| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Title: | Extra Functions to Cut, Label and Colour Dendrogram Clusters |
| Type: | Package |
| Description: | Provides extra functions to manipulate dendrograms that build on the base functions provided by the 'stats' package. The main functionality it is designed to add is the ability to colour all the edges in an object of class 'dendrogram' according to cluster membership i.e. each subtree is coloured, not just the terminal leaves. In addition it provides some utility functions to cut 'dendrogram' and 'hclust' objects and to set/get labels. |
| Version: | 0.2.3 |
| Suggests: | testthat |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2018-01-24 19:25:06 UTC; jefferis |
| Author: | Gregory Jefferis [aut, cre] |
| Maintainer: | Gregory Jefferis <jefferis@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2018-01-25 14:38:21 UTC |
Extra functions to cut, label and colour dendrogram clusters
Description
Extra functions to cut, label and colour dendrogram clusters
Cutting clusters
dendroextras provides the slice function as an
alternative to the base cut function. In contrast to
cut, slice returns group membership in dendrogram
order i.e. the first element in the group vector that is returned will be
the leftmost member of the leftmost cluster (cluster #1).
Colouring clusters
dendroextras provides colour_clusters to colour all of
the edges forming clusters cut by height or number of groups. You can also
set and retrieve the leaf colours (i.e. the terminal nodes) using
set_leaf_colours and leaf_colours.
Labels
dendroextras provides labels and
labels<- methods to get and set the labels of cluster
members.
See Also
dendrogram, hclust in stats
package.
Colour sub-clusters of a tree (dendrogram/hclust) object
Description
The distinctive feature of this function is to colour both the
terminal leaves of a cluster and the edges leading to those leaves.
The edgePar attribute of nodes will be augmented by a new list item col.
The groups will be defined by a call to slice using the k or h
parameters.
Usage
colour_clusters(d, k = NULL, h = NULL, col = rainbow,
groupLabels = NULL)
color_clusters(d, k = NULL, h = NULL, col = rainbow, groupLabels = NULL)
Arguments
d |
A |
k |
number of groups (passed to |
h |
height at which to cut tree (passed to |
col |
Function or vector of colours |
groupLabels |
If TRUE add numeric group label - see Details for options |
Details
If groupLabels=TRUE then numeric group labels will added to
each cluster. If a vector is supplied then these entries will be used as
the group labels. If a function is supplied then it will be passed a
numeric vector of groups (e.g. 1:5) and must return the formatted group
labels.
Value
a tree object of class dendrogram.
Author(s)
jefferis
See Also
Examples
d5=colour_clusters(hclust(dist(USArrests), "ave"),5)
plot(d5)
d5g=colour_clusters(hclust(dist(USArrests), "ave"),5,groupLabels=TRUE)
plot(d5g)
d5gr=colour_clusters(hclust(dist(USArrests), "ave"),5,groupLabels=as.roman)
plot(d5gr)
Set the labels of an object
Description
Set the labels of an object
Set the labels of a dendrogram
Usage
labels(x,...) <- value
labels(x,...) <- value
Arguments
x |
Object on which to set labels |
... |
Additional parameters passed to specific methods |
value |
New labels |
Value
object of class dendrogram
Author(s)
jefferis
See Also
Examples
hc <- hclust(dist(USArrests), "ave")
dend <- as.dendrogram(hc)
labels(dend)<-abbreviate(labels(dend),minlength=2)
Find labels of hclust object (in dendrogram order)
Description
NB will return labels in dendrogram order, not in the
order of the original labels retained in object$labels
ususally corresponding to the row or column names of
the dist object provided to hclust.
Usage
## S3 method for class 'hclust'
labels(object, ...)
Arguments
object |
hclust object from which to extract labels |
... |
Additional arguments (ignored) |
Value
character vector of labels in dendrogram order
Author(s)
jefferis
See Also
Examples
hc <- hclust(dist(USArrests), "ave")
dend <- as.dendrogram(hc)
stopifnot(all.equal(labels(hc),labels(dend)))
Return the leaf colours of a dendrogram
Description
Return the leaf colours of a dendrogram
Usage
leaf_colours(d, col_to_return = c("edge", "node", "label"))
Arguments
d |
the dendrogram |
col_to_return |
Character scalar - kind of colour attribute to return |
Details
The returned colours will be in dendrogram order.
Value
named character vector of colours, NA_character_ where missing
Author(s)
jefferis
See Also
Examples
d5=colour_clusters(hclust(dist(USArrests), "ave"),5)
leaf_colours(d5)
Set the leaf colours of a dendrogram
Description
Set the leaf colours of a dendrogram
Usage
set_leaf_colours(d, col, col_to_set = c("edge", "node", "label"))
set_leaf_colors(d, col, col_to_set = c("edge", "node", "label"))
Arguments
d |
the dendrogram |
col |
Single colour or named character vector of colours. When NA no colour will be set. |
col_to_set |
Character scalar - kind of colour attribute to set |
Author(s)
jefferis
See Also
Examples
d5=colour_clusters(hclust(dist(USArrests), "ave"),5)
dred=set_leaf_colours(d5,'red','edge')
stopifnot(isTRUE(all(leaf_colours(dred)=='red')))
d52=set_leaf_colours(d5,leaf_colours(d5),'edge')
stopifnot(all.equal(d5,d52))
Cut a tree-like object into groups numbered in tree order
Description
In comparison with cutree, the groups are numbered from left to right as per the tree when plotted in its standard horizontal form. Note also that the return value will have the leaves sorted in dendrogram order.
Usage
slice(x, k = NULL, h = NULL, ...)
Arguments
x |
tree like object |
k |
an integer scalar with the desired number of groups |
h |
numeric scalar with height where the tree should be cut |
... |
Additional parameters passed to methods |
Value
a named vector with group memberships
Author(s)
jefferis
See Also
cutree,cut.dendrogram,rect.hclust
Examples
hc <- hclust(dist(USArrests), "ave")
# return groups, leaves ordered by dendrogram
slice(hc,k=5)
# return groups, leaves ordered as originally passed to hclust
slice(hc,k=5)[order(hc$order)]