// Define functions to render linked interactive plots using d3.
// Another script should define e.g.
// <script>
//   var plot = new animint("#plot","path/to/plot.json");
// </script>
// Constructor for animint Object.
var animint = function (to_select, json_file) {
  var steps = [];
  var default_axis_px = 16;
  var grid_layout = false;
  var grid_layout_table;
  function wait_until_then(timeout, condFun, readyFun) {
    var args=arguments
    function checkFun() {
      if(condFun()) {
        readyFun(args[3],args[4]);
      } else{
        setTimeout(checkFun, timeout);
      }
    }
    checkFun();
  }

  function convert_R_types(resp_array, types){
    return resp_array.map(function (d) {
      for (var v_name in d) {
              if(!is_interactive_aes(v_name)){
          var r_type = types[v_name];
          if (r_type == "integer") {
            d[v_name] = parseInt(d[v_name]);
          } else if (r_type == "numeric") {
            d[v_name] = parseFloat(d[v_name]);
          } else if (r_type == "factor" || r_type == "rgb" 
                     || r_type == "linetype" || r_type == "label"
                     || r_type == "character") {
            // keep it as a character
          } else if (r_type == "character" & v_name == "outliers") {
            d[v_name] = parseFloat(d[v_name].split(" @ "));
          } 
              }
      }
      return d;
    });
  }

  // replacing periods in variable with an underscore this makes sure
  // that selector doesn't confuse . in name with css selectors
  function safe_name(unsafe_name){
    return unsafe_name.replace(/[ .]/g, '_');
  }
  function legend_class_name(selector_name){
    return safe_name(selector_name) + "_variable";
  }

  function is_interactive_aes(v_name){
    if(v_name.indexOf("clickSelects") > -1){
      return true;
    }
    if(v_name.indexOf("showSelected") > -1){
      return true;
    }
    return false;
  }

  var linetypesize2dasharray = function (lt, size) {
    var isInt = function(n) {
      return typeof n === 'number' && parseFloat(n) == parseInt(n, 10) && !isNaN(n);
    };
    if(isInt(lt)){ // R integer line types.
      if(lt == 1){
        return null;
      }
      var o = {
        0: size * 0 + "," + size * 10,
        2: size * 4 + "," + size * 4,
        3: size + "," + size * 2,
        4: size + "," + size * 2 + "," + size * 4 + "," + size * 2,
        5: size * 8 + "," + size * 4,
        6: size * 2 + "," + size * 2 + "," + size * 6 + "," + size * 2
      };
    } else { // R defined line types
      if(lt == "solid" || lt === null){
        return null;
      }
      var o = {
        "blank": size * 0 + "," + size * 10,
        "none": size * 0 + "," + size * 10,
        "dashed": size * 4 + "," + size * 4,
        "dotted": size + "," + size * 2,
        "dotdash": size + "," + size * 2 + "," + size * 4 + "," + size * 2,
        "longdash": size * 8 + "," + size * 4,
        "twodash": size * 2 + "," + size * 2 + "," + size * 6 + "," + size * 2,
        "22": size * 2 + "," + size * 2,
        "42": size * 4 + "," + size * 2,
        "44": size * 4 + "," + size * 4,"13": size + "," + size * 3,
        "1343": size + "," + size * 3 + "," + size * 4 + "," + size * 3,
        "73": size * 7 + "," + size * 3,
        "2262": size * 2 + "," + size * 2 + "," + size * 6 + "," + size * 2,
        "12223242": size + "," + size * 2 + "," + size * 2 + "," + size * 2 + "," + size * 3 + "," + size * 2 + "," + size * 4 + "," + size * 2,
        "F282": size * 15 + "," + size * 2 + "," + size * 8 + "," + size * 2,
        "F4448444": size * 15 + "," + size * 4 + "," + size * 4 + "," + size * 4 + "," + size * 8 + "," + size * 4 + "," + size * 4 + "," + size * 4,
        "224282F2": size * 2 + "," + size * 2 + "," + size * 4 + "," + size * 2 + "," + size * 8 + "," + size * 2 + "," + size * 16 + "," + size * 2,
        "F1": size * 16 + "," + size
      };
    }

    if (lt in o){
      return o[lt];
    } else{ // manually specified line types
      str = lt.split("");
      strnum = str.map(function (d) {
        return size * parseInt(d, 16);
      });
      return strnum;
    }
  };

  var isArray = function(o) {
    return Object.prototype.toString.call(o) === '[object Array]';
  };

  // create a dummy element, apply the appropriate classes,
  // and then measure the element
  // Inspired from http://jsfiddle.net/uzddx/2/
  var measureText = function(pText, pFontSize, pAngle, pStyle) {
    if (pText === undefined || pText === null || pText.length === 0) return {height: 0, width: 0};
    if (pAngle === null || isNaN(pAngle)) pAngle = 0;

    var container = element.append('svg');
    // do we need to set the class so that styling is applied?
    //.attr('class', classname);

    container.append('text')
      .attr({x: -1000, y: -1000})
      .attr("transform", "rotate(" + pAngle + ")")
      .attr("style", pStyle)
      .attr("font-size", pFontSize)
      .text(pText);

    var bbox = container.node().getBBox();
    container.remove();

    return {height: bbox.height, width: bbox.width};
  };

  var nest_by_group = d3.nest().key(function(d){ return d.group; });
  var dirs = json_file.split("/");
  dirs.pop(); //if a directory path exists, remove the JSON file from dirs
  var element = d3.select(to_select);
  this.element = element;
  var tooltip = element.append("div")
      .attr("class", "animint-tooltip")
      .style("opacity", 0);
  var hide_tooltip = function() {
    tooltip.style("opacity", 0);
  };
  var viz_id = element.attr("id");
  var plot_widget_table = element.append("table");
  var plot_td = plot_widget_table.append("tr").append("td");
  plot_td.attr("class","plot_content");
  var widget_td = plot_widget_table.append("tr").append("td");
  var Widgets = {};
  this.Widgets = Widgets;
  var Selectors = {};
  this.Selectors = Selectors;
  var Plots = {};
  this.Plots = Plots;
  var Geoms = {};
  this.Geoms = Geoms;
  // SVGs must be stored separately from Geoms since they are
  // initialized first, with the Plots.
  var SVGs = {};
  this.SVGs = SVGs;
  var Animation = {};
  this.Animation = Animation;
  var all_geom_names = {};
  this.all_geom_names = all_geom_names;

  //creating an array to contain the selectize widgets
  var selectized_array = [];
  var data_object_geoms = {
    "line":true,
    "path":true,
    "ribbon":true,
    "polygon":true
  };
  var css = document.createElement('style');
  css.type = 'text/css';
  var styles = [".axis path{fill: none;stroke: black;shape-rendering: crispEdges;}",
            ".axis line{fill: none;stroke: black;shape-rendering: crispEdges;}",
            ".axis text {font-family: sans-serif;font-size: 11px;}"];

  var add_geom = function (g_name, g_info) {
    // Determine if data will be an object or an array.
    // added geom properties in steps array
    var geom = g_info.classed;
    var title = g_info.params.title || g_info.classed;
    var helpText = g_info.params.help || '';
    var help_showSelected = g_info.params.help_showSelected || '';
    var help_clickSelects = g_info.params.help_clickSelects || '';
    var description = helpText;
    if(g_info.params.hasOwnProperty("showSelected")){
      if(description != "")description += '<br>';
      description += 'Data are shown for the current selection of: ' + help_showSelected;
    }
    if(g_info.params.hasOwnProperty("clickSelects")){
      if(description != "")description += '<br>';
      description += 'Click to select: ' + help_clickSelects;
    }
    if(description == ""){
      description = "No interactions available";
    }
    steps.push({  // this add the geom to the steps array for guided tour
      element: '#' + viz_id + ' .' + geom,
      popover: {
        title: title,
        description: description
      }
    });
    if(g_info.geom in data_object_geoms){
      g_info.data_is_object = true;
    }else{
      g_info.data_is_object = false;
    }
    // Add a row to the loading table.
    g_info.tr = Widgets["loading"].append("tr");
    g_info.tr.append("td").text(g_name);
    g_info.tr.append("td").attr("class", "chunk");
    g_info.tr.append("td").attr("class", "downloaded").text(0);
    g_info.tr.append("td").text(g_info.total);
    g_info.tr.append("td").attr("class", "status").text("initialized");

    // load chunk tsv
    g_info.data = {};
    g_info.download_status = {};
    Geoms[g_name] = g_info;
    // Determine whether common chunk tsv exists
    // If yes, load it
    if(g_info.hasOwnProperty("columns") && g_info.columns.common){
      var common_tsv = get_tsv(g_info, "_common");
      g_info.common_tsv = common_tsv;
      var common_path = getTSVpath(common_tsv);
      d3.tsv(common_path, function (error, response) {
        var converted = convert_R_types(response, g_info.types);
        g_info.data[common_tsv] = nest_by_group.map(converted);
      });
    } else {
      g_info.common_tsv = null;
    }
    // Save this geom and load it!
    update_geom(g_name, null);
  };
  var grid_layout_tr = null; //static between add_plot calls.
  var add_plot = function (p_name, p_info, grid_layout) {
    var plot_table;
    if(grid_layout) {
      var grid_info = p_info.span || {};
      if(grid_layout_tr === null) {
        grid_layout_tr = grid_layout_table.append("tr");
      }
      var grid_layout_td = grid_layout_tr.append("td");
      if(grid_info.rowspan > 0){
        grid_layout_td.attr("rowspan", grid_info.rowspan);
      }
      if(grid_info.colspan > 0){
        grid_layout_td.attr("colspan", grid_info.colspan);
      }
      plot_table = grid_layout_td.append("table")
      if(grid_info.last_in_row){
        grid_layout_tr = null;
      }
    }else{
      plot_table = plot_td.append("table").style("display", "inline-block");
    }
    var plot_tr = plot_table.append("tr");
    var tdLeft = plot_tr.append("td");
    var tdRight = plot_tr.append("td").attr("class", p_name+"_legend");
    if(viz_id === null){
      p_info.plot_id = p_name;
    }else{
      p_info.plot_id = viz_id + "_" + p_name;
    }
    var svg = tdLeft.append("svg")
      .attr("id", p_info.plot_id)
      .attr("height", p_info.options.height)
      .attr("width", p_info.options.width);
    
    // divvy up width/height based on the panel layout
    var nrows = Math.max.apply(null, p_info.layout.ROW);
    var ncols = Math.max.apply(null, p_info.layout.COL);
    var panel_names = p_info.layout.PANEL;
    var npanels = Math.max.apply(null, panel_names);

    // Note axis names are "shared" across panels (just like the title)
    var xtitlepadding = 5 + measureText(p_info["xtitle"], default_axis_px).height;
    var ytitlepadding = 5 + measureText(p_info["ytitle"], default_axis_px).height;

    // 'margins' are fixed across panels and do not
    // include title/axis/label padding (since these are not
    // fixed across panels). They do, however, account for
    // spacing between panels
    var text_height_pixels = measureText("foo", 11).height;
    var margin = {
      left: 0,
      right: text_height_pixels * p_info.panel_margin_lines,
      top: text_height_pixels * p_info.panel_margin_lines,
      bottom: 0
    };
    var plotdim = {
      width: 0,
      height: 0,
      xstart: 0,
      xend: 0,
      ystart: 0,
      yend: 0,
      graph: {
        width: 0,
        height: 0
      },
      margin: margin,
      xlab: {
        x: 0,
        y: 0
      },
      ylab: {
        x: 0,
        y: 0
      },
      title: {
        x: 0,
        y: 0
      }
    };

