plot3d.hclust: Methods to identify and plot groups of neurons cut from an...

In nat.nblast: NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

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	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

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)

nat.nblast documentation built on July 9, 2023, 6:12 p.m.