Error in palantir.plot.plot_diffusion_components(umap, dm_res)
st4302 opened this issue · comments
Hello,
I am following your tutorial but I keep getting an error at this step:
palantir.plot.plot_diffusion_components(umap, dm_res)
The error is:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
[<ipython-input-315-7cbcba274001>](https://localhost:8080/#) in <module>
----> 1 palantir.plot.plot_diffusion_components(umap, dm_res)
2 frames
[/usr/local/lib/python3.8/dist-packages/pandas/core/indexes/range.py](https://localhost:8080/#) in get_loc(self, key, method, tolerance)
386 except ValueError as err:
387 raise KeyError(key) from err
--> 388 raise KeyError(key)
389 return super().get_loc(key, method=method, tolerance=tolerance)
390
KeyError: 'x'
How can I fix this?
The UMAP looks like this:
0 1
AAACCCAAGATAGCTA-1-0 7.693128 10.518767
AAACCCATCCATAAGC-1-0 8.449496 12.627493
AAACGAATCGATGCAT-1-0 8.182425 11.091985
AAACGCTTCGCCAACG-1-0 7.905481 10.491224
AAAGAACCATACCATG-1-0 10.100371 8.583208
... ... ...
TTTCAGTTCCTAACAG-1-3 10.279884 4.997492
TTTCGATAGACGACGT-1-3 8.339639 6.235906
TTTGATCAGACCAGAC-1-3 10.603064 6.300741
TTTGATCCACTCTCGT-1-3 9.351139 5.385613
TTTGGTTGTACCGGCT-1-3 8.074388 5.161654
3489 rows × 2 columns
The dm_res like this:
{'T': <3489x3489 sparse matrix of type '<class 'numpy.float64'>'
with 165452 stored elements in Compressed Sparse Row format>,
'EigenVectors': 0 1 2 3 4
AAACCCAAGATAGCTA-1-0 -0.01693 -0.001429 0.005914 -0.010811 -0.004006
AAACCCATCCATAAGC-1-0 -0.01693 -0.001356 0.006489 -0.013253 -0.008432
AAACGAATCGATGCAT-1-0 -0.01693 -0.001479 0.005864 -0.011387 -0.003724
AAACGCTTCGCCAACG-1-0 -0.01693 -0.001493 0.005729 -0.009450 -0.006522
AAAGAACCATACCATG-1-0 -0.01693 -0.002563 0.002697 0.001889 0.007615
... ... ... ... ... ...
TTTCAGTTCCTAACAG-1-3 -0.01693 -0.003093 -0.003663 0.019242 0.012358
TTTCGATAGACGACGT-1-3 -0.01693 0.023604 -0.004408 0.011898 0.002167
TTTGATCAGACCAGAC-1-3 -0.01693 -0.002492 -0.000834 0.011405 0.006017
TTTGATCCACTCTCGT-1-3 -0.01693 -0.002674 -0.002274 0.018819 0.005962
TTTGGTTGTACCGGCT-1-3 -0.01693 -0.002431 -0.001375 0.015350 -0.000283
[3489 rows x 5 columns],
'EigenValues': 0 1.000000
1 0.969623
2 0.966975
3 0.949074
4 0.944321
dtype: float64,
'kernel': <3489x3489 sparse matrix of type '<class 'numpy.float64'>'
with 165452 stored elements in Compressed Sparse Row format>}
I have this error as well. How did you fix it?
I fixed it by this code-
umap.rename(columns={0:"x",1:"y"},inplace=True)