    // Draw the title
    var titlepadding = measureText(p_info.title, p_info.title_size).height;
    // why are we giving the title padding if it is undefined?
    if (p_info.title === undefined) titlepadding = 0;
    plotdim.title.x = p_info.options.width / 2;
    plotdim.title.y = titlepadding;
    svg.append("text")
      .text(p_info.title)
      .attr("class", "plottitle")
      .attr("font-family", "sans-serif")
      .attr("font-size", p_info.title_size)
      .attr("transform", "translate(" + plotdim.title.x + "," + 
        plotdim.title.y + ")")
      .style("text-anchor", "middle");

    // grab max text size over axis labels and facet strip labels
    var axispaddingy = 5;
    if(p_info.hasOwnProperty("ylabs") && p_info.ylabs.length){
      axispaddingy += Math.max.apply(null, p_info.ylabs.map(function(entry){
        // + 5 to give a little extra space to avoid bad axis labels
        // in shiny.
        return measureText(entry, p_info.ysize).width + 5;
      }));
    }
    var axispaddingx = 30; // distance between tick marks and x axis name.
    if(p_info.hasOwnProperty("xlabs") && p_info.xlabs.length){
      // TODO: throw warning if text height is large portion of plot height?
      axispaddingx += Math.max.apply(null, p_info.xlabs.map(function(entry){
             return measureText(entry, p_info.xsize, p_info.xangle).height;
      }));
      // TODO: carefully calculating this gets complicated with rotating xlabs
      //margin.right += 5;
    }
    plotdim.margin = margin;
    
    var strip_heights = p_info.strips.top.map(function(entry){ 
      return measureText(entry, p_info.strip_text_xsize).height;
    });
    var strip_widths = p_info.strips.right.map(function(entry){ 
      return measureText(entry, p_info.strip_text_ysize).height; 
    });

    // compute the number of x/y axes, max strip height per row, and
    // max strip width per columns, for calculating height/width of
    // graphing region.
    var row_strip_heights = [];
    var col_strip_widths = [];
    var n_xaxes = 0;
    var n_yaxes = 0;
    var current_row, current_col;
    for (var layout_i = 0; layout_i < npanels; layout_i++) {
      current_row = p_info.layout.ROW[layout_i] - 1;
      current_col = p_info.layout.COL[layout_i] - 1;
      if(row_strip_heights[current_row] === undefined){
        row_strip_heights[current_row] = [];
      }
      if(col_strip_widths[current_col] === undefined){
        col_strip_widths[current_col] = [];
      }
      row_strip_heights[current_row].push(strip_heights[layout_i]);
      col_strip_widths[current_col].push(strip_widths[layout_i]);
      if (p_info.layout.COL[layout_i] == 1) {
        n_xaxes += p_info.layout.AXIS_X[layout_i];
      }
      if (p_info.layout.ROW[layout_i] == 1) {
        n_yaxes += p_info.layout.AXIS_Y[layout_i];
      }
    }
    function cumsum_array(array_of_arrays){
      var cumsum = [], max_value, cumsum_value = 0;
      for(var i=0; i<array_of_arrays.length; i++){
        cumsum_value += d3.max(array_of_arrays[i]);
        cumsum[i] = cumsum_value;
      }
      return cumsum;
    }
    var cum_height_per_row = cumsum_array(row_strip_heights);
    var cum_width_per_col = cumsum_array(col_strip_widths);
    var strip_width = d3.max(cum_width_per_col);
    var strip_height = d3.max(cum_height_per_row);

    // the *entire graph* height/width
    var graph_width = p_info.options.width - 
        ncols * (margin.left + margin.right) -
        strip_width -
        n_yaxes * axispaddingy - ytitlepadding;
    var graph_height = p_info.options.height - 
        nrows * (margin.top + margin.bottom) -
        strip_height -
        titlepadding - n_xaxes * axispaddingx - xtitlepadding;

    // Impose the pixelated aspect ratio of the graph upon the width/height
    // proportions calculated by the compiler. This has to be done on the
    // rendering side since the precomputed proportions apply to the *graph*
    // and the graph size depends upon results of measureText()
    if (p_info.layout.coord_fixed[0]) {
      var aspect = (graph_height / nrows) / (graph_width / ncols);
    } else {
      var aspect = 1;
    }
    var wp = p_info.layout.width_proportion.map(function(x){
      return x * Math.min(1, aspect);
    })
    var hp = p_info.layout.height_proportion.map(function(x){
      return x * Math.min(1, 1/aspect);
    })

    // track the proportion of the graph that should be 'blank'
    // this is mainly used to implement coord_fixed()
    var graph_height_blank = 1;
    var graph_width_blank = 1;
    for (var layout_i = 0; layout_i < npanels; layout_i++) {
      if (p_info.layout.COL[layout_i] == 1) graph_height_blank -= hp[layout_i];
      if (p_info.layout.ROW[layout_i] == 1) graph_width_blank -= wp[layout_i];
    }
    // cumulative portion of the graph used
    var graph_width_cum = (graph_width_blank / 2) * graph_width;
    var graph_height_cum = (graph_height_blank / 2) * graph_height;

    // Bind plot data to this plot's SVG element
    svg.plot = p_info;
    Plots[p_name] = p_info;
    p_info.geoms.forEach(function (g_name) {
      var layer_g_element = svg.append("g").attr("class", g_name);
      panel_names.forEach(function(PANEL){
        layer_g_element.append("g").attr("class", "PANEL" + PANEL);
      });
      SVGs[g_name] = svg;
    });

    // create a grouping for strip labels (even if there are none).
    var topStrip = svg.append("g")
      .attr("class", "topStrip")
    ;
    var rightStrip = svg.append("g")
      .attr("class", "rightStrip")
    ;

    // this will hold x/y scales for each panel
    // eventually we inject this into Plots[p_name]
    var scales = {};
    n_xaxes = 0;
    n_yaxes = 0;
    // Draw a plot outline for every panel
    for (var layout_i = 0; layout_i < npanels; layout_i++) {
      var panel_i = layout_i + 1;
      var axis  = p_info["axis" + panel_i];

      //forces values to be in an array
      var xaxisvals = [];
      var xaxislabs = [];
      var yaxisvals = [];
      var yaxislabs = [];
      var outbreaks, outlabs;

      //function to write labels and breaks to their respective arrays
      var axislabs = function(breaks, labs, axis){
        if(axis=="x"){
          outbreaks = xaxisvals;
          outlabs = xaxislabs;
        } else {
          outbreaks = yaxisvals;
          outlabs = yaxislabs;
        } // set appropriate variable names
        if (isArray(breaks)) {
          breaks.forEach(function (d) {
            outbreaks.push(d);
          })
        } else {
          //breaks can be an object!
          for (key in breaks) {
            outbreaks.push(breaks[key]);
          }
        }
        if (labs){
          labs.forEach(function (d) {
            outlabs.push(d);
            // push each label provided into the array
          });
        } else {
          outbreaks.forEach(function (d) {
            outlabs.push("");
            // push a blank string to the array for each axis tick
            // if the specified label is null
          });
        }
      };

      if(axis["xticks"]){
        axislabs(axis.x, axis.xlab, "x");
      }
      if(axis["yticks"]){
        axislabs(axis.y, axis.ylab, "y");
      }

      // compute the current panel height/width
      plotdim.graph.height = graph_height * hp[layout_i];
      plotdim.graph.width = graph_width * wp[layout_i];

      current_row = p_info.layout.ROW[layout_i];
      current_col = p_info.layout.COL[layout_i];
      var draw_x = p_info.layout.AXIS_X[layout_i];
      var draw_y = p_info.layout.AXIS_Y[layout_i];
      // panels are drawn using a "typewriter approach" (left to right
      // & top to bottom) if the carriage is returned (ie, there is a
      // new row), change some parameters:
      var new_row = current_col <= p_info.layout.COL[layout_i - 1]
      if (new_row) {
        n_yaxes = 0;
        graph_width_cum = (graph_width_blank / 2) * graph_width;
        graph_height_cum += graph_height * hp[layout_i-1];
      }
      n_xaxes += draw_x;
      n_yaxes += draw_y;

      // calculate panel specific locations to be used in placing
      // axes, labels, etc.
      plotdim.xstart =  current_col * plotdim.margin.left +
        (current_col - 1) * plotdim.margin.right +
        graph_width_cum + n_yaxes * axispaddingy + ytitlepadding;
      // room for right strips should be distributed evenly across
      // panels to preserve aspect ratio
      plotdim.xend = plotdim.xstart + plotdim.graph.width;
      // total height of strips drawn thus far
      var strip_h = cum_height_per_row[current_row-1];
      plotdim.ystart = current_row * plotdim.margin.top +
        (current_row - 1) * plotdim.margin.bottom +
        graph_height_cum + titlepadding + strip_h;
      // room for xaxis title should be distributed evenly across
      // panels to preserve aspect ratio
      plotdim.yend = plotdim.ystart + plotdim.graph.height;
      // always add to the width (note it may have been reset earlier)
      graph_width_cum = graph_width_cum + plotdim.graph.width;

      // get the x position of the y-axis title (and add padding) when
      // rendering the first plot.
      if (layout_i === 0) {
        var ytitle_x = (plotdim.xstart - axispaddingy - ytitlepadding / 2);
        var xtitle_left = plotdim.xstart;
        var ytitle_top = plotdim.ystart;
      }
      // get the y position of the x-axis title when drawing the last
      // panel.
      if (layout_i === (npanels - 1)) {
        var xtitle_y = (plotdim.yend + axispaddingx);
        var xtitle_right = plotdim.xend;
        var ytitle_bottom = plotdim.yend;
      }

      var draw_strip = function(strip, side) {
        if (strip == "") {
          return(null);
        }
        var x, y, rotate, stripElement, strip_text_xy;
        if (side == "right") {
          x = plotdim.xend;
          y = (plotdim.ystart + plotdim.yend) / 2;
          rotate = 90;
          stripElement = rightStrip;
          strip_text_xy = "y";
        }else{ //top
          x = (plotdim.xstart + plotdim.xend) / 2;
          y = plotdim.ystart;
          rotate = 0;
          stripElement = topStrip;
          strip_text_xy = "x";
        }
        var trans_text = "translate(" + x + "," + y + ")";
        var rot_text = "rotate(" + rotate + ")";
        var strip_text_size = "strip_text_"+strip_text_xy+"size";
        stripElement
          .selectAll("." + side + "Strips")
          .data(strip)
          .enter()
          .append("text")
          .style("text-anchor", "middle")
          .style("font-size", p_info[strip_text_size])
          .text(function(d) { return d; })
        // NOTE: there could be multiple strips per panel
        // TODO: is there a better way to manage spacing?
          .attr("transform", trans_text + rot_text)
        ;
      }
      draw_strip([p_info.strips.top[layout_i]], "top");
      draw_strip([p_info.strips.right[layout_i]], "right");

