Merge pull request #4 from matsengrp/update_notebooks

updated notebooks, results, requirements, and gitignore
matsengrp · Mar 13, 2024 · f3137d7 · f3137d7
2 parents 66b9833 + 425701c
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,8 @@
+
+convergence_testing_2024-03-13/
+results/spike_analysis/*.png
+results/spike_analysis/7t*.csv
+results/spike_analysis/*pdb*
 **/Attic
 **/.ipynb_checkpoints
 **/hssp-3.1.5

diff --git a/README.md b/README.md
@@ -14,6 +14,11 @@ To run the notebook:
 ```
 git clone https://github.com/matsengrp/SARS-CoV-2_spike_multidms.git
 ```
+2. (recommended) create a new environment
+```
+mamba create --name multidms-spike python=3.11
+mamba activate multidms-spike
+```
 2. install the requirements
 ```
 pip install -r analysis_requirements.txt
@@ -24,6 +29,6 @@ jupyter notebook
 ```
 
 ## Key files
-1. [results/mutations_df.csv](results/mutations_df.csv) contains the respective parameters and phenotype effects for all mutations analyzed in this study.
-2. [results/training_functional_scores.csv](results/training_functional_scores.csv) contains the curated model training set of barcoded variants and their respective functional scores, for each of the two replicate.
+1. [results/spike_analysis/mutations_df.csv](results/spike_analysis/mutations_df.csv) contains the respective parameters and phenotype effects for all mutations analyzed in this study.
+2. [results/spike_analysis/training_functional_scores.csv](results/spike_analysis/training_functional_scores.csv) contains the curated model training set of barcoded variants and their respective functional scores, for each of the two replicate.
 
diff --git a/analysis_requirements.txt b/analysis_requirements.txt
@@ -1,4 +1,4 @@
-multidms==0.2.0
+multidms==0.4.0
 biopython
 notebook
 ipywidgets

