SignatureAnalyzer
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TypeError: Passing a dict as an indexer is not supported. Use a list instead.
Sorry for making a duplicate post, I wasn't sure if this issue was still being monitored. I am having the same issue with the same version of python and pandas. I installed signatureanalyzer from the repo also. Here is the full output from the run
---------------------------------------------------------
---------- S I G N A T U R E A N A L Y Z E R ----------
---------------------------------------------------------
* Creating output dir at cosmic3_ID
* Using hg38 build
* Using cosmic3_ID signatures
* Loading spectra from all_OCT.maf
* Mapping contexts: 360 / 361
* Saving ARD-NMF outputs to cosmic3_ID/nmf_output.h5
* Running ARD-NMF...
0/9: nit= 41 K=1 del=0.00000000
1/9: nit= 61 K=1 del=0.00000000
2/9: nit= 41 K=1 del=0.00000000
3/9: nit= 40 K=1 del=0.00000000
4/9: nit= 40 K=1 del=0.00000000
5/9: nit= 41 K=1 del=0.00000000
6/9: nit= 37 K=1 del=0.00000000
7/9: nit= 41 K=1 del=0.00000000
8/9: nit= 42 K=1 del=0.00000000
9/9: nit= 78 K=1 del=0.00000000
* Run 0 had lowest objective with mode (n=10) K = 1.
* Saving report plots to cosmic3_ID
Plotting Contributions Barplot:
Traceback (most recent call last):
File "/home/dylan/miniconda3/envs/signatureanalyzer/bin/signatureanalyzer", line 33, in <module>
sys.exit(load_entry_point('signatureanalyzer', 'console_scripts', 'signatureanalyzer')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/large_drive/runs/signatureanalyzer/getzlab-SignatureAnalyzer/signatureanalyzer/__main__.py", line 201, in main
run_maf(
File "/mnt/large_drive/runs/signatureanalyzer/getzlab-SignatureAnalyzer/signatureanalyzer/signatureanalyzer.py", line 155, in run_maf
plot_mutational_signatures(outdir, reference, aggr.K)
File "/mnt/large_drive/runs/signatureanalyzer/getzlab-SignatureAnalyzer/signatureanalyzer/utils.py", line 771, in plot_mutational_signatures
_ = signature_barplot_ID(W, contributions=np.sum(H))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/large_drive/runs/signatureanalyzer/getzlab-SignatureAnalyzer/signatureanalyzer/plotting/_muts.py", line 333, in signature_barplot_ID
W = W.loc[context83]
~~~~~^^^^^^^^^^^
File "/home/dylan/miniconda3/envs/signatureanalyzer/lib/python3.11/site-packages/pandas/core/indexing.py", line 1091, in __getitem__
check_dict_or_set_indexers(key)
File "/home/dylan/miniconda3/envs/signatureanalyzer/lib/python3.11/site-packages/pandas/core/indexing.py", line 2627, in check_dict_or_set_indexers
raise TypeError(
TypeError: Passing a dict as an indexer is not supported. Use a list instead.