README.md

In AllenInstitute/atlasplot: Easy Plotting of the Allen Brain Altases

atlasplot

Simple Reproducible Plots for the Allen Institute's Brain Atlases

This package aims to simplify the process of producing graphics for the expression data available in the Allen Institute's Brain Atlases. Additionally, it will be coupled with individual data packages, allowing anyone to easily access this vast data resource.

Install

To install the atlasplot package it is recommended to use the devtools package. This is a well trusted and reputable package from Hadley Wickham intended to streamline package development and installation.

In the R command line perform the following commands

# Install devtools package
install.package("devtools")

# Install atlasplot
# build_vignettes = TRUE creates the html vignette
devtools::install_github("AllenInstitute/atlasplot", build_vignettes = TRUE)

Usage

Here is a list of the current accompanying data packages: hbadata fetdata brspdata nhpdata

atlasplot additionally has an Allen Institute API wrapper for: Adult Mouse Brain Atlas Developing Mouse Brain Atlas

Caching

atlasplot makes use of a simple caching system to speed up access to commonly used resources. By caching common API calls locally, atlasplot can significantly reduce network communication time. Caching is initialized the first time you call a function that uses to web API. The cache file will always be located in ~/.json_cache. Files are saved as .rda objects, and are compressed to decrease their footprint.

There are two user functions associated with caching: set_cache_size clear_cache

By default, atlasplot limits its cache to 2 Gb. set_cache_size can be used to change this default

> set_cache_size(10000) # change cache size to 10 kb

Additionally, caching can be turned off by selecting a size of FALSE.

clear_cache deletes all current files in the users cache. It is called with no arguments and is only inteneded to be used when updated data has been added to the API.

License

The license for this package is available on Github at: https://github.com/AllenInstitute/atlasplot/blob/master/LICENSE

Level of Support

We do not plan any updates of this tool at this time. However, please contact Jeremy Miller (jeremym at alleninstitute dot org) with any questions, concerns, or if you have suggestions for additions to the package. We do plan to correct errors, so if you notice one, please email or submit an "Issue".

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/atlasplot/blob/master/CONTRIBUTING.md

Citation

This package was developed by Charlie Edelson in 2017 based off previous plots created by Jeremy Miller. It is currently unpublished, but we would encourage linkage to this GitHub repo as well as citation of the underlying Allen Brain Map data sets as described in the Citation Policy.

AllenInstitute/atlasplot documentation built on Aug. 11, 2021, 1:52 a.m.