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Reproducible Plots for the Allen Institutes Brain Atlases
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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.


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


Here is a list of the current accompanying data packages:

atlasplot additionally has an Allen Institute API wrapper for:

  • Adult Mouse Brain Atlas
  • Developing Mouse Brain Atlas


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.

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