PlotAggregate

Background

A way to visualize footprints is by the use of an "aggregate" plot across all sites. TOBIAS PlotAggregate makes it easy to plot and compare aggregates across different signals and different regions.

---

Input parameters

• --TFBS
  One or more .bed-file(s) of TFBS to plot aggregates for.
• --signals
  One or more .bigwig-file(s) to fetch scores from. For footprint visualization, this will most likely be the "*_corrected.bw"-file created by (ATACorrect)[ATACorrect.md].

Full input parameters can be found by running TOBIAS ATACorrect --help.

---

Output

• Figure visualizing the aggregate footprint across the sites in --TFBS.

---

Example commands

Visualize the difference in footprints between two conditions for all accessible sites:

$ TOBIAS PlotAggregate --TFBS test_data/BATF_all.bed  --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATFJUN_footprint_comparison_all.pdf --share_y both --plot_boundaries --signal-on-x

~3 seconds

Visualize the difference in footprints between two conditions exclusively for bound sites:

$ TOBIAS PlotAggregate --TFBS test_data/BATF_Bcell_bound.bed test_data/BATF_Tcell_bound.bed --signals test_data/Bcell_corrected.bw test_data/Tcell_corrected.bw --output BATF_footprint_comparison_subsets.png --share_y both --plot_boundaries

~5 seconds

Visualize the split of bound/unbound sites for one condition:

$ TOBIAS PlotAggregate --TFBS test_data/IRF1_all.bed test_data/IRF1_Bcell_bound.bed test_data/IRF1_Bcell_unbound.bed --signals test_data/Bcell_uncorrected.bw test_data/Bcell_expected.bw test_data/Bcell_corrected.bw --output IRF1_footprint.png --share_y sites --plot_boundaries

~8 seconds