targ_dir='/local/groux/scATAC-seq/results'
dest_dir='/local/groux/phd_thesis/images/ch_atac-seq'
script_dir='/local/groux/phd_thesis/scripts/ch_atac-seq'

mkdir -p $dest_dir

# fragment size distribution
cp $targ_dir/10xgenomics_PBMC_5k/fragment_lengths.png  $dest_dir/fragment_lengths.png

# read/fragment/edge/center aggregations around CTCF, SP1, myc, EBF1 motifs
Rscript $script_dir/figure_ctcf_sp1_myc_ebf1_footprint.R

# chromatin around CTCF sites
Rscript $script_dir/figure_ctcf_6classes.R

# chromatin around SP1 sites
Rscript $script_dir/figure_sp1_6classes.R

# AUC and ROC results
cp $targ_dir/toy_data.save/simulated_sequences_2class_flip_auc_roc.png $dest_dir/simulated_sequences_2class_flip_auc_roc.png
cp $targ_dir/toy_data.save/simulated_sequences_2class_flip_best_motifs.png $dest_dir/simulated_sequences_2class_flip_best_motifs.png

# SP1 binding sites
Rscripts $script_dir/figure_sp1_motifs.R