Sample code for the NeuroAnatomy Toolbox (nat) R package
- Library installation and basic example
- Grosjean et al 2011 Drosophila Projection Neuron Data
- Helmstaedter et al 2013 Mouse Retinal Connectome
- Sumbul et al 2014 Mouse Retinal Ganglion Cells
- Miyasaka et al 2014 Zebrafish Mitral Cell Projectome
- Lee et al 2012 Traced Drosophila neurons
- Heinze et al 2013 Traced Monarch butterfly neurons
Using these examples
- Install R for your platform
- Optionally install RStudio IDE
- Start R or RStudio
- Now install (once only) and load nat package from within R
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:
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.
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).
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.