code: def tophat_alignment_plot (self):
          
  
          # Specify the order of the different possible categories
          keys = OrderedDict()
          keys['aligned_not_multimapped_discordant'] = { 'color': '#437bb1', 'name': 'Aligned' }
          keys['aligned_multimap'] =   { 'color': '#f7a35c', 'name': 'Multimapped' }
          keys['aligned_discordant'] = { 'color': '#e63491', 'name': 'Discordant mappings' }
          keys['unaligned_total'] =    { 'color': '#7f0000', 'name': 'Not aligned' }
  
          # Config for the plot
          config = {
              'id': 'tophat_alignment',
              'title': 'Tophat: Alignment Scores',
              'ylab': '# Reads',
              'cpswitch_counts_label': 'Number of Reads'
          }
  
          self.add_section( plot =  bargraph.plot(self.tophat_data, keys, config) )
docs: Make the HighCharts HTML to plot the alignment rates