Figure4.md

A. Locus Plot

• Get contribution scores from synapse directory for the subsampled models
• Run 4a_locus_plot.ipynb to generate figures

B. JSD plots

• Get observed bigwigs and contribution scores from synpase for the subsampled models
• Generate predictions for the subsampled models on peaks generated for the 572M chromBPNet model, use chrombpnet pred_bw
• Use 4b_comparing_deepshap_subsample.ipynb and 4b_comparing_oberved_versus_predicted_subsample.ipynb to generate figures

C. Balloon plot with recalls

• Run FiNeMO using 572M modisco object on all the contribution scores from subsampled models - scripts
• First run 4c_comparing_hit_calls_finemo_profile.ipynb followed by 4c_balloon_plot_for_recall_finemo_profile.ipynb to get balloo plot

D. Marginal Footprints

• Run scripts in src/figures_factory/Fig4/scripts/marginal_footprinting/ to get marginal footprints
• Run 4d_marginal_footprinting_motifs.ipynb to get marginal footprinting plots