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getassaydata from scanpy object #870

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koalap-2018 opened this issue Oct 13, 2019 · 4 comments
Closed

getassaydata from scanpy object #870

koalap-2018 opened this issue Oct 13, 2019 · 4 comments
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@koalap-2018
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Hi guys,

I am trying to get the gene expression raw, log, scaled for just a couple of genes from the anndata object but i have tried doesnt seem to work. I just want a simple dataframe with the gene names as colum indexes and row info of the cells. this is waht i used to do in seurat. I am sure there is an easy way to do this in scanpy but just havent figure out.

geneX_df=as.data.frame(as.matrix(GetAssayData(object = anndata, slot = "data")["geneX",]))

Thanks!
@LuckyMD
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LuckyMD commented Oct 13, 2019 •
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Hi,

If adata is your anndata object, you can get the expression data from adata.X. Depending on what you did to the object before, that will contain differently pre-processed data.

If you want it for "Gene A", then you can use adata[:,'Gene A'].Xto get the expression value of Gene A in all cells.

You can of course put that into a pandas dataframe via pd.DataFrame()

@koalap-2018
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Thanks @LuckyMD

@flying-sheep
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Hi! I hope you’ll enjoy using scanpy. Beginner questions like this are more suited for https://scanpy.discourse.group/ or stackoverflow so we still have some overview over this bug tracker.

@koalap-2018
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Great thanks so much!

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@flying-sheep @LuckyMD @koalap-2018