ChaozhongLiu
commented
2 weeks ago Hi there, Thanks for you interests in TREASMO! From the error message, the problem seems to be with Muon, and it seems that they don't have clear error message on this. I suppose it could be due to version changes or your data.
Could you please try:
- what is the output of
mdata.shape? Does it contain any cell? - Switch to Muon version as the one my experiment used:
0.1.5
watermelon-flower
Hi TREASMO team, paper looked really cool! So I wanted to try and run on some of my own data and the code provided: rna = ad.read_h5ad('data/HSPC_Muon_RNA.h5ad') atac = ad.read_h5ad('data/HSPC_Muon_ATAC.h5ad') mdata = mu.MuData({"rna": rna, "atac": atac}) mu.pp.intersect_obs(mdata) mdata.shape mu.pp.neighbors(mdata, n_neighbors=20) mu.tl.umap(mdata) however, I get the following error message: Traceback (most recent call last): File "D:\PYTHON\lib\code.py", line 90, in runcode exec(code, self.locals) File "", line 78, in
File "D:\PYCHARM\TREASMO\XUNI\lib\site-packages\muon_core\preproc.py", line 623, in neighbors
mdata.obsp[conns_key] = connectivities
File "D:\PYCHARM\TREASMO\XUNI\lib\site-packages\anndata_core\aligned_mapping.py", line 181, in setitem
value = self._validate_value(value, key)
File "D:\PYCHARM\TREASMO\XUNI\lib\site-packages\anndata_core\aligned_mapping.py", line 68, in _validate_value
if self.parent.shape[axis] != dim_len(val, i):
File "D:\PYTHON\lib\functools.py", line 875, in wrapper
return dispatch(args[0].class)(*args, kw)
File "D:\PYCHARM\TREASMO\XUNI\lib\site-packages\anndata\utils.py", line 69, in dim_len
return x.shape[axis]
AttributeError: 'tuple' object has no attribute 'shape'**
can you tell me how can i solve it? Thank you!!!