I'm trying to subset from multiple obs in scanpy

Question

enter image description hereenter image description here enter image description here

Hello. I am a beginner who is studying scanpy. I'm trying to subset from multiple obs in scanpy.

I can subset clusters in one obs. However, I want to subset clusters of 'pEMT' and 'Oxphos' among 'obs' at the same time as one adata.

Is there a way?

Answer 1

The image shows that 'pEMT' and 'Oxphos' are columns in the obs dataframe.

If you are subsetting the adata object based on pMET as adata[adata.obs['pMET']==somevalue] and subsetting based on Oxphos as adata[adata.obs['Oxphos']==somevalue] you can "and" the conditions as this to subset based on the both of the columns:

adata[(adata.obs['pMET']==somevalue) & (adata.obs['Oxphos']==somevalue)]

Note that adata.obs['somecolumn']==somevalue returns a Series object of booleans. You can do element-wise boolean arithemtic on these, for example you can use & (and), | (or), ~ (not) operators.