---
title: "NBLAST Clustering"
author: "Gregory Jefferis"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Hierarchical clustering of neurons by NBLAST scores}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

# Startup
Install the package if required
```{r install, eval=FALSE}
install.packages('nat.nblast', dependencies = TRUE)
```

Load the package and set up for knitr / 3D snapshot figures
```{r, message=FALSE}
library(nat.nblast)
rgl::setupKnitr()
```



# 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

```{r, message=FALSE}
library(nat)
kcscores <- nblast_allbyall(kcs20)
```

## Clustering

Hierarchically cluster the Kenyon scores and divide the clustering into 3 groups
```{r}
hckcs <- nhclust(scoremat=kcscores)
library(dendroextras)
dkcs <- colour_clusters(hckcs, k=3)
```

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

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

## 3D plot
You can create interactive 3D plots using the rgl package where different
subgroups of neurons are coloured according to the calculated clustering.
```{r, rgl=TRUE, message=FALSE}
plot3d(hckcs, k=3, db=kcs20, soma=T)
par3d(userMatrix=diag(c(1,-1,-1,1), 4))
plot3d(MBL.surf, alpha=.1)
```