nat.examples

Sample code for the NeuroAnatomy Toolbox (nat) R package

Contents

1. Library installation and basic example
2. Grosjean et al 2011 Drosophila Projection Neuron Data
3. Helmstaedter et al 2013 Mouse Retinal Connectome
4. Sumbul et al 2014 Mouse Retinal Ganglion Cells
5. Miyasaka et al 2014 Zebrafish Mitral Cell Projectome
6. Lee et al 2012 Traced Drosophila neurons
7. Heinze et al 2013 Traced Monarch butterfly neurons

Using these examples

1. Install R for your platform
2. Optionally install RStudio IDE
3. Start R or RStudio
4. Now install (once only) and load nat package from within R

install.packages("nat")
library(nat)

Each example (except the very basic 01-setup) assumes that R's current working directory has been set to the relevant folder. This will be handled by the 00-setup.R script in each folder if it is called like this:

source('/path/to/nat.examples/02-grosjean20011/00-setup.R')

Do not use the chdir=TRUE option (even if your IDE wants to do this for you).

You can also set the path yourself manually e.g.

setwd('/path/to/nat.examples/02-grosjean20011/')

Once you have run the 00-setup.R script you can start start running bits of code interactively (e.g. with copy paste or RStudio's "Run selection* menu option).

Acknowledgements

We insist that you cite the original authors of each study if you make use of the data that they have released. Please also cite this repository (https://github.com/natverse/nat.examples) if you make use of specific example code along with the https://github.com/natverse/nat package.