      // for each of the x and y axes, there is a "real" and fake
      // version. The real version will be used for plotting the
      // data, and the fake version is just for the display of the
      // axes.
      scales[panel_i] = {};
      scales[panel_i].x = d3.scale.linear()
        .domain(axis.xrange)
        .range([plotdim.xstart, plotdim.xend]);
      scales[panel_i].y = d3.scale.linear()
        .domain(axis.yrange)
        .range([plotdim.yend, plotdim.ystart]);
      if(draw_x){
        var xaxis = d3.svg.axis()
          .scale(scales[panel_i].x)
          .tickValues(xaxisvals)
          .tickFormat(function (d) {
            return xaxislabs[xaxisvals.indexOf(d)].toString();
          })
          .orient("bottom")
        ;
  var axis_panel = "xaxis" + "_" + panel_i;
        var xaxis_g = svg.append("g")
          .attr("class", "xaxis axis " + axis_panel)
          .attr("transform", "translate(0," + plotdim.yend + ")")
          .call(xaxis);
        if(axis["xline"] == false){
          var axis_path = xaxis_g.select("path.domain");
          axis_path.remove();
        }
        xaxis_g.selectAll("text")
          .style("text-anchor", p_info.xanchor)
          .style("font-size", p_info.xsize)
          .attr("transform", "rotate(" + p_info.xangle + " 0 9)");
      }
      if(draw_y){
        var yaxis = d3.svg.axis()
          .scale(scales[panel_i].y)
          .tickValues(yaxisvals)
          .tickFormat(function (d) {
            return yaxislabs[yaxisvals.indexOf(d)].toString();
          })
          .orient("left");
  var axis_panel = "yaxis" + "_" + panel_i;
        var yaxis_g = svg.append("g")
          .attr("class", "yaxis axis " + axis_panel)
          .attr("transform", "translate(" + (plotdim.xstart) + ",0)")
          .call(yaxis);
        if(axis["yline"] == false){
          var axis_path = yaxis_g.select("path.domain");
          axis_path.remove();
        }
  yaxis_g.selectAll(".tick text")
    .style("font-size", p_info.ysize);
      }

      if(!axis.xline) {
            styles.push("#"+p_name+" #xaxis"+" path{stroke:none;}");
      }
      if(!axis.xticks) {
            styles.push("#"+p_name+" #xaxis .tick"+" line{stroke:none;}");
      }
      if(!axis.yline) {
            styles.push("#"+p_name+" #yaxis"+" path{stroke:none;}");
      }
      if(!axis.yticks) {
            styles.push("#"+p_name+" #yaxis .tick"+" line{stroke:none;}");
      }
      
      // creating g element for background, grid lines, and border
      // uses insert to draw it right before plot title
      var background = svg.insert("g", ".plottitle")
        .attr("class", "background bgr" + panel_i);
      
      // drawing background
      if(Object.keys(p_info.panel_background).length > 1) {
        background.append("rect")
          .attr("x", plotdim.xstart)
          .attr("y", plotdim.ystart)
          .attr("width", plotdim.xend - plotdim.xstart)
          .attr("height", plotdim.yend - plotdim.ystart)
          .attr("class", "background_rect")
          .style("fill", p_info.panel_background.fill)
          .style("stroke", p_info.panel_background.colour)
          .style("stroke-dasharray", function() {
            return linetypesize2dasharray(p_info.panel_background.linetype,
                                          p_info.panel_background.size);
          });
      }
      
      // drawing the grid lines
      ["grid_minor", "grid_major"].forEach(function(grid_class){
        var grid_background = p_info[grid_class];
        // if grid lines are defined
        if(grid_background.hasOwnProperty("size")) {
          var grid = background.append("g")
              .attr("class", grid_class);
          ["x","y"].forEach(function(scale_var){
            var const_var;
            if(scale_var == "x"){
              const_var = "y";
            }else{
              const_var = "x";
            }
            grid.append("g")
              .attr("class", scale_var)
              .selectAll("line")
              .data(grid_background.loc[scale_var][layout_i])
              .enter()
              .append("line")
              .attr(const_var + "1", plotdim[const_var + "start"])
              .attr(const_var + "2", plotdim[const_var + "end"])
              .attr(scale_var + "1", function(d) {
                return scales[panel_i][scale_var](d);
              })
              .attr(scale_var + "2", function(d) {
                return scales[panel_i][scale_var](d);
              })
              .style("stroke", grid_background.colour)
              .style("stroke-linecap", grid_background.lineend)
              .style("stroke-width", grid_background.size)
              .style("stroke-dasharray", linetypesize2dasharray(
                grid_background.linetype, grid_background.size))
            ;
          });
        }
      });
      
      // drawing border
      // uses insert to draw it right before the #plottitle
      if(Object.keys(p_info.panel_border).length > 1) {
        background.append("rect")
          .attr("x", plotdim.xstart)
          .attr("y", plotdim.ystart)
          .attr("width", plotdim.xend - plotdim.xstart)
          .attr("height", plotdim.yend - plotdim.ystart)
          .attr("class", "border_rect")
          .style("fill", p_info.panel_border.fill)
          .style("stroke", p_info.panel_border.colour)
          .style("stroke-dasharray", function() {
            return linetypesize2dasharray(p_info.panel_border.linetype,
                                          p_info.panel_border.size);
          });
      }

    } //end of for(layout_i
    // After drawing all backgrounds, we can draw the axis labels.
    if(p_info["ytitle"]){
      svg.append("text")
        .text(p_info["ytitle"])
        .attr("class", "ytitle")
        .style("text-anchor", "middle")
        .style("font-size", default_axis_px + "px")
        .attr("transform", "translate(" +
              ytitle_x +
              "," +
              (ytitle_top + ytitle_bottom)/2 +
              ")rotate(270)")
      ;
    }
    if(p_info["xtitle"]){
      svg.append("text")
        .text(p_info["xtitle"])
        .attr("class", "xtitle")
        .style("text-anchor", "middle")
        .style("font-size", default_axis_px + "px")
        .attr("transform", "translate(" +
              (xtitle_left + xtitle_right)/2 +
              "," +
              xtitle_y +
              ")")
      ;
    }
    Plots[p_name].scales = scales;
  }; //end of add_plot()

  function update_legend_opacity(v_name){
    var s_info = Selectors[v_name];
    s_info.legend_tds.style("opacity", s_info.legend_update_fun);
  }

  var add_selector = function (s_name, s_info) {
    Selectors[s_name] = s_info;
    if(s_info.type == "multiple"){
      if(!isArray(s_info.selected)){
        s_info.selected = [s_info.selected];
      }
      // legend_update_fun is evaluated in the context of the
      // td.legend_entry_label.
      s_info.legend_update_fun = function(d){
        var i_value = s_info.selected.indexOf(this.textContent);
        if(i_value == -1){
          return 0.5;
        }else{
          return 1;
        }
      }
    }else{
      s_info.legend_update_fun = function(d){
        if(this.textContent == s_info.selected){
          return 1;
        }else{
          return 0.5;
        }
      }
    }
    s_info.legend_tds = 
      element.selectAll("tr."+legend_class_name(s_name)+" td.legend_entry_label")
    ;
    update_legend_opacity(s_name);
  }; //end of add_selector()

  function get_tsv(g_info, chunk_id){
    return g_info.classed + "_chunk" + chunk_id + ".tsv";
  }
  function getTSVpath(tsv_name){
    return dirs.concat(tsv_name).join("/");
  }
  
  /**
   * copy common chunk tsv to varied chunk tsv, returning an array of
   * objects.
  */
  function copy_chunk(g_info, varied_chunk) {
    var varied_by_group = nest_by_group.map(varied_chunk);
    var common_by_group = g_info.data[g_info.common_tsv];
    var new_varied_chunk = [];
    for(group_id in varied_by_group){
      var varied_one_group = varied_by_group[group_id];
      var common_one_group = common_by_group[group_id];
      var group_size;
      if(varied_one_group.length>1){
        group_size = varied_one_group.length;
      }else{
        group_size = common_one_group.length;
      }
      for(var out_i=0; out_i < group_size; out_i++){
        // there are three cases about which common data to use:
        var common_i, varied_i;
        // there are two cases about which varied data to use:
        if(varied_one_group.length==1){
          varied_i = 0;
        }else{
          varied_i = out_i;
        }
        var varied_obj = varied_one_group[varied_i];
        if(common_one_group.length==1){
          // varied or common data has length 1.
          common_i = 0;
        }else if(varied_obj.hasOwnProperty("row_in_group")){
          // there were NA so length is smaller than common data, and
          // we have row_in_group to tell us what common data to use.
          common_i = varied_obj.row_in_group-1;
        }else{
          // each group of varied data has same length as common data.
          common_i = out_i;
        }
        var common_obj = common_one_group[common_i];
        var new_obj = {};
        Object.assign(new_obj, common_obj);
        Object.assign(new_obj, varied_obj);
        new_varied_chunk.push(new_obj);
      }
    }
    return new_varied_chunk;
  }

  // update_geom is called from add_geom and update_selector. It
  // downloads data if necessary, and then calls draw_geom.
  var update_geom = function (g_name, selector_name) {
    var g_info = Geoms[g_name];
    // First apply chunk_order selector variables.
    var chunk_id = g_info.chunks;
    g_info.chunk_order.forEach(function (v_name) {
      if(chunk_id == null){
        return; // no data in a higher up chunk var.
      }
      var value = Selectors[v_name].selected;
      if(chunk_id.hasOwnProperty(value)){
               chunk_id = chunk_id[value];
      }else{
               chunk_id = null; // no data to show in this subset.
      }
    });
    if(chunk_id == null){
      draw_panels(g_info, [], selector_name); //draw nothing.
      return;
    }
    var tsv_name = get_tsv(g_info, chunk_id);
    // get the data if it has not yet been downloaded.
    g_info.tr.select("td.chunk").text(tsv_name);
    if(g_info.data.hasOwnProperty(tsv_name)){
      draw_panels(g_info, g_info.data[tsv_name], selector_name);
    }else{
      g_info.tr.select("td.status").text("downloading");
      var svg = SVGs[g_name];
      var loading = svg.append("text")
        .attr("class", "loading"+tsv_name)
              .text("Downloading "+tsv_name+"...")
              .attr("font-size", 9)
              //.attr("x", svg.attr("width")/2)
        .attr("y", 10)
        .style("fill", "red");
      download_chunk(g_info, tsv_name, function(chunk){
              loading.remove();
        draw_panels(g_info, chunk, selector_name);
      });
    }
  };
  var draw_panels = function(g_info, chunk, selector_name) {
    // derive the plot name from the geometry name
    var g_names = g_info.classed.split("_");
    var p_name = g_names[g_names.length - 1];
    var panels = Plots[p_name].layout.PANEL;
    panels.forEach(function(panel) {
      draw_geom(g_info, chunk, selector_name, panel);
    });
  };

  function download_next(g_name){
    var g_info = Geoms[g_name];
    var selector_value = Animation.sequence[g_info.seq_i];
    var chunk_id = g_info.chunks[selector_value];
    var tsv_name = get_tsv(g_info, chunk_id);
    g_info.seq_count += 1;
    if(Animation.sequence.length == g_info.seq_count){
      Animation.done_geoms[g_name] = 1;
      return;
    }
    g_info.seq_i += 1;
    if(g_info.seq_i == Animation.sequence.length){
      g_info.seq_i = 0;
    }
    if(typeof(chunk_id) == "string"){
      download_chunk(g_info, tsv_name, function(chunk){
        download_next(g_name);
      })
    }else{
      download_next(g_name);
    }
  }

  // download_chunk is called from update_geom and download_next.
  function download_chunk(g_info, tsv_name, funAfter){
    if(g_info.download_status.hasOwnProperty(tsv_name)){
      var chunk;
      if(g_info.data_is_object){
        chunk = {};
      }else{
        chunk = [];
      }
      funAfter(chunk);
      return; // do not download twice.
    }
    g_info.download_status[tsv_name] = "downloading";
    // prefix tsv file with appropriate path
    var tsv_file = getTSVpath(tsv_name);
    d3.tsv(tsv_file, function (error, response) {
      // First convert to correct types.
      g_info.download_status[tsv_name] = "processing";
      response = convert_R_types(response, g_info.types);
      wait_until_then(500, function(){
        if(g_info.common_tsv) {
          return g_info.data.hasOwnProperty(g_info.common_tsv);
        }else{
          return true;
        }
      }, function(){
        if(g_info.common_tsv) {
          // copy data from common tsv to varied tsv
          response = copy_chunk(g_info, response);
        }
        var nest = d3.nest();
        g_info.nest_order.forEach(function (v_name) {
          nest.key(function (d) {
            return d[v_name];
          });
        });
        var chunk = nest.map(response);
        g_info.data[tsv_name] = chunk;
        g_info.tr.select("td.downloaded").text(d3.keys(g_info.data).length);
        g_info.download_status[tsv_name] = "saved";
        funAfter(chunk);
      });
    });
  }//download_chunk.

