mouselight_brain_info: Get information about the mouse brain compartments in the...

In natverse/mouselightr: Bridge HHMI Janelia MouseLight Database and nat R Package

Description

Query MouseLight's GraphQL API to retreive information about all of the brain volumes in the MouseLight project. These brain regions can be sub-volumes of other brain regions. An igraph object can be generated to explore these dependencies.

Usage

mouselight_brain_region_info(...)

mouselight_brain_graph(...)

Arguments

...	methods passed to mouselight_fetch

Value

Using mouselight_brain_graph will return an object of class igraph for use with the igraph R package. Using mouselight_brain_region_info, a data.frame with the following values is returned:

• acronym short name for a brain region

• safeName long, easily computer-readble name for a brain region

• structureId unique ID for brain region

• parentStructureId ID for a larger brain region, to which this brain region belongs

• structureIdPath a path of structure IDs to the 'root', the whole brain

References

Winnubst, Johan, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, et al. 2019. “Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain.” bioRxiv. https://doi.org/10.1101/537233. Economo, Michael N., Nathan G. Clack, Luke D. Lavis, Charles R. Gerfen, Karel Svoboda, Eugene W. Myers, and Jayaram Chandrashekar. 2016. “A Platform for Brain-Wide Imaging and Reconstruction of Individual Neurons.” eLife 5 (January): e10566.

See Also

mouselight_read_brain, mouselight_read_neurons

Examples

## Not run: 
## First we need to download all of the neurons
mbr = mouselight_brain_region_info()

## Leet's have a look at this data
View(mouselight_brain_region_info)

## Some brain regions are actually a subcompartment of others in this set.
### Hmm, so what would be good is if we could see those correspondences
g = mouselight_brain_graph()

## Let's plot these i na way we can easily see!
library(igraph)
f = igraph::layout_with_fr(g)
plot(g, layout = f)

## There are a lot of nodes here, we might want to move them about
tkplot(g, layout = f)


## End(Not run)

natverse/mouselightr documentation built on July 6, 2020, 2:09 p.m.