How to create heatmap scatter plot with weightings

I am currently using the function posted here: https://uk.mathworks.com/matlabcentral/fileexchange/47165-heatscatter-plot-for-variables-x-and-y.

    function outfile = heatscatter(X, Y, outpath, outname, numbins, markersize, marker, plot_colorbar, plot_lsf, xlab, ylab, title)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%heatscatter(X, Y, outpath, outname, numbins, markersize, marker, plot_colorbar, plot_lsf, xlab, ylab, title)
% mandatory:
%            X                  [x,1] array containing variable X
%            Y                  [y,1] array containing variable Y
%            outpath            path where the output-file should be saved.
%                                leave blank for current working directory
%            outname            name of the output-file. if outname contains
%                                filetype (e.g. png), this type will be used.
%                                Otherwise, a pdf-file will be generated
% optional:
%            numbins            [double], default 50
%                                number if bins used for the
%                                heat3-calculation, thus the coloring
%            markersize         [double], default 10
%                                size of the marker used in the scatter-plot
%            marker             [char], default 'o'
%                                type of the marker used in the scatter-plot
%            plot_colorbar      [double], boolean 0/1, default 1
%                                set whether the colorbar should be plotted
%                                or not
%            plot_lsf           [double], boolean 0/1, default 1
%                                set whether the least-square-fit line
%                                should be plotted or not (together with
%                                the correlation/p-value of the data
%            xlab               [char], default ''
%                                lable for the x-axis
%            ylab               [char], default ''
%                                lable for the y-axis
%            title              [char], default ''
%                                title of the figure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      %%%%mandatory
      if ~exist('X','var') || isempty(X)
          error('Param X is mandatory! --> EXIT!');
      end
      if ~exist('Y','var') || isempty(Y)
          error('Param Y is mandatory! --> EXIT!');
      end
      if ~exist('outpath','var')
          error('Param outpath is mandatory! --> EXIT!');
      end
      if ~exist('outname','var') || isempty(outname)
          error('Param outname is mandatory! --> EXIT!');
      end

      %%%%optional
      if ~exist('numbins','var') || isempty(numbins)
          numbins = 50;
      else
          % force number, not char input
          numbins = str2double(numbins);
      end
      if ~exist('markersize','var') || isempty(markersize)
          markersize = 10;
      else
          % force number, not char input
          markersize = str2double(markersize);
      end
      if ~exist('marker','var') || isempty(marker)
          marker = 'o';
      end
      if ~exist('plot_colorbar','var') || isempty(plot_colorbar)
          plot_colorbar = 1;
      end
      if ~exist('plot_lsf','var') || isempty(plot_lsf)
          plot_lsf = 1;
      end
      if ~exist('xlab','var') || isempty(xlab)
          xlab = '';
      end
      if ~exist('ylab','var') || isempty(ylab)
          ylab = '';
      end
      if ~exist('title','var') || isempty(title)
          title = '';
      end

      [values, centers] = hist3([X Y], [numbins numbins]);

      centers_X = centers{1,1};
      centers_Y = centers{1,2};

      binsize_X = abs(centers_X(2) - centers_X(1)) / 2;
      binsize_Y = abs(centers_Y(2) - centers_Y(1)) / 2;
      bins_X = zeros(numbins, 2);
      bins_Y = zeros(numbins, 2);

      for i = 1:numbins
          bins_X(i, 1) = centers_X(i) - binsize_X;
          bins_X(i, 2) = centers_X(i) + binsize_X;
          bins_Y(i, 1) = centers_Y(i) - binsize_Y;
          bins_Y(i, 2) = centers_Y(i) + binsize_Y;
      end

      scatter_COL = zeros(length(X), 1);

      onepercent = round(length(X) / 100);

      fprintf('Generating colormap...\n');

      for i = 1:length(X)

          if (mod(i,onepercent) == 0)
              fprintf('.');
          end            

          last_lower_X = NaN;
          last_higher_X = NaN;
          id_X = NaN;

          c_X = X(i);
          last_lower_X = find(c_X >= bins_X(:,1));
          if (~isempty(last_lower_X))
              last_lower_X = last_lower_X(end);
          else
              last_higher_X = find(c_X <= bins_X(:,2));
              if (~isempty(last_higher_X))
                  last_higher_X = last_higher_X(1);
              end
          end
          if (~isnan(last_lower_X))
              id_X = last_lower_X;
          else
              if (~isnan(last_higher_X))
                  id_X = last_higher_X;
              end
          end

          last_lower_Y = NaN;
          last_higher_Y = NaN;
          id_Y = NaN;

          c_Y = Y(i);
          last_lower_Y = find(c_Y >= bins_Y(:,1));
          if (~isempty(last_lower_Y))
              last_lower_Y = last_lower_Y(end);
          else
              last_higher_Y = find(c_Y <= bins_Y(:,2));
              if (~isempty(last_higher_Y))
                  last_higher_Y = last_higher_Y(1);
              end
          end
          if (~isnan(last_lower_Y))
              id_Y = last_lower_Y;
          else
              if (~isnan(last_higher_Y))
                  id_Y = last_higher_Y;
              end
          end

          scatter_COL(i) = values(id_X, id_Y);

      end

      fprintf(' Done!\n');

      fprintf('Plotting...');

      f = figure();
      scatter(X, Y, markersize, scatter_COL, marker);

      if (plot_colorbar)
          colorbar;
      end

      if (plot_lsf)
          [r,p] = corr(X, Y);
          str = {sprintf('corr: %.3f', r), sprintf('pval: %d', p)};
          l = lsline;
          set(l, 'Color', 'k');
          annotation('textbox', [0.14 0.80 0.1 0.1], 'String', str, 'EdgeColor', 'none');
      end

      if (~isempty(xlab))
          xlabel(xlab);
      end
      if (~isempty(ylab))
          ylabel(ylab);
      end
      if (~isempty(title))
          title(title);
      end

      [p,n,r] = fileparts(outname);
      if (isempty(r))
          r = '.pdf';
      end
      outname = strcat(p,n,r);
      outfile = fullfile(outpath, outname);
      saveas(f, outfile);
      fprintf(' Done!\n');

end

This is producing the heatmaps that I require. However, I now have data which lists the X and Y values along with number of times that those two values appear. Currently I am using the 'repmat' function to give the result below, within a for loop:

This is proving extremely slow to achieve as this currently turns 400,000 lines of data into ~14 million lines.

Is there any easier way to do this by adapting the function?