Contact maps and gene design plots

[ezingrebe]

Those plots should be generated by applying the following procedure:

• first, generate the summary_contact_grouped.txt file by running dist_genestages_grouped.py
• generate the figures by running Jupyter Notebook contact_maps.ipynb (the script doesn't function; attempts of debugging led to even more bugs, so I converted it to the contact_maps.py functioning and debugged Python script instead)

Python script contact_maps.py generates the following figures:

• contact_all.pdf --> contact map for all the genes
• contactRegionFocused.pdf --> contact map divided by regions
• byRegion.pdf
• byRegion_figure.pdf
• byRegion_new.pdf
• heatmap_pr.pdf --> relation between promoter length and activation rate for different gene designs
• heatmap_pr_figure.pdf
• heatmap_thr.pdf --> relation between activation rate and threshold for different gene designs
• surface.pdf

To be clarified:

• what do the following figures represent: byRegion.pdf, byRegion_figure.pdf, byRegion_new.pdf, heatmap_pr_figure.pdf, surface.pdf
• byRegion_new.pdf: what does the X-axis represent?
• file heatmap_pr_figure.pdf doesn't seem to contain any useful data - is it needed at all?