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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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Cluster extend possible issue #41

Closed lwhitmore closed 4 years ago

lwhitmore commented 4 years ago

Hi, I am unclear how cluster extend works. I have a cluster (number 12) that has 257 unknown cells , 552 Monocyte cells and few other cells in other classifications (i.e B cells, T cells etc...) It seems like the cluster extend should be assigning these cells as monocytes but is not assigning them any classifications and is keeping them as Unknown cells. I am not understanding why this would happen. I have the cluster_extend_max_frac_unknown = 1.

Thanks for your help! Leanne

hpliner commented 4 years ago

Apologies for the delay. How many cells are in the other classifications? Using the default cluster_extend_max_frac_incorrect of 0.1, if more than 10% of classified cells are something else (55 ish) then the cluster won't be extended.

lwhitmore commented 4 years ago

Not a problem! Even though when I set cluster_extend_max_frac_incorrect to 0 I still have some unknowns (although there are less)

lwhitmore commented 4 years ago

Hey at re examining this it seems like the cluster_extend_max_frac_incorrect does work but only for clusters whose main class is not unknown, which makes sense. Sorry for the mix up here.

Thanks for your help! Leanne

hpliner commented 4 years ago

Great, so ok to close?

lwhitmore commented 4 years ago

Yeah sounds good! Thanks again!