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Hi @avilella, If I understood correctly, all you need to do is to create a dummy import scanpy as sc
import scipy.sparse
# assuming your filtered dandelion object is called vdj
obs = pd.DataFrame(index = vdj.metadata.index)
n = vdj.metadata.shape[0]
# just create a random matrix
adata = sc.AnnData(X = scipy.sparse.random(n, 100), obs = obs)
# this is just to populate the neighbors slot
sc.pp.neighbors(adata)
# then transfer
ddl.tl.transfer(adata, vdj) |
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Would it be possible to run the airr_rearrangement.tsv file based clustering and 3D network plotting without supplying a filtered h5 file?
If one only has data for the VDJ library and not the 5'GEX, this filtered h5 file wouldn't exist, yet the airr_rearrangement.tsv file for the VDJ data is available. See below the steps that currently work for both:
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