Methods to identify and plot groups of neurons cut from an hclust object

plot3d.hclust uses plot3d to plot neurons from each group, cut from the hclust object, by colour.

# S3 method for hclust
plot3d(
  x,
  k = NULL,
  h = NULL,
  groups = NULL,
  col = rainbow,
  colour.selected = FALSE,
  ...
)

Arguments

x	an hclust object generated by nhclust.
k	number of clusters to cut from hclust object.
h	height to cut hclust object.
groups	numeric vector of groups to plot.
col	colours for groups (directly specified or a function).
colour.selected	When set to TRUE the colour palette only applies to the displayed cluster groups (default FALSE).
...	additional arguments for plot3d

Value

A list of rgl IDs for plotted objects (see plot3d).

Details

Note that the colours are in the order of the dendrogram as assigned by colour_clusters.

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)
#> The "ward" method has been renamed to "ward.D"; note new "ward.D2"
# 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)