Update README, additional figure panels

baymlab · Jan 20, 2024 · 5697fae · 5697fae
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diff --git a/Analysis/Part_3_TnSeq_analysis/README.md b/Analysis/Part_3_TnSeq_analysis/README.md
@@ -14,18 +14,22 @@ This contains jupyter notebooks that carry out the following data reformatting a
 This contains jupyter notebooks that carry out the following analysis
 
 - fitness_calculations.ipynb: here, I calculate the fitness effect of transposon insertion mutations by fitting a line to log(frequency) vs time. 
+    - also includes a panel for Fig S4
 - Essentiality threshold.ipynnb: here, I simulate the expected variability in the fitness estimates from TnSeq assays for essential genes and genes with significant growth deficit. The goal is to identify a threshold at which we can reliably distinguish between essentiality and fitness deficit.
+    - also includes a panel for Fig S8
 
 ### Processed_data_for_plotting
 
 All the intermediate data needed to generate the final plots is saved here such as fitness estimates, RNAseq expression levels, homolog pairs, etc.
 
-### final_analysis_plotting.ipynb
+### generate_figures_main.ipynb
 
-this is the main jupyter notebook where all the analysis comes together. I do the following analyses, and generate the corresponding plots for the paper:
+this is the main jupyter notebook where the analysis comes together. I do the following analyses, and generate the corresponding plots for the paper:
 - comparing the distribution of fitness effects for the ancestors and evolved clones
 - inferring differential gene essentiality between ancestors and evolved clones
 - parallelism analysis of gene essentiality changes
-- structural variation and gene essentiality changes
 - gene expression levels and gene essentiality changes
 
