Fortify isometric feature mapping results

Prepares fortified versions of results from vegan::isomap() objects.

Usage

# S3 method for class 'isomap'
fortify(model, data = NULL, axes = NULL, what = c("sites", "network"), ...)

# S3 method for class 'isomap'
tidy(x, data = NULL, axes = NULL, what = c("sites", "network"), ...)

Arguments

model, x

an object of class vegan::isomap().

data

data.frame; additional data to be added to the fortified object.

axes

numeric; which axes to return. For what = "network" this must be of length two only.

what

character; what aspect of the results should be fortified? "sites" returns to ordination scores from the multidimensional scaling part of the model. "network" returns the coordinates for edges joining points.

...

additional arguments for other methods. Currently ignored.

Value

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 additional variable is label, containing a label for each observation. For what = "network", the data frame contains four variables containing the coordinates in the chosen MDS axes for the start and end points of the network edges.

Details

Two different objects can be created from the results of an vegan::isomap() object. The first is the standard scores representation of fortified ordinations in vegan, which results in a wide data frame where rows contain observations and column 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".

Author

Gavin L. Simpson

Examples

library("vegan")

library("ggplot2")
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()
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.