deimos.plot.stem(): KeyError with res object

[jessieolough]

Hello,

I am trying to follow the DEIMoS documentation for the MS2 Extraction steps. At the end, where I have the final res object and I go to use the deimos.plot.stem() function, I get the following error message:

Traceback (most recent call last):
  File "C:\Users\jessieolough\AppData\Local\anaconda3\envs\deimos\Lib\site-packages\pandas\core\indexes\range.py", line 413, in get_loc
    return self._range.index(new_key)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: 61 is not in range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\jessieolough\AppData\Local\anaconda3\envs\deimos\Lib\site-packages\pandas\core\indexing.py", line 1183, in __getitem__
    return self.obj._get_value(*key, takeable=self._takeable)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jessieolough\AppData\Local\anaconda3\envs\deimos\Lib\site-packages\pandas\core\frame.py", line 4221, in _get_value
    row = self.index.get_loc(index)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\jessieolough\AppData\Local\anaconda3\envs\deimos\Lib\site-packages\pandas\core\indexes\range.py", line 415, in get_loc
    raise KeyError(key) from err
KeyError: 61

All the other preceding steps worked as expected and res is the same as the fragmentation spectra of the highest intensity MS1 feature table printed in the documentation.

Any help would be much appreciated.

Kind regards,
Jessica

[smcolby]

Looks like the exact row indices of the output might not match. What is the first index you see in the output of cell 14? I.e.,

[jessieolough]

Hi Sean,

Thanks for getting back. The output I get looks like this:

[smcolby]

Yep, see how the data frame index starts at 58, not 61? So to select the top feature, you'd need to grab the row with index 58, i.e.:

deimos.plot.stem(np.array(res.loc[58, 'mz_ms2']),
                 np.array(res.loc[58, 'intensity_ms2']),
                 width=1)
plt.tight_layout()
plt.show()

Is this using the same underlying example data, or your own? I probably need to regenerate the documentation if the example data is no longer producing the same result.

[jessieolough]

Hi Sean,

Thanks! Ah yes, that fixed the issue. This is using the same underlying example data.

Kind regards,
Jess