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…ck_trace based on debug mode of Django
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| import logging | |||
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this file should be deleted
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| # check if colormap is valid | ||
| try: | ||
| custom_cmap = copy(plt.get_cmap(color_map)) |
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when selecting "red-yellow-blue" as "Color mat used for heatmap" the following error occurres:
File "C:\Users\janni\PycharmProjects\PROTzilla2\protzilla\steps.py", line 76, in calculate
output_dict = self.method(self.inputs)
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\janni\PycharmProjects\PROTzilla2\protzilla\methods\data_analysis.py", line 757, in method
return multiflex_lf(**inputs)
^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\janni\PycharmProjects\PROTzilla2\protzilla\data_analysis\ptm_quantification\multiflex.py", line 224, in multiflex_lf
custom_cmap = copy(plt.get_cmap(color_map))
^^^^^^^^^
UnboundLocalError: cannot access local variable 'color_map' where it is not associated with a value```
| and facilitates the analysis of modification dynamics and coregulated modifications across large datasets without the need for preselecting specific proteins. | ||
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| Parts of the implementation have been adapted from https://gitlab.com/SteenOmicsLab/multiflex-lf. | ||
| """ |
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document input parameters
| end = time.time() | ||
| message = dict( | ||
| level=logging.INFO, | ||
| msg=f"Finished with MultiFLEX-LF analysis in ~{end-start:.1f} seconds.", |
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should this displayed to the user? (we never do this for other methods)
| elif colormap == 6: | ||
| color_map = "RdYlGn" | ||
| elif colormap == 7: | ||
| color_map = "RdYlBu" |
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Maybe use an array or dictionary here instead
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| # ignore nan-slice warnings | ||
| # with warnings.catch_warnings(): | ||
| # warnings.filterwarnings("ignore", r"All-NaN (slice|axis) encountered") |
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remove this code instead of commenting it
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Description
Adds new MulitFLEX-LF method to PROTzilla.
Changes
A new file was creared for MultiFLEX-LF. Changes where you would expect them for adding a new method.
Testing
Tests will be added in the future.