code: def bowtie_alignment_plot (self):
          
  
          # Specify the order of the different possible categories
          keys = OrderedDict()
          keys['reads_aligned'] = { 'color': '#8bbc21', 'name': 'Aligned' }
          keys['multimapped'] =   { 'color': '#2f7ed8', 'name': 'Multimapped' }
          keys['not_aligned'] =   { 'color': '#0d233a', 'name': 'Not aligned' }
  
          # Config for the plot
          config = {
              'id': 'bowtie1_alignment',
              'title': 'Bowtie 1: Alignment Scores',
              'ylab': '# Reads',
              'cpswitch_counts_label': 'Number of Reads'
          }
  
          self.add_section(
              description = 'This plot shows the number of reads aligning to the reference in different ways.',
              helptext = '''
              There are 3 possible types of alignment:
              * **Aligned**: Read has only one occurence in the reference genome.
              * **Multimapped**: Read has multiple occurence.
              * **Not aligned**: Read has no occurence.
              ''',
              plot = bargraph.plot(self.bowtie_data, keys, config)
          )
docs: Make the HighCharts HTML to plot the alignment rates