Commit b52a797

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Merge pull request #142 from MikeLippincott/figures_redo

Update figures from computation rerun

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.RData
.gitignore
2.Nomic_nELISA_Analysis
- 0.Exploratory_Analysis/PBMC
  - 1.finding_ground_truth.ipynb
  - figures
    - selected_cytokines.png
- Data/clean/Plate2
  - nELISA_plate_430420_PBMC_clean.parquet
  - nELISA_plate_430420_SHSY5Y_clean.parquet
4.sc_Morphology_Neural_Network_MLP_Model
- 0.hyperparameter_optimization
  - notebooks
    - Hyperparameter_Optimization_model_multiclass.ipynb
  - scripts
    - Hyperparameter_Optimization_model_multiclass.py
- 1.model_training
  - notebooks
    - train_multiclass_model.ipynb
  - scripts
    - Multi_Classifier_Call.sh
    - train_multiclass_model.py
- 2.model_testing/notebooks
  - sample-3573600.out
- figures/Multi_Class/MultiClass_MLP/PBMC
- trained_models
  - architectures/Multi_Class/PBMC
    - Multi_Class_MultiClass_MLP.json
  - model_save_states/Multi_Class/PBMC
    - Multi_Class_MultiClass_MLP.pt
    - Multi_Class_MultiClass_MLP_shuffle.pt
8.cytopick_analysis/notebooks
- find_prediction_images.ipynb
env_R.yaml
env_python.yaml
figures
- 0.manuscript_stats
  - notebooks
    - stats_notebook.ipynb
  - scripts
    - stats_notebook.py
- 2.figure2
  - figure2.ipynb
  - figures
    - figure2.png
  - notebooks
    - figure2.ipynb
  - scripts
    - figure2.r
- 3.figure3
  - README.md
  - figures
  - notebooks
  - scripts
- 4.figure4
  - figures
    - figure4.png
    - filtered_features.png
    - regression/PBMC
      - aggregated_with_nomic
        global_prediction_trend.png
        global_variance_r2.png
        local_variance_r2.png
      - top_abs_val_coefficients_enet.pdf
  - notebooks
    - figure4.ipynb
- 5.figure5
  - figures
    - Multi_Class/MultiClass_MLP/PBMC
    - figure5.png
  - notebooks
    - 2.add_scale_bars.ipynb
    - figure5.ipynb
  - scripts
    - figure5.r
- S1
  - figures
  - notebooks
    - S1.ipynb
    - figure_S1.ipynb
  - scripts
    - figure_S1.r
- S10
  - figures
  - notebooks
    - S10.ipynb
  - scripts
    - S10.r
- S11
  - figures
  - notebooks
    - S11.ipynb
  - scripts
    - S11.r
- S12
  - figures
    - S12.png
    - f1_score.png
  - notebooks
    - S12.ipynb
  - scripts
    - S12.r
- S13
  - figures
    - S13.png
    - f1_score.png
  - imageJ_macros
    - channel_change.ijm
  - notebooks
    - S13.ipynb
    - add_scale_bars.ipynb
  - scripts
    - S13.r
    - add_scale_bars.py
- S14
  - data
  - figures
  - notebooks
    - S14.ipynb
    - add_scale_bars.ipynb
  - scripts
- S2
  - figures
  - notebooks
    - figure_S2.ipynb
- S2_3
  - figures
  - notebooks
    - S2_3.ipynb
  - scripts
    - S2_3.r
- S3_4
  - figures
  - notebooks
    - S3_4.ipynb
- S4
  - S4.png
- S5
  - figures
    - S5.png
  - notebooks
    - S5.ipynb
  - scripts
    - S5.r
- S6
  - figures
    - PBMCS6.png
  - notebooks
    - S6.ipynb
  - scripts
    - S6.r
- S7_8_9
  - figures/regression/PBMC
  - notebooks
    - S7_8_9.ipynb
  - scripts
    - S7_8_9.r
- STable1/results
  - 2023_Interstellar_Table_S1.csv
  - consensus_cytokine_results.csv
  - consensus_cytokine_results_cleaned.md
- STable2
  - notebooks
    - STable.ipynb
    - Stable2.ipynb
  - results
  - scripts
    - Stable1.py
- STable3
  - notebooks
    - STable.ipynb
  - results
    - all_features.csv
    - all_features.md
  - scripts
    - STable.py
- STable4
  - 2023_Interstellar_Table_S4.csv
- STable5
  - 2023_Pyroptosis_Table_S5.csv

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+45699

-42965

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`‎.RData`

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`‎.gitignore`

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 # logs
 .mAP/notebooks/*.log
 .mAP/scripts/*.log
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