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?
Those plots should be generated by applying the following procedure:
Python script contact_maps.py generates the following figures:
To be clarified: