4. Visualization

Simple plots for one or two csv files of reactIDR

• --window : sliding window of averaging

python ../src/plot_bargraph.py --window 1 --ignore --idr --output vivo_vitro test_vivo_all.csv  test_vitro_all.csv 
python ../src/plot_bargraph.py --window 100 --ignore --idr --output vivo_vitro test_vivo_all.csv  test_vitro_all.csv 

Structure prediction

• --struct : define accessible and stem class when posterior is higher than t

python ../src/plot_bargraph.py --ignore --idr --output vivo_vitro --struct 0.5 test_vivo_all.csv  test_vitro_all.csv  > a.txt

Reactivity scores

• --bed
• --threshold : thresholds after filtering out the scores less than t
• --segment: output the contiguous regions rather than each nucleotide

python ../src/plot_bargraph.py --ignore --idr --output vivo_vitro --bed output --threshold 0.1 --segment test_vivo_all.csv  test_vitro_all.csv