Install the package if required

install.packages('nat.nblast', dependencies = TRUE)

Load the package and set up for knitr / 3D snapshot figures


Clustering with NBLAST scores

All by all scores

First we create a 20 x 20 NBLAST all by all score matrix for 20 Kenyon cells included with the nat package

kcscores <- nblast_allbyall(kcs20)


Hierarchically cluster the Kenyon scores and divide the clustering into 3 groups

hckcs <- nhclust(scoremat=kcscores)
## The "ward" method has been renamed to "ward.D"; note new "ward.D2"
dkcs <- colour_clusters(hckcs, k=3)

Plot a dendrogram of the clustering, with leaves labelled by true neuron type

labels(dkcs) <- with(kcs20[labels(dkcs)], type)
par(cex=.7) # so labels are legible

plot of chunk unnamed-chunk-4

3D plot

You can create interactive 3D plots using the rgl package where different subgroups of neurons are coloured according to the calculated clustering.

plot3d(hckcs, k=3, db=kcs20, soma=T)
par3d(userMatrix=diag(c(1,-1,-1,1), 4))
plot3d(, alpha=.1)

plot of chunk unnamed-chunk-5