diff --git a/results/manuscript_figures/convergence_all_lasso_lines.png b/results/manuscript_figures/convergence_all_lasso_lines.png
diff --git a/results/manuscript_figures/global_epistasis_and_prediction_correlations.png b/results/manuscript_figures/global_epistasis_and_prediction_correlations.png
diff --git a/results/manuscript_figures/interactive_chart_w_beta.html b/results/manuscript_figures/interactive_chart_w_beta.html
diff --git a/results/manuscript_figures/interactive_chart_wo_beta.html b/results/manuscript_figures/interactive_chart_wo_beta.html
diff --git a/results/manuscript_figures/percent_shifts_under_x_lineplot.png b/results/manuscript_figures/percent_shifts_under_x_lineplot.png
diff --git a/results/manuscript_figures/raw_data_summary_barcodes_backgrounds_hist.png b/results/manuscript_figures/raw_data_summary_barcodes_backgrounds_hist.png
diff --git a/results/manuscript_figures/reference_model_comparison_params_scatter.pdf b/results/manuscript_figures/reference_model_comparison_params_scatter.pdf
diff --git a/results/manuscript_figures/reference_model_comparison_params_scatter.png b/results/manuscript_figures/reference_model_comparison_params_scatter.png
diff --git a/results/manuscript_figures/replicate_functional_score_correlation_scatter.pdf b/results/manuscript_figures/replicate_functional_score_correlation_scatter.pdf
diff --git a/results/manuscript_figures/replicate_functional_score_correlation_scatter.png b/results/manuscript_figures/replicate_functional_score_correlation_scatter.png
diff --git a/results/manuscript_figures/shift_by_site_heatmap_zoom.pdf b/results/manuscript_figures/shift_by_site_heatmap_zoom.pdf
diff --git a/results/manuscript_figures/shift_by_site_heatmap_zoom.png b/results/manuscript_figures/shift_by_site_heatmap_zoom.png
diff --git a/results/manuscript_figures/shift_corr_Delta_BA2.pdf b/results/manuscript_figures/shift_corr_Delta_BA2.pdf
diff --git a/results/manuscript_figures/shift_corr_Delta_BA2.png b/results/manuscript_figures/shift_corr_Delta_BA2.png
diff --git a/results/manuscript_figures/shift_distribution_correlation_effect.pdf b/results/manuscript_figures/shift_distribution_correlation_effect.pdf
diff --git a/results/manuscript_figures/shift_distribution_correlation_effect.png b/results/manuscript_figures/shift_distribution_correlation_effect.png
diff --git a/results/manuscript_figures/shift_distribution_correlation_naive.pdf b/results/manuscript_figures/shift_distribution_correlation_naive.pdf
diff --git a/results/manuscript_figures/shift_distribution_correlation_naive.png b/results/manuscript_figures/shift_distribution_correlation_naive.png
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots.pdf b/results/manuscript_figures/shrinkage_analysis_trace_plots.pdf
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots.png b/results/manuscript_figures/shrinkage_analysis_trace_plots.png
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots_beta.pdf b/results/manuscript_figures/shrinkage_analysis_trace_plots_beta.pdf
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots_beta.png b/results/manuscript_figures/shrinkage_analysis_trace_plots_beta.png
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots_with_epistasis.pdf b/results/manuscript_figures/shrinkage_analysis_trace_plots_with_epistasis.pdf
diff --git a/results/manuscript_figures/shrinkage_analysis_trace_plots_with_epistasis.png b/results/manuscript_figures/shrinkage_analysis_trace_plots_with_epistasis.png
diff --git a/results/manuscript_figures/structural_statistics_max_abs_S.pdf b/results/manuscript_figures/structural_statistics_max_abs_S.pdf
diff --git a/results/manuscript_figures/structural_statistics_max_abs_S.png b/results/manuscript_figures/structural_statistics_max_abs_S.png
diff --git a/results/manuscript_figures/sum_shift_by_site.pdf b/results/manuscript_figures/sum_shift_by_site.pdf
diff --git a/results/manuscript_figures/sum_shift_by_site.png b/results/manuscript_figures/sum_shift_by_site.png
diff --git a/results/manuscript_figures/validation_titer_fold_change.pdf b/results/manuscript_figures/validation_titer_fold_change.pdf
diff --git a/results/manuscript_figures/validation_titer_fold_change.png b/results/manuscript_figures/validation_titer_fold_change.png
diff --git a/results/model-ch-sig-I-act/mut_df.csv b/results/model-ch-sig-I-act/mut_df.csv