  // update_geom is responsible for obtaining a chunk of downloaded
  // data, and then calling draw_geom to actually draw it.
  var draw_geom = function(g_info, chunk, selector_name, PANEL){
    g_info.tr.select("td.status").text("displayed");
    var svg = SVGs[g_info.classed];
    // derive the plot name from the geometry name
    var g_names = g_info.classed.split("_");
    var p_name = g_names[g_names.length - 1];
    var scales = Plots[p_name].scales[PANEL];
    var selected_arrays = [ [] ]; //double array necessary.
    var has_clickSelects = g_info.aes.hasOwnProperty("clickSelects");
    var has_clickSelects_variable =
      g_info.aes.hasOwnProperty("clickSelects.variable");
    g_info.subset_order.forEach(function (aes_name) {
      var selected, values;
      var new_arrays = [];
      if(0 < aes_name.indexOf(".variable")){ 
        selected_arrays.forEach(function(old_array){
          var some_data = chunk;
          old_array.forEach(function(value){
            if(some_data.hasOwnProperty(value)) {
              some_data = some_data[value];
            } else {
              some_data = {};
            }
          })
          values = d3.keys(some_data);
          values.forEach(function(s_name){
            var selected = Selectors[s_name].selected;
            var new_array = old_array.concat(s_name).concat(selected);
            new_arrays.push(new_array);
          })
        })
      }else{//not .variable aes:
        if(aes_name == "PANEL"){
          selected = PANEL;
        }else{
          var s_name = g_info.aes[aes_name];
          selected = Selectors[s_name].selected;
        }
        if(isArray(selected)){
          values = selected; //multiple selection.
        }else{
          values = [selected]; //single selection.
        }
        values.forEach(function(value){
          selected_arrays.forEach(function(old_array){
            var new_array = old_array.concat(value);
            new_arrays.push(new_array);
          })
        })
      }
      selected_arrays = new_arrays;
    });
    // data can be either an array[] if it will be directly involved
    // in a data-bind, or an object{} if it will be involved in a
    // data-bind by group (e.g. geom_line).
    var data;
    if(g_info.data_is_object){
      data = {};
    }else{
      data = [];
    }
    selected_arrays.forEach(function(value_array){
      var some_data = chunk;
      value_array.forEach(function(value){
        if (some_data.hasOwnProperty(value)) {
          some_data = some_data[value];
        } else {
          if(g_info.data_is_object){
            some_data = {};
          }else{
            some_data = [];
          }
        }
      });
      if(g_info.data_is_object){
        if(isArray(some_data) && some_data.length){
          data["0"] = some_data;
        }else{
          for(k in some_data){
            data[k] = some_data[k];
          }
        }
      }else{//some_data is an array.
        data = data.concat(some_data);
      }
    });
    var aes = g_info.aes;
    var toXY = function (xy, a) {
      return function (d) {
        return scales[xy](d[a]);
      };
    };
    var layer_g_element = svg.select("g." + g_info.classed);
    var panel_g_element = layer_g_element.select("g.PANEL" + PANEL);
    var elements = panel_g_element.selectAll(".geom");

    // helper functions so we can write code that works for both
    // grouped and ungrouped geoms. get_one_row returns one row of
    // data (not one group), in both cases.
    var get_fun = function(fun){
      return function(input){
        var d = get_one_row(input);
        return fun(d);
      };
    };
    var get_attr = function(attr_name){
      return get_fun(function(d){
        return d[attr_name];
      });
    };

    var fontsize = 12;
    var get_fontsize;
    if (aes.hasOwnProperty("size")){
      get_fontsize = get_attr("size")
    }else if(g_info.params.hasOwnProperty("size")){
      get_fontsize = function(d) { return g_info.params.size; };
    }else{
      get_fontsize = function(d) { return fontsize; };
    }
    var size = 2;
    var get_size;
    if(aes.hasOwnProperty("size")){
      get_size = get_attr("size");
    }else{
      get_size = function(d){
        return size;
      };
    }
    var get_style_on_stroke_width = get_size;
    
    // stroke_width for geom_point
    var stroke_width = 1;  // by default ggplot2 has 0.5, animint has 1
    var get_stroke_width;
    if(aes.hasOwnProperty("stroke")){
      get_stroke_width = get_attr("stroke");
    }else{
      get_stroke_width = function(d){
        return stroke_width;
      };
    }
    
    var linetype = "solid";
    var get_linetype;
    if(aes.hasOwnProperty("linetype")){
      get_linetype = get_attr("linetype");
    }else{
      get_linetype = function(d){
        return linetype;
      };
    }
    var get_dasharray = function(d){
      var lt = get_linetype(d);
      return linetypesize2dasharray(lt, get_size(d));
    };

    var alpha = 1, alpha_off = 0.5;
    var get_alpha;
    var get_alpha_off = function (d) {
      return alpha_off;
    };
    if(aes.hasOwnProperty("alpha")){
      get_alpha = get_attr("alpha");
      get_alpha_off = get_attr("alpha");
    } else {
      get_alpha = function(d){
        return alpha;
      };
    }
    
    var colour = "black", colour_off;
    var get_colour;
    var get_colour_off = function (d) {
      return colour_off;
    };
    if(aes.hasOwnProperty("colour")){
      get_colour = get_attr("colour");
      get_colour_off = get_colour;
    }else{
      get_colour = function (d) {
        return colour;
      };
    }
    var get_colour_off_default = get_colour;
    if (g_info.geom == "label_aligned") {
      var fill = "white", fill_off = "white";
    }else{
      var fill = "black", fill_off = "black";
    }
    var get_fill = function (d) {
      return fill;
    };
    var get_fill_off = function (d) {
      return fill_off;
    };

    var get_hjust;
    var default_hjust = 0.5; // default center
    if(aes.hasOwnProperty("hjust")){
      get_hjust = get_attr("hjust");
    }else if(g_info.params.hasOwnProperty("hjust")){
      get_hjust = function(d){ return g_info.params.hjust; };
    }else{
      get_hjust = function(d){ return default_hjust; };
    }
    var get_vjust;
    var default_vjust = 0.5; // default center
    if(aes.hasOwnProperty("vjust")){
      get_vjust = get_attr("vjust");
    }else if(g_info.params.hasOwnProperty("vjust")){
      get_vjust = function(d){ return g_info.params.vjust; };
    }else{
      get_vjust = function(d){ return default_vjust; };
    }
    var angle = 0;
    var get_angle;
    if(aes.hasOwnProperty("angle")){
      get_angle = get_attr("angle");
    }else{
      get_angle = function(d){
        return angle;
      };
    }
    var get_rotate = function(d){
      // x and y are the coordinates to rotate around, we choose the center 
      // point of the text because otherwise it will rotate around (0,0) of its 
      // coordinate system, which is the top left of the plot
      x = scales["x"](d["x"]);
      y = scales["y"](d["y"]);
      var angle = get_angle(d);
      // ggplot expects angles to be in degrees CCW, SVG uses degrees CW, so 
      // we negate the angle.
      return `rotate(${-angle}, ${x}, ${y})`;
    };
    
    // For aes(hjust) the compiler should make an "anchor" column.
    var text_anchor = "middle";
    var get_text_anchor;
    if(g_info.aes.hasOwnProperty("hjust")) {
      get_text_anchor = function(d){
        return d["anchor"];
      }
    }else{
      get_text_anchor = function(d){
        return text_anchor;
      }
    }

    var eActions, eAppend;
    var key_fun = null;
    if(g_info.aes.hasOwnProperty("key")){
      key_fun = function(d){
        return d.key;
      };
    }
    var get_one_row;//different for grouped and ungrouped geoms.
    var data_to_bind;
    g_info.style_list = [
      "opacity","stroke","stroke-width","stroke-dasharray","fill"];
    var line_style_list = [
      "opacity","stroke","stroke-width","stroke-dasharray"];
    var fill_comes_from="fill", fill_off_comes_from="fill_off";
    if(g_info.data_is_object) {

      // Lines, paths, polygons, and ribbons are a bit special. For
      // every unique value of the group variable, we take the
      // corresponding data rows and make 1 path. The tricky part is
      // that to use d3 I do a data-bind of some "fake" data which are
      // just group ids, which is the kv variable in the code below

      // // case of only 1 line and no groups.
      // if(!aes.hasOwnProperty("group")){
      //     kv = [{"key":0,"value":0}];
      //     data = {0:data};
      // }else{
      //     // we need to use a path for each group.
      //     var kv = d3.entries(d3.keys(data));
      //     kv = kv.map(function(d){
      //         d[aes.group] = d.value;
      //         return d;
      //     });
      // }

      // For an example consider breakpointError$error which is
      // defined using this R code

      // geom_line(aes(segments, error, group=bases.per.probe,
      //    clickSelects=bases.per.probe), data=only.error, lwd=4)

      // Inside update_geom the variables take the following values
      // (pseudo-Javascript code)

      // var kv = [{"key":"0","value":"133","bases.per.probe":"133"},
      //           {"key":"1","value":"2667","bases.per.probe":"2667"}];
      // var data = {"133":[array of 20 points used to draw the line for group 133],
      //             "2667":[array of 20 points used to draw the line for group 2667]};

      // I do elements.data(kv) so that when I set the d attribute of
      // each path, I need to select the correct group before
      // returning anything.

      // e.attr("d",function(group_info){
      //     var one_group = data[group_info.value];
      //     return lineThing(one_group);
      // })

      // To make color work I think you just have to select the group
      // and take the color of the first element, e.g.

      // .style("stroke",function(group_info){
      //     var one_group = data[group_info.value];
      //     var one_row = one_group[0];
      //     return get_color(one_row);
      // }

      // In order to get d3 lines to play nice, bind fake "data" (group
      // id's) -- the kv variable. Then each separate object is plotted
      // using path (case of only 1 thing and no groups).

