Plot Brain region-specific data on a 2D brain map

I have some brain region-specific RNA-seq data to plot. After searching available resouces, I found the gganatogram R package, this is the closest R package that fits my purpose. However, this package treats the mouse brain as one organ.

Another brain-heatmap project brain-heatmap which fits my purpose is 6 years old and doesn’t work for me. How can I do a similar thing on ggplot2? In the R environment, we can plot the value to each State on the map easily, like population, crime, and so on. Is there any method to label the different brain regions like different States on the map and then visualize data quickly?

Or in this community, some available shapefiles already there? Like Geographic Information Systems (GIS) Data, so I can open it in R and add value to different brain regions.


Hello Shuai

The Allen Institute does make available different atlases including an API to access vector graphics for individual structures. I’m not familiar with an R package that will make it simple for you to incorporate this into your project.

Best regards,