diff --git a/results/model-ch-sig-I-act/shifts_by_site.csv b/results/model-ch-sig-I-act/shifts_by_site.csv
diff --git a/results/multidms02/convergence_all_lasso_lines.pdf b/results/multidms02/convergence_all_lasso_lines.pdf
diff --git a/results/multidms02/percent_shifts_under_x_lineplot.pdf b/results/multidms02/percent_shifts_under_x_lineplot.pdf
diff --git a/results/multidms02/raw_data_summary_barcodes_backgrounds_hist.pdf b/results/multidms02/raw_data_summary_barcodes_backgrounds_hist.pdf
diff --git a/results/multidms02/reference_model_comparison_params_scatter.pdf b/results/multidms02/reference_model_comparison_params_scatter.pdf
diff --git a/results/multidms02/replicate_functional_score_correlation_scatter.pdf b/results/multidms02/replicate_functional_score_correlation_scatter.pdf
diff --git a/results/multidms02/shift_by_site_heatmap_zoom.pdf b/results/multidms02/shift_by_site_heatmap_zoom.pdf
diff --git a/results/multidms02/shift_corr_Delta_BA2.pdf b/results/multidms02/shift_corr_Delta_BA2.pdf
diff --git a/results/multidms02/shift_distribution_correlation_naive.pdf b/results/multidms02/shift_distribution_correlation_naive.pdf
diff --git a/results/multidms02/shrinkage_analysis_trace_plots_beta.pdf b/results/multidms02/shrinkage_analysis_trace_plots_beta.pdf
diff --git a/results/mutations_df.csv b/results/mutations_df.csv
diff --git a/...t_figures/convergence_all_lasso_lines.pdf → ..._analysis/convergence_all_lasso_lines.pdf b/...t_figures/convergence_all_lasso_lines.pdf → ..._analysis/convergence_all_lasso_lines.pdf
diff --git a/...epistasis_and_prediction_correlations.pdf → ...epistasis_and_prediction_correlations.pdf b/...epistasis_and_prediction_correlations.pdf → ...epistasis_and_prediction_correlations.pdf
diff --git a/results/spike_analysis/interactive_shift_chart.html b/results/spike_analysis/interactive_shift_chart.html
diff --git a/...epistasis_and_prediction_correlations.pdf → results/spike_analysis/mutations_df.csv b/...epistasis_and_prediction_correlations.pdf → results/spike_analysis/mutations_df.csv
diff --git a/...gures/percent_shifts_under_x_lineplot.pdf → ...lysis/percent_shifts_under_x_lineplot.pdf b/...gures/percent_shifts_under_x_lineplot.pdf → ...lysis/percent_shifts_under_x_lineplot.pdf
diff --git a/...ata_summary_barcodes_backgrounds_hist.pdf → ...ata_summary_barcodes_backgrounds_hist.pdf b/...ata_summary_barcodes_backgrounds_hist.pdf → ...ata_summary_barcodes_backgrounds_hist.pdf
diff --git a/results/spike_analysis/reference_model_comparison_params_scatter.pdf b/results/spike_analysis/reference_model_comparison_params_scatter.pdf
diff --git a/results/spike_analysis/replicate_functional_score_correlation_scatter.pdf b/results/spike_analysis/replicate_functional_score_correlation_scatter.pdf
diff --git a/results/spike_analysis/shift_by_site_heatmap_zoom.pdf b/results/spike_analysis/shift_by_site_heatmap_zoom.pdf
diff --git a/results/spike_analysis/shift_corr_Delta_BA2.pdf b/results/spike_analysis/shift_corr_Delta_BA2.pdf
diff --git a/results/spike_analysis/shift_distribution_correlation_naive.pdf b/results/spike_analysis/shift_distribution_correlation_naive.pdf
diff --git a/results/spike_analysis/shrinkage_analysis_linear_models.pdf b/results/spike_analysis/shrinkage_analysis_linear_models.pdf
diff --git a/results/spike_analysis/shrinkage_analysis_trace_plots_beta.pdf b/results/spike_analysis/shrinkage_analysis_trace_plots_beta.pdf
diff --git a/results/spike_analysis/structural_statistics_max_abs_S.pdf b/results/spike_analysis/structural_statistics_max_abs_S.pdf
diff --git a/results/training_functional_scores.csv → ...e_analysis/training_functional_scores.csv b/results/training_functional_scores.csv → ...e_analysis/training_functional_scores.csv
diff --git a/...ltidms02/validation_titer_fold_change.pdf → ...analysis/validation_titer_fold_change.pdf b/...ltidms02/validation_titer_fold_change.pdf → ...analysis/validation_titer_fold_change.pdf
diff --git a/results/spike_structure_analysis/nbr_score_df.csv b/results/spike_structure_analysis/nbr_score_df.csv
diff --git a/results/spike_structure_analysis/pdb7tl9.ent b/results/spike_structure_analysis/pdb7tl9.ent
diff --git a/results/spike_structure_analysis/pdb7tl9.pdb b/results/spike_structure_analysis/pdb7tl9.pdb
diff --git a/simulation_manuscript_figures.ipynb b/simulation_manuscript_figures.ipynb
diff --git a/simulation_validation.ipynb b/simulation_validation.ipynb