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Hi there,
Thanks for trying conga! It looks like there's an "unrecognized" TCR gene name. That could mean that there's a mismatch between the "TCR" (or BCR) type and the organism. Can you double-check that the organism being passed into the plotting function is "human_ig"? Are you running this from the notebook or the command line?
You could investigate with a snippet of code like this:
organism = 'human_ig'
tcrs = conga.preprocess.retrieve_tcrs_from_adata(adata)
for tcr in tcrs:
print(tcr)
va, ja = tcr[0][:2]
vb, jb = tcr[1][:2]
assert va in conga.tcrdist.all_genes.all_genes[organism]
assert ja in conga.tcrdist.all_genes.all_genes[organism]
assert vb in conga.tcrdist.all_genes.all_genes[organism]
assert jb in conga.tcrdist.all_genes.all_genes[organism]
Hi!
I'm trying to run CoNGA on some B cell data. I get the
AssertionError
when I runconga.plotting.make_graph_vs_graph_logos
:The logos plot is only produced until the TCR logo.
adata.uns['conga_stats']
Thanks a lot for your help and great package!
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