Decouple dataset from statistics #329
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Base automatically changed from
decouple-dataset-from-enrichment
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September 20, 2024 13:27
# Conflicts: # alphastats/DataSet_Statistics.py # alphastats/gui/utils/overview_helper.py # alphastats/statistics/DifferentialExpressionAnalysis.py # tests/test_DataSet.py
JuliaS92
reviewed
Sep 24, 2024
| ).calculate() | ||
| return res, plot_list | ||
| # @ignore_warning(RuntimeWarning) | ||
| # def multicova_analysis( # TODO never used outside of tests .. how does this relate to multicova.py? |
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In MultiCovaAnalysis multicova.py is imported from the calculate function.
def calculate(self):
from alphastats.multicova import multicova
This is defenitely a feature we want in the tool, so it should remain active but we need a ticket for putting it in the interface.
JuliaS92
reviewed
Sep 24, 2024
| @@ -386,7 +386,3 @@ def load_options(): | |||
| st.session_state[StateKeys.STATISTIC_OPTIONS] = statistic_options(st.session_state) | |||
| # TODO: Check if this should be reintroduced or removed | |||
| # st.session_state["interpretation_options"] = interpretation_options | |||
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| def gui_multicova_analysis(): | |||
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Add big todo here instead of removing it.
JuliaS92
reviewed
Sep 24, 2024
| @@ -152,7 +175,7 @@ def _sam_calculate_fdr_line(self): | |||
| ) | |||
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| @lru_cache(maxsize=20) | |||
| def _sam(self): | |||
| def _sam(self): # TODO duplicated? | |||
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Only the last two lines differ from the function in DifferentialExpressionAnalysis
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This is a huge one, but could not be separated in a sensible way..
check the individual commits for the line of reasoning (the bug in fc calculation in de72c6e is removed again later
I think now I see where this could be going: the
DataSetclass will contain the data (mat,metadata) and beside that be just a convenient interface for the frontend. It will offer all operations that can be done on the data (statistics, plots, preprocessing), but delegate the logic to dedicated classes. Two things are missing still:Plotsinit(i.e. the actual data loading) to another class (similar toStatistics, ..)