Add MulitFLEX-LF to PROTzilla #521
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ck_trace based on debug mode of Django
| @@ -0,0 +1,567 @@ | |||
| import logging | |||
Collaborator
There was a problem hiding this comment.
this file should be deleted
|
|
||
| # check if colormap is valid | ||
| try: | ||
| custom_cmap = copy(plt.get_cmap(color_map)) |
Collaborator
There was a problem hiding this comment.
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. | ||
|
|
||
| Parts of the implementation have been adapted from https://gitlab.com/SteenOmicsLab/multiflex-lf. | ||
| """ |
Collaborator
There was a problem hiding this comment.
document input parameters
| end = time.time() | ||
| message = dict( | ||
| level=logging.INFO, | ||
| msg=f"Finished with MultiFLEX-LF analysis in ~{end-start:.1f} seconds.", |
Collaborator
There was a problem hiding this comment.
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" |
Collaborator
There was a problem hiding this comment.
Maybe use an array or dictionary here instead
|
|
||
| # ignore nan-slice warnings | ||
| # with warnings.catch_warnings(): | ||
| # warnings.filterwarnings("ignore", r"All-NaN (slice|axis) encountered") |
Collaborator
There was a problem hiding this comment.
remove this code instead of commenting it
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.