+### generate_figures.ipynb
+
+this notebook has the older versions of the plots that are now reimplemented in generate_figures_main.ipynb, but include a few supplementary figures which have remained unchanged through the review
diff --git a/Analysis/Plots_for_paper/.DS_Store b/Analysis/Plots_for_paper/.DS_Store
diff --git a/Analysis/Plots_for_paper/DFE_comparison_ridgeplot.pdf b/Analysis/Plots_for_paper/DFE_comparison_ridgeplot.pdf
diff --git a/Analysis/Plots_for_paper/FigS_dfe_noness.ai b/Analysis/Plots_for_paper/FigS_dfe_noness.ai
diff --git a/Analysis/Plots_for_paper/FigS_dfe_noness.png b/Analysis/Plots_for_paper/FigS_dfe_noness.png
diff --git a/Analysis/Plots_for_paper/ara-2_exclusion.pdf b/Analysis/Plots_for_paper/ara-2_exclusion.pdf
diff --git a/Analysis/Plots_for_paper/bar.pdf b/Analysis/Plots_for_paper/bar.pdf
diff --git a/Analysis/Plots_for_paper/diff_essentiality_not_struct.pdf b/Analysis/Plots_for_paper/diff_essentiality_not_struct.pdf
diff --git a/Analysis/Plots_for_paper/differential_essentiality_media_new.pdf b/Analysis/Plots_for_paper/differential_essentiality_media_new.pdf
diff --git a/Analysis/Plots_for_paper/differential_essentiality_new.pdf b/Analysis/Plots_for_paper/differential_essentiality_new.pdf
diff --git a/Analysis/Plots_for_paper/essentiality_threshold_simulation.pdf b/Analysis/Plots_for_paper/essentiality_threshold_simulation.pdf
diff --git a/Analysis/Plots_for_paper/expression_diff_ess.pdf b/Analysis/Plots_for_paper/expression_diff_ess.pdf
diff --git a/Analysis/Plots_for_paper/expression_lvls.pdf b/Analysis/Plots_for_paper/expression_lvls.pdf
diff --git a/Analysis/Plots_for_paper/fig2_DFE.pdf b/Analysis/Plots_for_paper/fig2_DFE.pdf
diff --git a/Analysis/Plots_for_paper/fig2_bcde.png b/Analysis/Plots_for_paper/fig2_bcde.png
diff --git a/Analysis/Plots_for_paper/fraction_genes_represented.pdf b/Analysis/Plots_for_paper/fraction_genes_represented.pdf
diff --git a/Analysis/Plots_for_paper/freq_significant_fe.pdf b/Analysis/Plots_for_paper/freq_significant_fe.pdf
diff --git a/Analysis/Plots_for_paper/gene_overlap_with_REL606.pdf b/Analysis/Plots_for_paper/gene_overlap_with_REL606.pdf
diff --git a/Analysis/Plots_for_paper/heatmap_fitness_deleterious.pdf b/Analysis/Plots_for_paper/heatmap_fitness_deleterious.pdf
diff --git a/Analysis/Plots_for_paper/heatmap_fitness_essential_new.pdf b/Analysis/Plots_for_paper/heatmap_fitness_essential_new.pdf
diff --git a/Analysis/Plots_for_paper/heatmap_fitness_neutral.pdf b/Analysis/Plots_for_paper/heatmap_fitness_neutral.pdf
diff --git a/Analysis/Plots_for_paper/heatmap_fitness_nonessential_new.pdf b/Analysis/Plots_for_paper/heatmap_fitness_nonessential_new.pdf
diff --git a/Analysis/Plots_for_paper/insertion_map.pdf b/Analysis/Plots_for_paper/insertion_map.pdf
diff --git a/Analysis/Plots_for_paper/insertion_numbers.pdf b/Analysis/Plots_for_paper/insertion_numbers.pdf
diff --git a/Analysis/Plots_for_paper/legend_fig3.pdf b/Analysis/Plots_for_paper/legend_fig3.pdf
diff --git a/Analysis/Plots_for_paper/legend_fig3_2.pdf b/Analysis/Plots_for_paper/legend_fig3_2.pdf
diff --git a/Analysis/Plots_for_paper/mean_DFE_noness.pdf b/Analysis/Plots_for_paper/mean_DFE_noness.pdf
diff --git a/Analysis/Plots_for_paper/not_reproducibility_fitness_araP4.png b/Analysis/Plots_for_paper/not_reproducibility_fitness_araP4.png
diff --git a/Analysis/Plots_for_paper/parallel_essentiality_DM25.pdf b/Analysis/Plots_for_paper/parallel_essentiality_DM25.pdf
diff --git a/Analysis/Plots_for_paper/parallel_essentiality_LB.pdf b/Analysis/Plots_for_paper/parallel_essentiality_LB.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_diff_ess.pdf b/Analysis/Plots_for_paper/parallelism_diff_ess.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_essentiality.pdf b/Analysis/Plots_for_paper/parallelism_essentiality.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_essentiality_am2_ap4.pdf b/Analysis/Plots_for_paper/parallelism_essentiality_am2_ap4.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_fitness_effects.pdf b/Analysis/Plots_for_paper/parallelism_fitness_effects.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_fitness_effects_am2_ap4.pdf b/Analysis/Plots_for_paper/parallelism_fitness_effects_am2_ap4.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_thresh=-0.15_-0.4.pdf b/Analysis/Plots_for_paper/parallelism_thresh=-0.15_-0.4.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_thresh=-0.1_-0.3.pdf b/Analysis/Plots_for_paper/parallelism_thresh=-0.1_-0.3.pdf
diff --git a/Analysis/Plots_for_paper/parallelism_thresh=-0.1_-0.4.pdf b/Analysis/Plots_for_paper/parallelism_thresh=-0.1_-0.4.pdf
diff --git a/Analysis/Plots_for_paper/params_1.pdf b/Analysis/Plots_for_paper/params_1.pdf
diff --git a/Analysis/Plots_for_paper/params_2.pdf b/Analysis/Plots_for_paper/params_2.pdf
diff --git a/Analysis/Plots_for_paper/params_3.pdf b/Analysis/Plots_for_paper/params_3.pdf
diff --git a/Analysis/Plots_for_paper/params_4.pdf b/Analysis/Plots_for_paper/params_4.pdf
diff --git a/Analysis/Plots_for_paper/params_5.pdf b/Analysis/Plots_for_paper/params_5.pdf
diff --git a/Analysis/Plots_for_paper/params_6.pdf b/Analysis/Plots_for_paper/params_6.pdf
diff --git a/Analysis/Plots_for_paper/redundant.pdf b/Analysis/Plots_for_paper/redundant.pdf
diff --git a/Analysis/Plots_for_paper/significant_fitness_effects.png b/Analysis/Plots_for_paper/significant_fitness_effects.png
diff --git a/Analysis/Plots_for_paper/trajectories_comp_bluegray.png b/Analysis/Plots_for_paper/trajectories_comp_bluegray.png
diff --git a/Analysis/Plots_for_paper/umi_correction.pdf b/Analysis/Plots_for_paper/umi_correction.pdf
diff --git a/Analysis/Plots_for_paper/umi_correction_difference.pdf b/Analysis/Plots_for_paper/umi_correction_difference.pdf
diff --git a/Analysis/Plots_for_paper/umi_r2_correction.pdf b/Analysis/Plots_for_paper/umi_r2_correction.pdf