      // we need to use a path for each group.
      var keyed_data = {}, one_group, group_id, k;
      var by_na_group, na_group_id, one_na_group;
      for(group_id in data){
        one_group = data[group_id];
        one_row = one_group[0];
        if(one_row.hasOwnProperty("na_group")){
          by_na_group = d3.nest().key(function(d){ return d.na_group; }).map(one_group);
          for(na_group_id in by_na_group){
            one_na_group = by_na_group[na_group_id];
            k = group_id + "_" + na_group_id;
            keyed_data[k] = one_na_group;
          }
        }else{
          keyed_data[group_id] = one_group;
        }
      }
      var kv_array = d3.entries(d3.keys(keyed_data));
      get_one_row = function(group_info) {
        var one_group = keyed_data[group_info.value];
        var one_row = one_group[0];
        return one_row;
      };
      var kv = kv_array.map(function (group_info) {
        //d[aes.group] = d.value;
        // Need to store the clickSelects value that will
        // be passed to the selector when we click on this
        // item.
        var one_row = get_one_row(group_info);
        Object.assign(group_info, one_row);
        return group_info;
      });
      // line, path, and polygon use d3.svg.line(),
      // ribbon uses d3.svg.area()
      // we have to define lineThing accordingly.
      if (g_info.geom == "ribbon") {
        var lineThing = d3.svg.area()
          .x(toXY("x", "x"))
          .y(toXY("y", "ymax"))
          .y0(toXY("y", "ymin"));
      } else {
        var lineThing = d3.svg.line()
          .x(toXY("x", "x"))
          .y(toXY("y", "y"));
      }
      if(["line","path"].includes(g_info.geom)){
        fill = "none";
        fill_off = "none";
      }
      data_to_bind = kv;
      eActions = function (e) {
        e.attr("d", function (d) {
          return lineThing(keyed_data[d.value]);
        })
      };
      eAppend = "path";
    }else{
      get_one_row = function(d){
        return d;
      }
      data_to_bind = data;
      if (g_info.geom == "segment") {
  g_info.style_list = line_style_list;
  // helper: get slope and intercept for datum
  function getLineParams(d) {
    var slope = d.slope !== undefined ? +d.slope :
      (g_info.abline_params && g_info.abline_params.slopes) ? g_info.abline_params.slopes[d.i] : 1;
    var intercept = d.intercept !== undefined ? +d.intercept :
      (g_info.abline_params && g_info.abline_params.intercepts) ? g_info.abline_params.intercepts[d.i] : 0;
    return { slope, intercept };
  }
  // helper: compute clipped coordinate for one endpoint
  function computeEndpoint(x, slope, intercept, xDomain, yDomain) {
    var y = slope * x + intercept;
    if (y < yDomain[0]) x = (yDomain[0] - intercept) / slope;
    if (y > yDomain[1]) x = (yDomain[1] - intercept) / slope;
    return { x, y };
  }
  // helper: compute abline endpoints
  function getAblineCoords(d, scales) {
    var { slope, intercept } = getLineParams(d);
    var xDomain = scales.x.domain();
    var yDomain = scales.y.domain();
    function get_ab_y(x) {
      return Math.max(yDomain[0], Math.min(yDomain[1], slope * x + intercept));
    }
    // Compute both endpoints
    var start = computeEndpoint(xDomain[0], slope, intercept, xDomain, yDomain);
    var end = computeEndpoint(xDomain[1], slope, intercept, xDomain, yDomain);
    return {
      x1: scales.x(start.x),
      y1: scales.y(get_ab_y(xDomain[0])),
      x2: scales.x(end.x),
      y2: scales.y(get_ab_y(xDomain[1]))
    };
  }
  if (g_info.is_abline) {
    eActions = function(e) {
      e.attr("x1", d => getAblineCoords(d, scales).x1)
       .attr("y1", d => getAblineCoords(d, scales).y1)
       .attr("x2", d => getAblineCoords(d, scales).x2)
       .attr("y2", d => getAblineCoords(d, scales).y2);
    };
  } else {
    // Regular segment case
    eActions = function(e) {
      e.attr("x1", toXY("x", "x"))
        .attr("y1", toXY("y", "y"))
        .attr("x2", toXY("x", "xend"))
        .attr("y2", toXY("y", "yend"));
    };
  }
  eAppend = "line";
      }
      if (g_info.geom == "linerange") {
        g_info.style_list = line_style_list;
        eActions = function (e) {
          e.attr("x1", function (d) {
            return scales.x(d["x"]);
          })
            .attr("x2", function (d) {
              return scales.x(d["x"]);
            })
            .attr("y1", function (d) {
              return scales.y(d["ymax"]);
            })
            .attr("y2", function (d) {
              return scales.y(d["ymin"]);
            })
          ;
        };
        eAppend = "line";
      }
      if (g_info.geom == "vline") {
        g_info.style_list = line_style_list;
        eActions = function (e) {
          e.attr("x1", toXY("x", "xintercept"))
            .attr("x2", toXY("x", "xintercept"))
            .attr("y1", scales.y.range()[0])
            .attr("y2", scales.y.range()[1])
          ;
        };
        eAppend = "line";
      }
      if (g_info.geom == "hline") {
        g_info.style_list = line_style_list;
        eActions = function (e) {
          e.attr("y1", toXY("y", "yintercept"))
            .attr("y2", toXY("y", "yintercept"))
            .attr("x1", scales.x.range()[0])
            .attr("x2", scales.x.range()[1])
          ;
        };
        eAppend = "line";
      }
      if (g_info.geom == "text") {
        size = 12;//default
        get_colour = function(d){
          return "none";
        };
        get_colour_off = function(d) {
          return "none";
        };
        fill_comes_from = "colour";
        fill_off_comes_from = "colour_off";
        g_info.style_list = [
          "opacity","fill"];
        eActions = function (e) {
          e.attr("x", toXY("x", "x"))
            .attr("y", toXY("y", "y"))
            .attr("font-size", get_size)
            .style("text-anchor", get_text_anchor)
            .attr("transform", get_rotate)
            .text(function (d) {
              return d.label;
            })
          ;
        };
        eAppend = "text";
      }
      if (g_info.geom == "point") {
        // point is special because it takes SVG fill from ggplot
        // colour, if fill is not specified.
        if(!(
          g_info.params.hasOwnProperty("fill") ||
            aes.hasOwnProperty("fill")
        )){
          fill_comes_from = "colour";
        }
        if(!g_info.params.hasOwnProperty("fill_off")){
          fill_off_comes_from = "colour_off";
        }
        get_style_on_stroke_width = get_stroke_width;//not size.
        eActions = function (e) {
          e.attr("cx", toXY("x", "x"))
            .attr("cy", toXY("y", "y"))
            .attr("r", get_size)
          ;
        };
        eAppend = "circle";
      }
      // function to calculate the size of boxes in geom_label_aligned according to the inside text
      var calcLabelBox = function(d) {
        var textStyle = [
            "font-family:" + (d.family || "sans-serif"),
            "font-weight:" + (d.fontface == 2 ? "bold" : "normal"),
            "font-style:" + (d.fontface == 3 ? "italic" : "normal")
        ].join(";");
        // Use d.size for font size (always current value)
        var fontsize = d.size;
        var textSize = measureText(d.label, fontsize, d.angle, textStyle);
        d.boxWidth = textSize.width;
        d.boxHeight = textSize.height;
        d.scaledX = scales.x(d.x);
        d.scaledY = scales.y(d.y);
      }
      if (g_info.geom == "label_aligned") {
          // Get parameters
          var alignment = g_info.params.alignment || "vertical";
          var min_distance = g_info.params.min_distance || 0.1;
          var background_rect = g_info.params.background_rect !== false; // Default true
          // Set d.size and d.originalFontsize for each datum
          data.forEach(function(d) {
              if (typeof d.originalFontsize === "undefined") {
                  d.size = get_fontsize(d);
                  d.originalFontsize = d.size;
              }
              // Always reset to original before shrinking
              d.size = d.originalFontsize;
              calcLabelBox(d);
          });
          var plot_limits;
          if (alignment === "vertical") {
            var yRange = scales.y.range();
            plot_limits = [Math.min.apply(null, yRange), Math.max.apply(null, yRange)];
          } else {
            var xRange = scales.x.range();
            plot_limits = [Math.min.apply(null, xRange), Math.max.apply(null, xRange)];
          }
          // using quadprog.js for optimizing positions of colliding boxes
          optimizeAlignedLabels(data, alignment, min_distance, plot_limits, function(d){return d.size;}, calcLabelBox);

          eAppend = "g";
          eActions = function(groups) {
            // Handle transitions seperately due to unique structure of geom_label_aligned
            var transitionDuration = 0;
            if (Selectors.hasOwnProperty(selector_name)) {
              transitionDuration = +Selectors[selector_name].duration || 0;
            }
            groups.each(function(d) {
              var group = d3.select(this);
              // Select existing elements (if any)
              var rect = group.select("rect");
              var text = group.select("text");
              var rectIsNew = false, textIsNew = false;
              // If elements don't exist, create them
              if (rect.empty()) {rect = group.append("rect"); rectIsNew = true;}
              if (text.empty()) {text = group.append("text"); textIsNew = true;}
              // Apply transitions to both elements
              if (!rectIsNew && transitionDuration > 0) {
                rect = rect.transition().duration(transitionDuration);
              }
              if (!textIsNew && transitionDuration > 0) {
                text = text.transition().duration(transitionDuration);
              }
              if (background_rect) {
                rect
                  .attr("x", function(d) { 
                    if (alignment == "vertical") {
                      return d.scaledX - d.boxWidth * get_hjust(d);
                    } else {
                      return d.optimizedPos - d.boxWidth / 2;
                    }
                  })
                  .attr("y", function(d) {
                    if (alignment == "vertical") {
                      return d.optimizedPos - d.boxHeight / 2;
                    } else {
                      return d.scaledY - d.boxHeight * (1 - get_vjust(d));
                    }
                  })
                  .attr("width", function(d) { return d.boxWidth; })
                  .attr("height", function(d) { return d.boxHeight; })
                  .style("opacity", get_alpha)
                  .style("stroke", get_colour)
                  .style("fill", get_fill)
                  .attr("rx", g_info.params.label_r || 0)
                  .attr("ry", g_info.params.label_r || 0);
              }
              text
                .attr("x", function(d) {
                  if (alignment == "vertical") {
                    return d.scaledX - d.boxWidth * get_hjust(d) + d.boxWidth / 2;
                  } else {
                    return d.optimizedPos;
                  }
                })
                .attr("y", function(d) {
                  if (alignment == "vertical") {
                    return d.optimizedPos;
                  } else {
                    return d.scaledY - d.boxHeight * (1 - get_vjust(d)) + d.boxHeight / 2 ;
                  }
                })
                .attr("dominant-baseline", "middle")
                .attr("font-size", function(d) { return d.size + "px"; })
                .style("text-anchor", "middle")
                .style("fill", get_colour)
                .text(function(d) { return d.label; });
            });
          };
        }

