Dia entrapment peptide level#1065
Open
Cajac102 wants to merge 20 commits into
Open
Conversation
…teobench/ProteoBench into DIA_entrapment_peptide_level
![github-code-quality[bot]](https://avatars.githubusercontent.com/u/9919?s=60&v=4){kind=small}
Comment on lines
+95
to
+102
| def benchmarking( | ||
| self, | ||
| input_file: str, | ||
| input_format: str, | ||
| user_input: dict, | ||
| all_datapoints: Optional[pd.DataFrame], | ||
| input_file_secondary: str = None, | ||
| ) -> Tuple[DataFrame, DataFrame, DataFrame]: |
Comment on lines
+32
to
+35
| def generate_intermediate( | ||
| self, | ||
| filtered_df: pd.DataFrame, | ||
| ) -> pd.DataFrame: |
Comment on lines
+16
to
+18
| def generate_in_depth_plots( | ||
| self, performance_data: pd.DataFrame, parse_settings: Any, **kwargs | ||
| ) -> Dict[str, go.Figure]: |
| cols_to_drop = [c for c in ("color", "hover_text", "scatter_size", "marker") if c in all_datapoints.columns] | ||
| all_datapoints_clean = all_datapoints.drop(columns=cols_to_drop) | ||
|
|
||
| f = open(os.path.join(self.t_dir_pr, "results.json"), "w") |
| This allows immediate feedback when AlphaDIA is selected. | ||
| """ | ||
| st.subheader("Input files") | ||
| st.markdown(open(variables.description_input_file_md, "r", encoding="utf-8").read()) |
|
|
||
| # Display description if available | ||
| if hasattr(variables, "description_table_md") and os.path.exists(variables.description_table_md): | ||
| st.markdown(open(variables.description_table_md, "r", encoding="utf-8").read()) |
| return "valid" | ||
| elif lower_bound > fdr: | ||
| return "invalid" | ||
| elif lower_bound <= fdr < upper_bound: |
| st.markdown(variables.texts.ShortMessages.submission_processing_warning) | ||
| try: | ||
| st.write(f"Follow your submission approval here: [{pr_url}]({pr_url})") | ||
| except UnboundLocalError: |
| """Streamlit-based web interface for ProteoBench.""" | ||
|
|
||
| import copy | ||
| import logging |
| import copy | ||
| import logging | ||
| import uuid | ||
| from typing import Any, Dict |
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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.
First Draft of DIA Entrapment module. Absolutely WIP, but push now to show during meeting.
-Added infrastructure
-Added first draft of main plot
-Added two FDP calculations that are shown in main plot
TBD:
-Paired method calculation needs file that is too big for github, will upload to server next week
-In depth plot: FDP vs FDR across different FDR levels