plot3d.hclust {nat.nblast} | R Documentation |
Methods to identify and plot groups of neurons cut from an hclust
object
Description
plot3d.hclust
uses plot3d
to plot neurons from
each group, cut from the hclust
object, by colour.
Usage
## S3 method for class 'hclust'
plot3d(
x,
k = NULL,
h = NULL,
groups = NULL,
col = rainbow,
colour.selected = FALSE,
...
)
Arguments
x |
|
k |
number of clusters to cut from |
h |
height to cut |
groups |
numeric vector of groups to plot. |
col |
colours for groups (directly specified or a function). |
colour.selected |
When set to |
... |
additional arguments for |
Details
Note that the colours are in the order of the dendrogram as assigned
by colour_clusters
.
Value
A list of rgl
IDs for plotted objects (see
plot3d
).
See Also
nhclust, plot3d, slice,
colour_clusters
Examples
# 20 Kenyon cells
data(kcs20, package='nat')
# calculate mean, normalised NBLAST scores
kcs20.aba=nblast_allbyall(kcs20)
kcs20.hc=nhclust(scoremat = kcs20.aba)
# plot the resultant dendrogram
plot(kcs20.hc)
# now plot the neurons in 3D coloured by cluster group
# note that specifying db explicitly could be avoided by use of the
# \code{nat.default.neuronlist} option.
plot3d(kcs20.hc, k=3, db=kcs20)
# only plot first two groups
# (will plot in same colours as when all groups are plotted)
plot3d(kcs20.hc, k=3, db=kcs20, groups=1:2)
# only plot first two groups
# (will be coloured with a two-tone palette)
plot3d(kcs20.hc, k=3, db=kcs20, groups=1:2, colour.selected=TRUE)
[Package nat.nblast version 1.6.7 Index]