      var rect_geoms = ["tallrect","widerect","rect"];
      if(rect_geoms.includes(g_info.geom)){
        eAppend = "rect";
        if (g_info.geom == "tallrect") {
          eActions = function (e) {
            e.attr("x", toXY("x", "xmin"))
              .attr("width", function (d) {
                return scales.x(d["xmax"]) - scales.x(d["xmin"]);
              })
              .attr("y", scales.y.range()[1])
              .attr("height", scales.y.range()[0] - scales.y.range()[1])
            ;
          };
        }
        if (g_info.geom == "widerect") {
          eActions = function (e) {
            e.attr("y", toXY("y", "ymax"))
              .attr("height", function (d) {
                return scales.y(d["ymin"]) - scales.y(d["ymax"]);
              })
              .attr("x", scales.x.range()[0])
              .attr("width", scales.x.range()[1] - scales.x.range()[0])
            ;
          };
        }
        if (g_info.geom == "rect") {
          alpha_off = alpha;
          colour_off = "transparent";
          get_colour_off_default = get_colour_off;
          eActions = function (e) {
            e.attr("x", toXY("x", "xmin"))
              .attr("width", function (d) {
                return Math.abs(scales.x(d.xmax) - scales.x(d.xmin));
              })
              .attr("y", toXY("y", "ymax"))
              .attr("height", function (d) {
                return Math.abs(scales.y(d.ymin) - scales.y(d.ymax));
              })
            ;
          };
        }
      }
    }
    // set params after geom-specific code, because each geom may have
    // a different default.
    if (g_info.params.hasOwnProperty("stroke")) {
      stroke_width = g_info.params.stroke;
    }
    if (g_info.params.hasOwnProperty("linetype")) {
      linetype = g_info.params.linetype;
    }
    if(g_info.params.hasOwnProperty("alpha")){
      alpha = g_info.params.alpha;
      alpha_off = alpha - 0.5
    }
    if(g_info.params.hasOwnProperty("alpha_off")){
      alpha_off = g_info.params.alpha_off;
    }
    if(g_info.params.hasOwnProperty("anchor")){
      text_anchor = g_info.params["anchor"];
    }
    if(g_info.params.hasOwnProperty("colour")){
      colour = g_info.params.colour;
    }
    if(g_info.params.hasOwnProperty("colour_off")){
      colour_off = g_info.params.colour_off;
    }else{
      get_colour_off = get_colour_off_default;
    }
    if (g_info.params.hasOwnProperty("angle")) {
      angle = g_info.params["angle"];
    }
    if (g_info.params.hasOwnProperty(fill_comes_from)) {
      fill = g_info.params[fill_comes_from];
    }
    if (g_info.params.hasOwnProperty(fill_off_comes_from)) {
      fill_off = g_info.params[fill_off_comes_from];
    }else{
      fill_off = fill;
    }
    if(aes.hasOwnProperty(fill_comes_from)){
      get_fill = get_attr(fill_comes_from);
      get_fill_off = get_attr(fill_comes_from);
    };
    if (g_info.params.hasOwnProperty("size")) {
      size = g_info.params.size;
    }
    var styleActions = function(e){
      if (g_info.geom == "label_aligned") return;  // Do NOT call styleActions(e) for geom_label_aligned
      g_info.style_list.forEach(function(s){
        e.style(s, function(d) {
          var style_on_fun = style_on_funs[s];
          return style_on_fun(d);
        });
      });
    };
    var style_on_funs = {
      "opacity": get_alpha,
      "stroke": get_colour,
      "fill": get_fill,
      "stroke-width": get_style_on_stroke_width,
      "stroke-dasharray": get_dasharray
    };
    var style_off_funs = {
      "opacity": get_alpha_off,
      "stroke": get_colour_off,
      "fill": get_fill_off
    };
    // TODO cleanup.
    var select_style_default = ["opacity","stroke","fill"];
    g_info.select_style = select_style_default.filter(
      X => g_info.style_list.includes(X));
    var styles_to_apply = (g_info.geom === "label_aligned") ? ["opacity"] : g_info.select_style;
    // (Only apply opacity to geom_label_aligned 
    // due to its structure difference -- to avoid double styling in both <g> and <text> inside <g>)
    var over_fun = function(e){
      styles_to_apply.forEach(function(s){
        e.style(s, function (d) {
          return style_on_funs[s](d);
        });
      });
    };
    var out_fun = function(e){
      styles_to_apply.forEach(function(s){
        e.style(s, function (d) {
          var select_on = style_on_funs[s](d);
          var select_off = style_off_funs[s](d);
          if(has_clickSelects){
            return ifSelectedElse(
              d.clickSelects,
              g_info.aes.clickSelects,
              select_on, select_off);
          }else if(has_clickSelects_variable){
            return ifSelectedElse(
              d["clickSelects.value"],
              d["clickSelects.variable"],
              select_on, select_off);
          }
        });
      });
    };
    elements = elements.data(data_to_bind, key_fun);
    elements.exit().remove();
    var enter = elements.enter();
    if(g_info.aes.hasOwnProperty("href")){
      enter = enter.append("svg:a")
        .append("svg:"+eAppend);
    }else{
      enter = enter.append(eAppend)
        .attr("class", "geom");
    }
    var moreActions = function(e){};
    if (has_clickSelects || has_clickSelects_variable) {
      moreActions = out_fun;
      elements.call(out_fun)
        .on("mouseover", function (d) {
          d3.select(this).call(over_fun);
        })
        .on("mouseout", function (d) {
          d3.select(this).call(out_fun);
        })
      ;
      if(has_clickSelects){
        elements.on("click", function (d) {
            var s_name = g_info.aes.clickSelects;
            update_selector(s_name, d.clickSelects);
        });
      }else{
        elements.on("click", function(d){
          var s_name = d["clickSelects.variable"];
          var s_value = d["clickSelects.value"];
          update_selector(s_name, s_value);
        });
      }
    }
    // Set attributes of only the entering elements. This is needed to
    // prevent things from flying around from the upper left when they
    // enter the plot.
    var doActions = function(e) {
      eActions(e);
      styleActions(e);
      moreActions(e)
    };
    doActions(enter);  // DO NOT DELETE!
    var has_tooltip = g_info.aes.hasOwnProperty("tooltip");
    function positionTooltip(tooltip, content) {
      var mouseX = 0, mouseY = 0;
      if (d3.event) {
        mouseX = d3.event.pageX;
        mouseY = d3.event.pageY;
      }
      var safeHtml = String(content).replace(/\n/g, '<br/>');
      tooltip
        .html(safeHtml)
        .style("left", (mouseX + TOOLTIP_HORIZONTAL_OFFSET) + "px")
        .style("top", (mouseY - TOOLTIP_VERTICAL_OFFSET) + "px")
        .style("opacity", 0.7);
    }
    if(has_clickSelects || has_tooltip || has_clickSelects_variable){
      // Tooltip positioning constants
      var TOOLTIP_HORIZONTAL_OFFSET = 10; // pixels right of mouse pointer
      var TOOLTIP_VERTICAL_OFFSET = 28;   // pixels above mouse pointer
      var text_fun;
      if(has_tooltip){
        text_fun = function(d){
          return d.tooltip;
        };
      }else if(has_clickSelects){
        text_fun = function(d){
          var v_name = g_info.aes.clickSelects;
          return v_name + " " + d.clickSelects;
        };
      }else{ //clickSelects_variable
        text_fun = function(d){
          return d["clickSelects.variable"] + " " + d["clickSelects.value"];
        };
      }
      // Add tooltip handlers
      elements
        .on("mouseover.tooltip", function(d) {
          if (!d || typeof text_fun !== 'function') return;
          var content = text_fun(d);
          positionTooltip(tooltip, content);
        })
        .on("mouseout.tooltip", hide_tooltip)
        .on("mousemove.tooltip", function() {
          positionTooltip(tooltip, tooltip.html());
        });
    }
    if(Selectors.hasOwnProperty(selector_name)){
      var milliseconds = Selectors[selector_name].duration;
      elements = elements.transition().duration(milliseconds);
    }
    if(g_info.aes.hasOwnProperty("id")){
      elements.attr("id", get_attr("id"));
    }
    if(g_info.aes.hasOwnProperty("href")){
      // elements are <a>, children are e.g. <circle>
      var linked_geoms = elements.select(eAppend);
      doActions(linked_geoms);
      elements.attr("xlink:href", get_attr("href"))
        .attr("target", "_blank")
        .attr("class", "geom");
    }else{
      // elements are e.g. <circle>
      doActions(elements); // Set the attributes of all elements (enter/exit/stay)
    }
  };
  
  var value_tostring = function(selected_values) {
      //function that is helpful to change the format of the string
      var selector_url="#"
      for (var selc_var in selected_values){
          if(selected_values.hasOwnProperty(selc_var)){
              var values_str=selected_values[selc_var].join();
              var sub_url=selc_var.concat("=","{",values_str,"}");
              selector_url=selector_url.concat(sub_url);
          }
      }
      var url_nohash=window.location.href.match(/(^[^#]*)/)[0];
      selector_url=url_nohash.concat(selector_url);
      return  selector_url;
 };
  
  var get_values=function(){
      // function that is useful to get the selected values
      var selected_values={}
      for(var s_name in Selectors){
          var s_info=Selectors[s_name];
          var initial_selections = [];
          if(s_info.type==="single"){
              initial_selections=[s_info.selected];
          }
          else{
          for(var i in s_info.selected) {
            initial_selections[i] =  s_info.selected[i];
          }
          }
          selected_values[s_name]=initial_selections;    
      }
      return selected_values;
  };

  // DEAD CODE FOR COVERAGE TESTING
    function deadCodeForCoverage() {
      // This function is never called and should show as uncovered in coverage reports.
      var unused = 42;
      if (unused === 43) {
        console.log("This should never be printed.");
      }
    }
  
  // update scales for the plots that have update_axes option in
  // theme_animint
  function update_scales(p_name, axes, v_name, value){
    // Get pre-computed domain
    var axis_domains = Plots[p_name]["axis_domains"];
    if(!isArray(axes)){
      axes = [axes];
    }
    if(axis_domains != null){
      axes.forEach(function(xyaxis){
        // For Each PANEL, update the axes
        Plots[p_name].layout.PANEL.forEach(function(panel_i, i){
          // Determine whether this panel has a scale or not
          // If not we just update the scales according to the common
          // scale and skip the updating of axis
          var draw_axes = Plots[p_name].layout["AXIS_"+ xyaxis.toUpperCase()][i];
          if(draw_axes){
            var use_panel = panel_i;
          }else{
            var use_panel = Plots[p_name].layout.PANEL[0];
          }
          // We update the current selection of the plot every time
          // and use it to index the correct domain
          var curr_select = axis_domains[xyaxis].curr_select;
          if(axis_domains[xyaxis].selectors.indexOf(v_name) > -1){
            curr_select[v_name] = value;
            var str = use_panel+".";
            for(selec in curr_select){
              str = str + curr_select[selec] + "_";
            }
            str = str.substring(0, str.length - 1); // Strip off trailing underscore
            var use_domain = axis_domains[xyaxis]["domains"][str];
          }
          if(use_domain != null){
            Plots[p_name]["scales"][panel_i][xyaxis].domain(use_domain);
            var scales = Plots[p_name]["scales"][panel_i][xyaxis];
            // major and minor grid lines as calculated in the compiler
            var grid_vals = Plots[p_name]["axis_domains"][xyaxis]["grids"][str];

            // Once scales are updated, update the axis ticks if needed
            if(draw_axes){
              // Tick values are same as major grid lines
              update_axes(p_name, xyaxis, panel_i, grid_vals[1]);
            }
            // Update major and minor grid lines
            update_grids(p_name, xyaxis, panel_i, grid_vals, scales);
          }
        });
      });
    }
  }

  // Update the axis ticks etc. once plot is zoomed in/out
  // currently called from update_scales.
  function update_axes(p_name, axes, panel_i, tick_vals){
    var orientation;
    if(axes == "x"){
      orientation = "bottom";
    }else{
      orientation = "left";
    }
    if(!isArray(tick_vals)){
      tick_vals = [tick_vals];
    }
    var xyaxis = d3.svg.axis()
          .scale(Plots[p_name]["scales"][panel_i][axes])
          .orient(orientation)
          .tickValues(tick_vals);
    // update existing axis
    var xyaxis_g = element.select("#plot_"+p_name).select("."+axes+"axis_"+panel_i)
          .transition()
          .duration(1000)
          .call(xyaxis);
  }

  // Update major/minor grids once axes ticks have been updated
  function update_grids(p_name, axes, panel_i, grid_vals, scales){
    // Select panel to update
    var bgr = element.select("#plot_"+p_name).select(".bgr"+panel_i);
    // Update major and minor grid lines
    ["minor", "major"].forEach(function(grid_class, j){
      var lines = bgr.select(".grid_"+grid_class).select("."+axes);
      var xy1, xy2;
      if(axes == "x"){
        xy1 = lines.select("line").attr("y1");
        xy2 = lines.select("line").attr("y2");
      }else{
        xy1 = lines.select("line").attr("x1");
        xy2 = lines.select("line").attr("x2");
      }
      
      // Get default values for grid lines like colour, stroke etc.
      var grid_background = Plots[p_name]["grid_"+grid_class];
      var col = grid_background.colour;
      var lt = grid_background.linetype;
      var size = grid_background.size;
      var cap = grid_background.lineend;

