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camlab-bioml / cytomarker

Interactive design and validation of antibody panels using single-cell atlases
https://camlab.shinyapps.io/cytomarker/
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Bug in cell type removal (NA cell type) #81

Closed kieranrcampbell closed 2 years ago

kieranrcampbell commented 2 years ago

When I run the current version of cytosel (at the lab shinyapps account) using the pbmc_new.rds file I get the following error:

Screen Shot 2022-09-12 at 10 18 48 PM

Any thoughts on what's causing this?

matt-sd-watson commented 2 years ago

i think that there is an NA value in the annotation column for this particular object. Since there is only one NA count, it is removed because it does not meet the minimum category count of 2. I remember this when I used this object before, and I just changed the NA to "Unknown".

This isn't so much a bug with the filtering steps as opposed to not knowing specifically how to handle NA or null values in metadata columns. We could build this into the checks, but the low cell type filtering is working as intended and the warning is triggered in the appropriate context.

kieranrcampbell commented 2 years ago

Ah ok. How about we check for NA (either as the actual R NA value, or as "NA" encoded as text) and just add an information box (like those that appear on the right hand side) saying NAs were found and will be discarded?