nat.nblast (version 1.5)

plot3d.hclust: 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, ...)

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).

...

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
x=nblast(kcs20, kcs20, normalised=TRUE)
x=(x+t(x))/2
# note that specifying db explicitly could be avoided by use of the
# \\code{nat.default.neuronlist} option.
plot3d(hclust(as.dist(x)), k=3, db=kcs20)