missing annotations

[ohmstead]

missing annotations

[jkanche]

@ohmstead: Just pushed a version that does not truncate the annotation list anymore. Let me know if that works for you! Thank you for the feedback 👍🏽

[jkanche]

The "supplied" annotations dropdown list is missing several of the metadata columns I have in my adata.obs object. Is there a way for me to structure my AnnData object so I can have them included?

@ohmstead, The reason they are missing from the dropdown is these annotations have way too many categories (> 50). Any visualization on these columns is not super helpful. But i can see how this is confusing to the user.

The gene information is sorted by ensemble gene ID and not gene symbols. My gene symbols are stored in adata.var.index. How can I access these instead of ensembl IDs?

The table ranks marker genes, they are not sorted alphabetically. (i) icon provide more information for each of these panels.

We let the user choose what to display (defaults to ensembl ids, if the dataset contains one) in this table. click on gene_id label should show a dropdown of all available feature columns:

AnnData's index for var maps to "rowNames" in the R/Bioconductor world

[ohmstead]

@jkanche Thank you for showing me where to find gene symbols! I see them now.

I respectfully disagree that columns with many categories aren't helpful for visualizing. For example, in my case I have 63 cell types in my sample, but only about a dozen large clusters. It would be very nice to visualize all my cell types.

[ohmstead]

Your responsiveness is amazing! Thanks so much