      // Remove old lines
      lines.selectAll("line")
        .remove();

      if(!isArray(grid_vals[j])){
        grid_vals[j] = [grid_vals[j]];
      }

      if(axes == "x"){
        lines.selectAll("line")
          .data(grid_vals[j])
          .enter()
          .append("line")
          .attr("y1", xy1)
          .attr("y2", xy2)
          .attr("x1", function(d) { return scales(d); })
          .attr("x2", function(d) { return scales(d); })
          .style("stroke", col)
          .style("stroke-linecap", cap)
          .style("stroke-width", size)
          .style("stroke-dasharray", function() {
            return linetypesize2dasharray(lt, size);
          });
      }else{
        lines.selectAll("line")
          .data(grid_vals[j])
          .enter()
          .append("line")
          .attr("x1", xy1)
          .attr("x2", xy2)
          .attr("y1", function(d) { return scales(d); })
          .attr("y2", function(d) { return scales(d); })
          .style("stroke", col)
          .style("stroke-linecap", cap)
          .style("stroke-width", size)
          .style("stroke-dasharray", function() {
            return linetypesize2dasharray(lt, size);
          });
      }
    });
  }

  var update_selector = function (v_name, value) {
    if(!Selectors.hasOwnProperty(v_name)){
      return;
    }
    value = value + "";
    var s_info = Selectors[v_name];
    if(s_info.type == "single"){
      // value is the new selection.
      s_info.selected = value;
    }else{
      // value should be added or removed from the selection.
      var i_value = s_info.selected.indexOf(value);
      if(i_value == -1){
        // not found, add to selection.
        s_info.selected.push(value);
      }else{
        // found, remove from selection.
        hide_tooltip()
        s_info.selected.splice(i_value, 1);
      }
    }
    // update_selector_url()
    // if there are levels, then there is a selectize widget which
    // should be updated.
    if(isArray(s_info.levels)){
      // the jquery ids
      if(s_info.type == "single") {
        var selected_ids = v_name.concat("___", value);
      } else {
        var selected_ids = [];
        for(i in s_info.selected) {
          selected_ids[i] = v_name.concat("___", s_info.selected[i]);
        }
      }
      // from
      // https://github.com/brianreavis/selectize.js/blob/master/docs/api.md:
      // setValue(value, silent) If "silent" is truthy, no change
      // event will be fired on the original input.
      selectized_array[v_name].setValue(selected_ids, true);
    }

    // For each updated geom, check if the axes of the plot need to be
    // updated and update them
    s_info.update.forEach(function(g_name){
      var plot_name = g_name.split("_").pop();
      var axes = Plots[plot_name]["options"]["update_axes"];
      if(axes != null){
        update_scales(plot_name, axes, v_name, value);
      }
    });

    update_legend_opacity(v_name);
    s_info.update.forEach(function(g_name){
      update_geom(g_name, v_name);
    });
  };

  var ifSelectedElse = function (s_value, s_name, selected, not_selected) {
    var is_selected;
    var s_info = Selectors[s_name];
    if(s_info.type == "single"){
      is_selected = s_value == s_info.selected;
    }else{
      is_selected = s_info.selected.indexOf(s_value) != -1;
    }
    if(is_selected){
      return selected;
    } else {
      return not_selected;
    }
  };
  
  function update_next_animation(){
    var values = d3.values(Animation.done_geoms);
    if(d3.sum(values) == values.length){
      // If the values in done_geoms are all 1, then we have loaded
      // all of the animation-related chunks, and we can start
      // playing the animation.
      var v_name = Animation.variable;
      var cur = Selectors[v_name].selected;
      var next = Animation.next[cur];
      update_selector(v_name, next);
    }
  }

  // The main idea of how legends work:

  // 1. In getLegend in animint.R I export the legend entries as a
  // list of rows that can be used in a data() bind in D3.

  // 2. Here in add_legend I create a <table> for every legend, and
  // then I bind the legend entries to <tr>, <td>, and <svg> elements.
  var add_legend = function(p_name, p_info){
    // case of multiple legends, d3 reads legend structure in as an array
    var tdRight = element.select("td."+p_name+"_legend");
    var legendkeys = d3.keys(p_info.legend);
    for(var i=0; i<legendkeys.length; i++){
      var legend_key = legendkeys[i];
      var l_info = p_info.legend[legend_key];
      // the table that contains one row for each legend element.
      var legend_table = tdRight.append("table")
        .attr("class", "legend")
      ;
      var legend_class = legend_class_name(l_info["class"]);
      var legend_id = p_info.plot_id + "_" + legend_class;
      // the legend table with breaks/value/label .
      // TODO: variable and value should be set in the compiler! What
      // if label is different from the data value?
      for(var entry_i=0; entry_i < l_info.entries.length; entry_i++){
        var entry = l_info.entries[entry_i];
        entry.variable = l_info.selector;
        entry.value = entry.label;
        entry.id = safe_name(legend_id + "_" + entry["label"]);
          entry.text_size = l_info.text_size;
      }
      var legend_rows = legend_table.selectAll("tr")
        .data(l_info.entries)
        .enter()
        .append("tr")
      // in a good data viz there should not be more than one legend
      // that shows the same thing, so there should be no duplicate
      // id.
        .attr("id", function(d) { return d["id"]; })
        .attr("class", legend_class)
      ;
      if(l_info.selector != null){
        legend_rows
          .on("click", function(d) {
            update_selector(d.variable, d.value);
          })
          .attr("title", function(d) {
            return "Toggle " + d.value;
          })
          .attr("style", "cursor:pointer")
        ;
      }
      var first_tr = legend_table.insert("tr", "tr");
      var first_th = first_tr.append("th")
        .attr("align", "left")
        .attr("colspan", 2)
        .text(l_info.title)
        .attr("class", legend_class)
        .style("font-size", l_info.title_size)
      ;
      var legend_svgs = legend_rows.append("td")
        .append("svg")
              .attr("id", function(d){return d["id"]+"_svg";})
              .attr("height", 14)
              .attr("width", 20);
      var pointscale = d3.scale.linear().domain([0,7]).range([1,4]);
      // scale points so they are visible in the legend. (does not
      // affect plot scaling)
      var linescale = d3.scale.linear().domain([0,6]).range([1,4]);
      // scale lines so they are visible in the legend. (does not
      // affect plot scaling)
      if(l_info.geoms.indexOf("polygon")>-1){
        // aesthetics that would draw a rect
        legend_svgs.append("rect")
          .attr("x", 2)
                .attr("y", 2)
                .attr("width", 10)
                .attr("height", 10)
          .style("stroke-width", function(d){return d["polygonsize"]||1;})
          .style("stroke-dasharray", function(d){
            return linetypesize2dasharray(d["polygonlinetype"], d["size"]||2);
          })
          .style("stroke", function(d){return d["polygoncolour"] || "#000000";})
          .style("fill", function(d){return d["polygonfill"] || "#FFFFFF";})
          .style("opacity", function(d){return d["polygonalpha"]||1;});
      }
      if(l_info.geoms.indexOf("text")>-1){
        // aesthetics that would draw a rect
        legend_svgs.append("text")
                .attr("x", 10)
                .attr("y", 14)
                  .style("fill", function(d){return d["textcolour"]||1;})
                .style("text-anchor", "middle")
                  .attr("font-size", function(d){return d["textsize"]||1;})
                .text("a");
      }
      if(l_info.geoms.indexOf("path")>-1){
        // aesthetics that would draw a line
        legend_svgs.append("line")
          .attr("x1", 1).attr("x2", 19).attr("y1", 7).attr("y2", 7)
          .style("stroke-width", function(d){
            return linescale(d["pathsize"])||2;
          })
          .style("stroke-dasharray", function(d){
            return linetypesize2dasharray(d["pathlinetype"], d["pathsize"] || 2);
          })
          .style("stroke", function(d){return d["pathcolour"] || "#000000";})
          .style("opacity", function(d){return d["pathalpha"]||1;});
      }
      if(l_info.geoms.indexOf("point")>-1){
        // aesthetics that would draw a point
        legend_svgs.append("circle")
          .attr("cx", 10)
          .attr("cy", 7)
          .attr("r", function(d){return pointscale(d["pointsize"])||4;})
          .style("stroke", function(d){return d["pointcolour"] || "#000000";})
          .style("fill", function(d){
            return d["pointfill"] || d["pointcolour"] || "#000000";
          })
          .style("opacity", function(d){return d["pointalpha"]||1;});
      }
      legend_rows.append("td")
        .attr("align", "left") // TODO: right for numbers?
        .attr("class", "legend_entry_label")
        .attr("id", function(d){ return d["id"]+"_label"; })
          .style("font-size", function(d){ return d["text_size"]})
        .text(function(d){ return d["label"];});
    }
  }

  // Download the main description of the interactive plot.
  d3.json(json_file, function (error, response) {
    if(response.hasOwnProperty("title")){
      // This selects the title of the web page, outside of wherever
      // the animint is defined, usually a <div> -- so it is OK to use
      // global d3.select here.
      d3.select("title").text(response.title);
    }
    // checking for layout structure
    for(var p_name in response.plots) {
      let attributes = response.plots[p_name].span;
        if(attributes.rowspan > 0 || attributes.colspan > 0 || attributes.last_in_row) {
          grid_layout = true;
          break;
        }
    }
    if(grid_layout){
      grid_layout_table = plot_td.append("table")
    }
    // Add plots.
    for (var p_name in response.plots) {
      add_plot(p_name, response.plots[p_name], grid_layout);
      add_legend(p_name, response.plots[p_name]);
      // Append style sheet to document head.
      css.appendChild(document.createTextNode(styles.join(" ")));
      document.head.appendChild(css);
    }
    // Then add selectors and start downloading the first data subset.
    for (var s_name in response.selectors) {
      add_selector(s_name, response.selectors[s_name]);
    }
    
    // Update the scales/axes of the plots if needed
    // We do this so that the plots zoom in initially after loading
    for (var p_name in response.plots) {
      if(response.plots[p_name].axis_domains !== null){
        for(var xy in response.plots[p_name].axis_domains){
          var selectors = response.plots[p_name].axis_domains[xy].selectors;
          if(!isArray(selectors)){
            selectors = [selectors];
          }
          update_scales(p_name, xy, selectors[0],
            response.selectors[selectors[0]].selected);
        }
      }
    }

    ////////////////////////////////////////////
    // Widgets at bottom of page
    ////////////////////////////////////////////
     // Function to start the tour
     var element = d3.select('body');
    if(response.hasOwnProperty("source")){
      widget_td.append("a")
        .attr("class","a_source_href")
        .attr("href", response.source)
        .text("source");
    }
    widget_td
      .append('button')
      .attr('class', 'animint_start_tour')
      .text('Start Tour')
      .on('click', function () {
        const driver = window.driver.js.driver;
        const driverObj = driver({
          showProgress: true,
          steps: steps,
        });
        driverObj.drive();
      });
    // loading table.
    var show_hide_table = widget_td.append("button")
      .text("Show download status table");
    show_hide_table
      .on("click", function(){
        if(this.textContent == "Show download status table"){
          loading.style("display", "");
          show_hide_table.text("Hide download status table");
        }else{
          loading.style("display", "none");
          show_hide_table.text("Show download status table");
        }
      });
    var loading = widget_td.append("table")
      .style("display", "none");
    Widgets["loading"] = loading;
    var tr = loading.append("tr");
    tr.append("th").text("geom");
    tr.append("th").attr("class", "chunk").text("selected chunk");
    tr.append("th").attr("class", "downloaded").text("downloaded");
    tr.append("th").attr("class", "total").text("total");
    tr.append("th").attr("class", "status").text("status");
    
    // Add geoms and construct nest operators.
    for (var g_name in response.geoms) {
      add_geom(g_name, response.geoms[g_name]);
    }
    
