Group Plot for Basal Ganglia cell types

1

How can I get a “Group Plot” like the ones I used to get from

http:/celltypes.brain-map.org/rnaseq/human/mtg

for Basal Ganglia cell types?

2

Hi @Harker ,

Thanks for reaching out. Could you clarify what type of plot you are looking for? For the Basal Ganglia data, you could try https://viewer.cytosplore.org/ from our BICAN collaborators. It offers additional visualization capabilities for these data sets.

Best,

Elysha

1 Like
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Hi Elysha,

Thank you for your very prompt response.

Jeremy Miller showed me how to answer the specific question I have right now using the ABC Atlas. But going forward I’m going to have more complicated questions that I thought would require that I write some Python or R code. A quick look at Cytosplore suggests that it may save me the trouble of doing that. I’ll get back to you if I need help with Cytosplore, but I’m all set for right now.

Thanks,

Harker

4

For completeness, and to aid the community, here was my email response to Harker, modified to remove any project-specific content:

The short answer is that there is no easy tool for generating dot plots like this for these data, yet. That said, you have a few options for looking at gene expression for these genes:

  1. Use the ABC Atlas. It’s by far the easiest approach, but you can only see one gene at a time.
  2. Access the data and create heatmaps programmatically: (e.g., adapt this notebook). This will get you the closest to what you want, but requires a bit of programming knowledge. You can also access the data directly from here and make your own dot plots, if you are very programmatically inclined.
  3. Use the R Shiny tool, CHARGE, which is a direct descendant of the MTG tool you listed below. Right now this only includes the macaque BG taxonomy and does not have an easy way to search for genes, but my goal by the end of the year is to have functionality to make dot plots for specific genes and to also include human and marmoset BG data sets, so this might be the way to go if you are not it in a rush.