ideogram/src/js/ideogram.filter.js

Chromosome visualization with D3.js

/* Decompresses ideogram's annotations for crossfilter initialization
By default, annotations are clustered by chromosome, e.g.
[
  {"chr": "1", "annots": [{"from": 100, "to", 101, "chr": "1", ...}, ...]},
  {"chr": "2", "annots": [{"from": 500, "to", 501, "chr": "2", ...}, ...]},
  ...
]
This method flattens that structure to e.g.
[
  {"from": 100, "to": 101, "chr": "1", ...},
  ...
  {"from": 500, "to": 501, "chr": "2", ...},
]
See also: packAnnots
*/
Ideogram.prototype.unpackAnnots = function() {

  var chr, annots, i,
      unpackedAnnots = [],
      ideo = this,
      chrs = ideo.annots;

  for (i = 0; i < chrs.length; i++) {
    chr = chrs[i];
    annots = chr.annots;
    unpackedAnnots = unpackedAnnots.concat(annots);
  }

  return unpackedAnnots;

}

/*
  Compresses annots back to default state.  Inverse of unpackAnnots.
*/
Ideogram.prototype.packAnnots = function(unpackedAnnots) {

  var chr, annot, i,
      annots = [],
      ideo = this,
      chrs = ideo.annots;

  for (var chr in chrs) {
    annots.push({'chr': chrs[chr].chr, annots: []});
  }

  for (i = 0; i < unpackedAnnots.length; i++) {
    annot = unpackedAnnots[i];
    annots[annot.chrIndex]['annots'].push(annot);
  }

  return annots;

}

/*
  Initializes crossfilter.  Needed for client-side filtering.
  More: https://github.com/square/crossfilter/wiki/API-Reference
*/
Ideogram.prototype.initCrossFilter = function() {
  var ideo = this,
      keys = ideo.rawAnnots.keys,
      i, facet;

  ideo.unpackedAnnots = ideo.unpackAnnots();
  ideo.crossfilter = crossfilter(ideo.unpackedAnnots);

  ideo.annotsByFacet = {};

  ideo.facets = keys.slice(3, keys.length);

  for (i = 0; i < ideo.facets.length; i++) {
    facet = ideo.facets[i];
    ideo.annotsByFacet[facet] =
      ideo.crossfilter
        .dimension(function(d) {
          return d[facet];
        })
  }
}

/*
  Filters annotations based on the given selections
  "selections" is an object of objects, e.g.

    {
      "tissue-type": {          <-- a facet
        "cerebral-cortex": 1,   <-- a filter; "1" means it is selected
        "liver": 1
      },
      "gene-type": {
        mirna": 1
      }
    }

  Translation:
  select where:
      (tissue-type is cerebral-cortex OR liver) and (gene-type is mirna)

  TODO:
    * Filter counts
    * Range filters
    * Integrate server-side filtering for very large datasets
*/
Ideogram.prototype.filterAnnots = function(selections) {

  var t0 = Date.now();

  var i, facet,
      prevFacet = null,
      results, fn,
      counts = {},
      ideo = this;

  if (Object.keys(selections).length == 0) {
    results = ideo.unpackedAnnots;
  } else {
    for (i = 0; i < ideo.facets.length; i++) {
      facet = ideo.facets[i];
      if (facet in selections) {
        fn = function(d) {
          if (d in selections[facet]) {
            return true;
          }
        };
      } else {
        fn = null;
      }
      ideo.annotsByFacet[facet].filter(fn);
      counts[facet] = ideo.annotsByFacet[facet].group().top(Infinity);
    }

    results = ideo.annotsByFacet[facet].top(Infinity);
  }

  for (i < 0; i < ideo.facets.length; i++) {
    ideo.annotsByFacet[facet].filterAll(); // clear filters
  }

  results = ideo.packAnnots(results);

  d3.selectAll("polygon.annot").remove();
  ideo.drawAnnots(results);

  console.log("Time in filterAnnots: " + (Date.now() - t0) + " ms");

  return counts;
}