R/stat-spantree.r
stat_spantree.RdThis stat layer identifies the \(n-1\) pairs among \(n\)
points that form a minimum spanning tree, then calculates the segments
between these poirs in the two dimensions x and y.
stat_spantree(
mapping = NULL,
data = NULL,
geom = "segment",
position = "identity",
engine = "mlpack",
method = "euclidean",
show.legend = NA,
inherit.aes = TRUE,
...
)Set of aesthetic mappings created by aes(). If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
The data to be displayed in this layer. There are three options:
If NULL, the default, the data is inherited from the plot
data as specified in the call to ggplot().
A data.frame, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame, and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10)).
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint.
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point(),
give the geom as "point".
For more information and other ways to specify the geom, see the layer geom documentation.
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter().
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter(), give the position as "jitter".
For more information and other ways to specify the position, see the layer position documentation.
A single character string specifying the package implementation
to use; "mlpack", "vegan", or "ade4".
Passed to stats::dist() if engine is "vegan" or "ade4",
ignored if "mlpack".
logical. Should this layer be included in the legends?
NA, the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display.
If FALSE, overrides the default aesthetics,
rather than combining with them. This is most useful for helper functions
that define both data and aesthetics and shouldn't inherit behaviour from
the default plot specification, e.g. borders().
Additional arguments passed to ggplot2::layer().
A ggproto layer.
A minimum spanning tree (MST) on the point cloud \(X\) is a minimal
connected graph on \(X\) with the smallest possible sum of distances (or
dissimilarities) between linked points. These layers call stats::dist() to
calculate a distance/dissimilarity object and an engine from mlpack,
vegan, or ade4 to calculate the MST. The result is formatted with
position aesthetics readable by ggplot2::geom_segment().
An MST calculated on x and y reflects the distances among the points in
\(X\) in the reduced-dimension plane of the biplot. In contrast, one
calculated on the full set of coordinates reflects distances in
higher-dimensional space. Plotting this high-dimensional MST on the
2-dimensional biplot provides a visual cue as to how faithfully two
dimensions can encapsulate the "true" distances between points (Jolliffe,
2002).
ggbiplot() uses ggplot2::fortify() internally to produce a single data
frame with a .matrix column distinguishing the subjects ("rows") and
variables ("cols"). The stat layers stat_rows() and stat_cols() simply
filter the data frame to one of these two.
The geom layers geom_rows_*() and geom_cols_*() call the corresponding
stat in order to render plot elements for the corresponding factor matrix.
geom_dims_*() selects a default matrix based on common practice, e.g.
points for rows and arrows for columns.
This statistical transformation is compatible with the convenience function
ord_aes().
Some transformations (e.g. stat_center()) commute with projection to the
lower (1 or 2)-dimensional biplot space. If they detect aesthetics of the
form ..coord[0-9]+, then ..coord1 and ..coord2 are converted to x and
y while any remaining are ignored.
Other transformations (e.g. stat_spantree()) yield different results in a
lower-dimensional biplot when they are computed before versus after
projection. If the stat layer detects these aesthetics, then the
transformation is performed before projection, and the results in the first
two dimensions are returned as x and y.
A small number of transformations (stat_rule()) are incompatible with
ordination aesthetics but will accept ord_aes() without warning.
These are calculated during the statistical transformation and can be accessed with delayed evaluation.
xend,yend,x,yendpoints of tree branches (segments)
Jolliffe IT (2002) Principal Component Analysis, Second Edition. Springer Series in Statistics, ISSN 0172-7397. doi:10.1007/b98835 https://link.springer.com/book/10.1007/b98835
Other stat layers:
stat_center(),
stat_chull(),
stat_cone(),
stat_projection(),
stat_rule(),
stat_scale()
if (FALSE) { # \dontrun{
# classical multidimensional scaling of road distances between European cities
euro_mds <- ordinate(eurodist, cmdscale_ord, k = 11)
# biplot with minimal spanning tree based on full-dimensional distances
# (as implemented in {mlpack})
euro_mds %>%
negate_ord("PCo2") %>%
ggbiplot() +
stat_cols_spantree(
ord_aes(euro_mds), engine = "mlpack",
alpha = .5, linetype = "dotted"
) +
geom_cols_text(aes(label = name), size = 3) +
ggtitle(
"MDS biplot of road distances between European cities",
"Dotted segments constitute the minimal spanning tree"
)
} # }