what = "network"
.
A data frame. For what = "sites"
, the data frame contains one variable per dimension of the multidimensional scaling embedding of the dissimilarities. Variables are named "DimX"
with "X"
being an integer. An adidtional variable is label
, containing a label for each observation. For what = "network"
, the data frame contains four variables cotaining the coordinates in the chosen MDS axes for the start and end points of the network edges.
Gavin L. Simpson
data(BCI)
dis <- vegdist(BCI)
ord <- isomap(dis, k = 3)
df <- fortify(ord, data = data.frame(Richness = specnumber(BCI)))
net <- fortify(ord, what = "network", axes = 1:2)
ggplot(df, aes(x = Dim1, y = Dim2)) +
geom_segment(data = net,
aes(x = xfrom, y = yfrom,
xend = xto, yend = yto),
colour = "grey85", size = 0.8) +
geom_point(aes(size = Richness)) +
coord_fixed()
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