    // Animation control widgets.
    var show_message = "Show animation controls";
    // add a button to view the animation widgets
    var show_hide_animation_controls = widget_td.append("button")
      .text(show_message)
      .attr("id", viz_id + "_show_hide_animation_controls")
      .on("click", function(){
        if(this.textContent == show_message){
          time_table.style("display", "");
          show_hide_animation_controls.text("Hide animation controls");
        }else{
          time_table.style("display", "none");
          show_hide_animation_controls.text(show_message);
        }
      })
    ;
    // table of the animint widgets
    var time_table = widget_td.append("table")
      .style("display", "none");
    var first_tr = time_table.append("tr");
    var first_th = first_tr.append("th");
    // if there's a time variable, add a button to pause the animint
    if(response.time){
      Animation.next = {};
      Animation.ms = response.time.ms;
      Animation.variable = response.time.variable;
      Animation.sequence = response.time.sequence;
      Widgets["play_pause"] = first_th.append("button")
        .text("Play")
        .attr("id", "play_pause")
        .on("click", function(){
          if(this.textContent == "Play"){
            Animation.play();
          }else{
            Animation.pause(false);
          }
        })
      ;
    }
    first_tr.append("th").text("milliseconds");
    if(response.time){
      var second_tr = time_table.append("tr");
      second_tr.append("td").text("updates");
      second_tr.append("td").append("input")
        .attr("id", "updates_ms")
        .attr("type", "text")
        .attr("value", Animation.ms)
        .on("change", function(){
          Animation.pause(false);
          Animation.ms = this.value;
          Animation.play();
        })
      ;
    }
    for(s_name in Selectors){
      var s_info = Selectors[s_name];
      if(!s_info.hasOwnProperty("duration")){
        s_info.duration = 0;
      }
    }
    var selector_array = d3.keys(Selectors);
    var duration_rows = time_table.selectAll("tr.duration")
      .data(selector_array)
      .enter()
      .append("tr");
    duration_rows
      .append("td")
      .text(function(s_name){return s_name;});
    var duration_tds = duration_rows.append("td");
    var duration_inputs = duration_tds
      .append("input")
      .attr("id", function(s_name){
        return viz_id + "_duration_ms_" + s_name;
      })
      .attr("type", "text")
      .on("change", function(s_name){
        Selectors[s_name].duration = this.value;
      })
      .attr("value", function(s_name){
        return Selectors[s_name].duration;
      });
    // selector widgets
    var toggle_message = "Show selection menus";
    var show_or_hide_fun = function(){
      if(this.textContent == toggle_message){
        selector_table.style("display", "");
        show_hide_selector_widgets.text("Hide selection menus");
        d3.select(".urltable").style("display","")
      }else{
        selector_table.style("display", "none");
        show_hide_selector_widgets.text(toggle_message);
        d3.select(".urltable").style("display","none")
      }
    }
    var show_hide_selector_widgets = widget_td.append("button")
      .text(toggle_message)
      .attr("class", "show_hide_selector_widgets")
      .on("click", show_or_hide_fun)
    ;
    // adding a table for selector widgets
    var selector_table = widget_td.append("table")
      .style("display", "none")
      .attr("class", "table_selector_widgets")
    ;
    var selector_first_tr = selector_table.append("tr");
    selector_first_tr
      .append("th")
      .text("Variable")
    ;
    selector_first_tr
      .append("th")
      .text("Selected value(s)")
    ;
    // video link
    if(response.hasOwnProperty("video")){
      widget_td.append("a")
        .attr("class","a_video_href")
        .attr("href", response.video)
        .text("video");
    }
    // looping through and adding a row for each selector
    for(s_name in Selectors) {
      var s_info = Selectors[s_name];
      // for .variable .value selectors, levels is undefined and we do
      // not want to make a selectize widget.

      // TODO: why does it take so long to initialize the selectize
      // widget when there are many (>1000) values?
      if(isArray(s_info.levels)){
        // If there were no geoms that specified clickSelects for this
        // selector, then there is no way to select it other than the
        // selectize widgets (and possibly legends). So in this case
        // we show the selectize widgets by default.
        var selector_widgets_hidden =
          show_hide_selector_widgets.text() == toggle_message;
        var has_no_clickSelects =
          !Selectors[s_name].hasOwnProperty("clickSelects")
        var has_no_legend =
          !Selectors[s_name].hasOwnProperty("legend")
        if(selector_widgets_hidden && has_no_clickSelects && has_no_legend){
          var node = show_hide_selector_widgets.node();
          show_or_hide_fun.apply(node);
        }
        // removing "." from name so it can be used in ids
        var s_name_id = legend_class_name(s_name);

        // adding a row for each selector
        var selector_widget_row = selector_table
          .append("tr")
          .attr("class", function() { return s_name_id + "_selector_widget"; })
        ;
        selector_widget_row.append("td").text(s_name);
        // adding the selector
        var selector_widget_select = selector_widget_row
          .append("td")
          .append("select")
          .attr("class", function() { return s_name_id + "_input"; })
          .attr("placeholder", function() { return "Toggle " + s_name; });
        // adding an option for each level of the variable
        selector_widget_select.selectAll("option")
          .data(s_info.levels)
          .enter()
          .append("option")
          .attr("value", function(d) { return d; })
          .text(function(d) { return d; });
        // making sure that the first option is blank
        selector_widget_select
          .insert("option")
          .attr("value", "")
          .text(function() { return "Toggle " + s_name; });
        // calling selectize
        var selectize_selector = to_select + ' .' + s_name_id + "_input";
        if(s_info.type == "single") {
          // setting up array of selector and options
          var selector_values = [];
          for(i in s_info.levels) {
            selector_values[i] = {
              id: s_name.concat("___", s_info.levels[i]),
              text: s_info.levels[i]
            };
          }
          // the id of the first selector
          var selected_id = s_name.concat("___", s_info.selected);

          // if single selection, only allow one item
          var $temp = $(selectize_selector)
            .selectize({
              create: false, 
              valueField: 'id',
              labelField: 'text',
              searchField: ['text'],
              options: selector_values, 
              items: [selected_id],
              maxItems: 1, 
              allowEmptyOption: true,
              onChange: function(value) {
                // extracting the name and the level to update
                var selector_name = value.split("___")[0];
                var selected_level = value.split("___")[1];
                // updating the selector
                update_selector(selector_name, selected_level);
              }
            })
          ;
        } else { // multiple selection:
          // setting up array of selector and options
          var selector_values = [];
          if(typeof s_info.levels == "object") {
            for(i in s_info.levels) {
              selector_values[i] = {
                id: s_name.concat("___", s_info.levels[i]),
                text: s_info.levels[i]
              };
            }
          } else {
            selector_values[0] = {
              id: s_name.concat("___", s_info.levels), 
              text: s_info.levels
            };
          }
          // setting up an array to contain the initally selected elements
          var initial_selections = [];
          for(i in s_info.selected) {
            initial_selections[i] = s_name.concat("___", s_info.selected[i]);
          }
          
          // construct the selectize
          var $temp = $(selectize_selector)
            .selectize({
              create: false, 
              valueField: 'id',
              labelField: 'text',
              searchField: ['text'],
              options: selector_values, 
              items: initial_selections,
              maxItems: s_info.levels.length, 
              allowEmptyOption: true,
              onChange: function(value) { 
                // if nothing is selected, remove what is currently selected
                if(value == null) {
                  // extracting the selector ids from the options
                  var the_ids = Object.keys($(this)[0].options);
                  // the name of the appropriate selector
                  var selector_name = the_ids[0].split("___")[0];
                  // the previously selected elements
                  var old_selections = Selectors[selector_name].selected;
                  // updating the selector for each of the old selections
                  old_selections.forEach(function(element) {
                    update_selector(selector_name, element);
                  });
                } else { // value is not null:
                  // grabbing the name of the selector from the selected value
                  var selector_name = value[0].split("___")[0];
                  // identifying the levels that should be selected
                  var specified_levels = [];
                  for(i in value) {
                    specified_levels[i] = value[i].split("___")[1];
                  }
                  // the previously selected entries
                  old_selections = Selectors[selector_name].selected;
                  
                  // the levels that need to have selections turned on
                  specified_levels
                    .filter(function(n) {
                      return old_selections.indexOf(n) == -1;
                    })
                    .forEach(function(element) {
                      update_selector(selector_name, element);
                    })
                  ;
                  // the levels that need to be turned off
                  // - same approach
                  old_selections
                    .filter(function(n) {
                      return specified_levels.indexOf(n) == -1;
                    })
                    .forEach(function(element) {
                      update_selector(selector_name, element);
                    })
                  ;
                }//value==null
              }//onChange
            })//selectize
          ;
        }//single or multiple selection.
        selectized_array[s_name] = $temp[0].selectize;
      }//levels, is.variable.value
    } // close for loop through selector widgets
    // If this is an animation, then start downloading all the rest of
    // the data, and start the animation.
    if (response.time) {
      var i, prev, cur;
      for (var i = 0; i < Animation.sequence.length; i++) {
        if (i == 0) {
          prev = Animation.sequence[Animation.sequence.length-1];
        } else {
          prev = Animation.sequence[i - 1];
        }
        cur = Animation.sequence[i];
        Animation.next[prev] = cur;
      }
      Animation.timer = null;
      Animation.play = function(){
        if(Animation.timer == null){ // only play if not already playing.
              // as shown on http://bl.ocks.org/mbostock/3808234
              Animation.timer = setInterval(update_next_animation, Animation.ms);
              Widgets["play_pause"].text("Pause");
        }
      };
      Animation.play_after_visible = false;
      Animation.pause = function(play_after_visible){
        Animation.play_after_visible = play_after_visible;
        clearInterval(Animation.timer);
        Animation.timer = null;
        Widgets["play_pause"].text("Play");
      };
      var s_info = Selectors[Animation.variable];
      Animation.done_geoms = {};
      s_info.update.forEach(function(g_name){
        var g_info = Geoms[g_name];
        if(g_info.chunk_order.length == 1 &&
           g_info.chunk_order[0] == Animation.variable){
          g_info.seq_i = Animation.sequence.indexOf(s_info.selected);
          g_info.seq_count = 0;
          Animation.done_geoms[g_name] = 0;
          download_next(g_name);
        }
      });
      Animation.play();
      all_geom_names = d3.keys(response.geoms);

      // This code starts/stops the animation timer when the page is
      // hidden, inspired by
      // http://stackoverflow.com/questions/1060008
      function onchange (evt) {
        if(document.visibilityState == "visible"){
          if(Animation.play_after_visible){
            Animation.play();
          }
        }else{
          if(Widgets["play_pause"].text() == "Pause"){
            Animation.pause(true);
          }
        }
      };
      document.addEventListener("visibilitychange", onchange);
    }
    // update_selector_url()
    var check_func=function(){
      var status_array = $('.status').map(function(){
        return $.trim($(this).text());
      }).get();
      status_array=status_array.slice(1)
      return status_array.every(function(elem){ return elem === "displayed"});           
    }
    if(window.location.hash) {
      var fragment=window.location.hash;
      fragment=fragment.slice(1);
      fragment=decodeURI(fragment)
      var frag_array=fragment.split(/(.*?})/);
      frag_array=frag_array.filter(function(x){ return x!=""})
      frag_array.forEach(function(selector_string){ 
        var selector_hash=selector_string.split("=");
        var selector_nam=selector_hash[0];
        var selector_values=selector_hash[1];
        var re = /\{(.*?)\}/;
        selector_values = re.exec(selector_values)[1];
        var array_values = selector_values.split(',');
        if(Selectors.hasOwnProperty(selector_nam)){
          var s_info = Selectors[selector_nam]
          if(s_info.type=="single"){//TODO fix
            array_values.forEach(function(element) {
              wait_until_then(100, check_func, update_selector,selector_nam,element)
              if(response.time)Animation.pause(true)
            });   
          }else{
            var old_selections = Selectors[selector_nam].selected;
            // the levels that need to have selections turned on
            array_values
              .filter(function(n) {
                return old_selections.indexOf(n) == -1;
              })
              .forEach(function(element) {
                wait_until_then(100, check_func, update_selector,selector_nam,element)
                if(response.time){
                  Animation.pause(true)
                }
              });
            old_selections
              .filter(function(n) {
                return array_values.indexOf(n) == -1;
              })
              .forEach(function(element) {
                wait_until_then(100, check_func, update_selector,selector_nam,element)
                if(response.time){
                  Animation.pause(true)
                }
              });     
          }//if(single) else multiple selection
        }//if(Selectors.hasOwnProperty(selector_nam))
      })//frag_array.forEach
    }//if(window.location.hash)
  });
};
