Reporting tool

reporting based on a structure:

• create summary stats:

  • imposed hic restraints:
    • cis / trans : need to refactor igm code to keep track of those
    • distribution by chromosome : same
    • distribution by genomic distance : same
  • violations histograms by type: ok
  • histogram of number of restraint per bead: need to keep track

• create contact map and compare with the input

  • visual matrix images: ok
  • in/out scatter plot: ok
  • compute correlation: ok

• structural features:

  • summary stats:
    • average radius of each shell
    • total radius of gyration
  • plot of average number of neighbors per bead
  • histogram of number of neighbors
  • radius of gyration per chromosome

• radial positions

  • plots of radial positions per bead
  • plots of radial position per chromosome
  • identification of peaks and dips

• five shells analysis

  • ?

• damid

  • scatter plot in/out (or expected/out)
  • plots of damid profile by chromosome (so, what are we using here?)