How to use the refinem.plots.scatter.Scatter function in refinem

highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_pc1_cov,
                                        True)
        else:
            deltaGC_td_plot = Scatter(self.options)  
            deltaGC_td_plot.plot_on_axes(self.fig,
                                        np_abs(delta_gc), td, label_plot_order,
                                        '|delta GC| (mean = %.1f)' % genome_stats.mean_gc,
                                        'tetranucleotide distance',
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_deltaGC_td,
                                        True)
                                        
            pc1_td_plot = Scatter(self.options)                                     
            pc1_td_plot.plot_on_axes(self.fig,
                                        pc1, 
                                        td, 
                                        label_plot_order,
                                        'PC 1 (%.1f%%)' % (tetra.variance[0] * 100),
                                        'tetranucleotide distance',
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_pc1_td,
                                        True)

        mpld3.plugins.connect(self.fig, mpld3.plugins.LinkedBrush(scatter))

        self.fig.tight_layout(pad=1.0, w_pad=0.1, h_pad=0.1)
        self.draw()

highlight_scaffold_ids,
                              link_scaffold_ids,
                              axes_tetra_pc1_pc3, True)
             
        if len(genome_stats.mean_coverage) >= 1:
            td_cov_plot = Scatter(self.options)  
            td_cov_plot.plot_on_axes(self.fig,
                                        td, cov, label_plot_order,
                                        'tetranucleotide distance',
                                        'Coverage (mean = %.1f)' % np_mean(genome_stats.mean_coverage),
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_td_cov,
                                        True)
                                             
            pc1_cov_plot = Scatter(self.options)                                     
            pc1_cov_plot.plot_on_axes(self.fig,
                                        pc1, cov, label_plot_order,
                                        'PC 1 (%.1f%%)' % (tetra.variance[0] * 100),
                                        'Coverage (mean = %.1f)' % np_mean(genome_stats.mean_coverage),
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_pc1_cov,
                                        True)
        else:
            deltaGC_td_plot = Scatter(self.options)  
            deltaGC_td_plot.plot_on_axes(self.fig,
                                        np_abs(delta_gc), td, label_plot_order,
                                        '|delta GC| (mean = %.1f)' % genome_stats.mean_gc,
                                        'tetranucleotide distance',
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,

highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_td_cov,
                                        True)
                                             
            pc1_cov_plot = Scatter(self.options)                                     
            pc1_cov_plot.plot_on_axes(self.fig,
                                        pc1, cov, label_plot_order,
                                        'PC 1 (%.1f%%)' % (tetra.variance[0] * 100),
                                        'Coverage (mean = %.1f)' % np_mean(genome_stats.mean_coverage),
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_pc1_cov,
                                        True)
        else:
            deltaGC_td_plot = Scatter(self.options)  
            deltaGC_td_plot.plot_on_axes(self.fig,
                                        np_abs(delta_gc), td, label_plot_order,
                                        '|delta GC| (mean = %.1f)' % genome_stats.mean_gc,
                                        'tetranucleotide distance',
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_deltaGC_td,
                                        True)
                                        
            pc1_td_plot = Scatter(self.options)                                     
            pc1_td_plot.plot_on_axes(self.fig,
                                        pc1, 
                                        td, 
                                        label_plot_order,
                                        'PC 1 (%.1f%%)' % (tetra.variance[0] * 100),
                                        'tetranucleotide distance',

tetra = TetraPcaPlot(self.options)
        _, pc1, _, _ = tetra.plot_on_axes(self.fig, 0, 1,
                                                          genome_scaffold_stats,
                                                          highlight_scaffold_ids,
                                                          link_scaffold_ids,
                                                          axes_tetra_pc1_pc2, True)

        tetra.plot_on_axes(self.fig, 0, 2,
                              genome_scaffold_stats,
                              highlight_scaffold_ids,
                              link_scaffold_ids,
                              axes_tetra_pc1_pc3, True)
             
        if len(genome_stats.mean_coverage) >= 1:
            td_cov_plot = Scatter(self.options)  
            td_cov_plot.plot_on_axes(self.fig,
                                        td, cov, label_plot_order,
                                        'tetranucleotide distance',
                                        'Coverage (mean = %.1f)' % np_mean(genome_stats.mean_coverage),
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,
                                        axes_td_cov,
                                        True)
                                             
            pc1_cov_plot = Scatter(self.options)                                     
            pc1_cov_plot.plot_on_axes(self.fig,
                                        pc1, cov, label_plot_order,
                                        'PC 1 (%.1f%%)' % (tetra.variance[0] * 100),
                                        'Coverage (mean = %.1f)' % np_mean(genome_stats.mean_coverage),
                                        highlight_scaffold_ids,
                                        link_scaffold_ids,