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czbiohub-sf / tabula-muris-senis

Tabula Muris Senis
http://tabula-muris-senis.ds.czbiohub.org
BSD 3-Clause "New" or "Revised" License
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Mapping from cell ontology class number to labels? #12

Closed joycekang closed 4 years ago

joycekang commented 4 years ago

Hello! Thanks for making this dataset well-organized. I might be missing something obvious, but is there a file that provides a mapping of cell ontology class numbers (int) to the actual name of the cell type ("B cell")? Also, what is the difference between "cell.ontology.class", "cell.ontology.id", and "free.annotation" columns in the @meta.data in droplet_filtered.h5ad? Thanks so much!

aopisco commented 4 years ago

hi @joycekang the mapping you're missing might have to do with you reading the h5ad file in R instead of Python. Have you try using the loom file and convert it to RDS first?

joycekang commented 4 years ago

Thanks for the response! I was indeed trying to read the h5ad file in R. Where is the loom file located? I downloaded the processed data from the tms_gene_data folder from https://figshare.com/projects/Tabula_Muris_Senis/64982 but don't see any loom files.

joycekang commented 4 years ago

Update: I was able to resolve this by reading in the h5ad file using scanpy then exporting the .obs dataframe as a .csv file to read into R. Thanks!