Plotting updates

[FerriolCalvet]

• PLOTNEEDLES(muts_all_samples, sequence_information_df)

  • Move plotting module here
  • Add consequence type coloring
  • Plot by bins? Needle plots by bins #159
  • Add essential splice mutations? Assign a position to essential splice mutations #155

• PLOTSELECTION(positive_selection_results_ready, seqinfo_df) #357

  • fig 2a omega per sample
  • plot selection at cohort/group level, all the different methods available
  • plot explanatory positive selection

• PLOTSATURATION() #358

  • plot gene + site selection + omega selection per domain in gene
  • plot domain selection
  • plot saturation per exon, domain and consequence type
  • ? plot saturation kinetics curves

• PLOTMETRICSQC #336

  • mutation density per gene cohort-level
  • mutation density per gene & sample
    • synonymous
    • protein-affecting
    • truncating
    • missense