ideogram/src/js/annotations/process.js

Chromosome visualization for the web

import {add2dAnnotsForChr} from './heatmap-2d';
import {setAnnotRanks} from './annotations';

// Default colors for tracks of annotations
var colorMap = [
  ['F00'], // If there is 1 track, then color it red.
  ['F00', '88F'], // If 2 tracks, color one red and one light blue.
  ['F00', 'CCC', '88F'], // If 3, color one red, one grey, one light blue.
  ['F00', 'FA0', '0AF', '88F'], // And so on.
  ['F00', 'FA0', 'CCC', '0AF', '88F'],
  ['F00', 'FA0', '875', '578', '0AF', '88F'],
  ['F00', 'FA0', '875', 'CCC', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', '0A7', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', 'CCC', '0A7', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', '552', '255', '0A7', '578', '0AF', '88F']
];

/**
 * Ensure annotation containers are ordered by chromosome.
 */
function orderAnnotContainers(annots, ideo) {
  var unorderedAnnots, i, j, annot, chr, chrs;

  unorderedAnnots = annots;
  annots = [];
  chrs = ideo.chromosomesArray;
  for (i = 0; i < chrs.length; i++) {
    chr = chrs[i].name;
    for (j = 0; j < unorderedAnnots.length; j++) {
      annot = unorderedAnnots[j];
      if (annot.chr === chr) {
        annots.push(annot);
      }
    }
  }

  return annots;
}

/**
 * Add client annotations, as in annotations-tracks.html
 */
function addClientAnnot(annots, annot, ra, m, ideo) {
  var annotTrack;

  annot.trackIndex = ra[3];
  annotTrack = ideo.config.annotationTracks[annot.trackIndex];
  if (annotTrack.color) {
    annot.color = annotTrack.color;
  }
  if (annotTrack.shape) {
    annot.shape = annotTrack.shape;
  }

  annots[m].annots.push(annot);

  return annots;
}

/**
 * Add sparse server annotations, as in annotations-track-filters.html
 */
function addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo) {
  var colors = colorMap[ideo.numAvailTracks - 1];

  annot.trackIndex = ra[3];
  annot.trackIndexOriginal = ra[4];
  annot.color = '#' + colors[annot.trackIndexOriginal];

  // Catch annots that will be omitted from display
  if (annot.trackIndex > ideo.config.numTracks - 1) {
    if (annot.trackIndex in omittedAnnots) {
      omittedAnnots[annot.trackIndex].push(annot);
    } else {
      omittedAnnots[annot.trackIndex] = [annot];
    }
    return [annots, omittedAnnots];
  }
  annots[m].annots.push(annot);

  return [annots, omittedAnnots];
}

/**
 * Basic client annotations, as in annotations-basic.html
 * and annotations-external.html
 */
function addBasicClientAnnot(annots, annot, m, ideo) {
  annot.trackIndex = 0;
  if (!annot.color) {
    annot.color = ideo.config.annotationsColor;
  }
  if (!annot.shape) {
    annot.shape = 'triangle';
  }
  annots[m].annots.push(annot);

  return annots;
}

function addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo) {

  if (ideo.config.annotationTracks) {
    annots = addClientAnnot(annots, annot, ra, m, ideo);
  } else if (keys[3] === 'trackIndex' && ideo.numAvailTracks !== 1) {
    [annots, omittedAnnots] =
      addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo);
  // } else if (
  //   keys.length > 3 &&
  //   keys[3] in {trackIndex: 1, color: 1, shape: 1} === false &&
  //   keys[4] === 'trackIndexOriginal'
  // ) {
  //   annots = addDenseServerAnnot(keys, annots, annot, m);
  } else {
    annots = addBasicClientAnnot(annots, annot, m, ideo);
  }

  return [annots, omittedAnnots];
}

function getAnnotDomId(chrIndex, annotIndex) {
  return '_c' + chrIndex + '_a' + annotIndex;
}

function addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel,
  m, keys, ideo) {
  var j, k, annot, ra;

  // Assign DOM ID if annots are rendered as individual DOM elements
  const shouldAssignDomId = (
    !ideo.config.annotationsLayout ||
    ideo.config.annotationsLayout === 'tracks'
  );

  for (j = 0; j < annotsByChr.annots.length; j++) {
    ra = annotsByChr.annots[j];
    annot = {};

    for (k = 0; k < keys.length; k++) {
      annot[keys[k]] = ra[k];
    }

    annot.stop = annot.start + annot.length;

    annot.chr = annotsByChr.chr;
    annot.chrIndex = m;
    annot.startPx = ideo.convertBpToPx(chrModel, annot.start);
    annot.stopPx = ideo.convertBpToPx(chrModel, annot.stop);
    annot.px = Math.round((annot.startPx + annot.stopPx) / 2);
    if (shouldAssignDomId) annot.domId = getAnnotDomId(m, j);

    [annots, omittedAnnots] =
      addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo);
  }

  if (shouldAssignDomId) {
    if (ideo.annotSortFunction) {
      annots[m].annots = setAnnotRanks(annots[m].annots, ideo);
      annots[m].annots.sort((a, b) => {
        // Reverse-sort, so first annots are drawn last, and thus at top layer
        return -ideo.annotSortFunction(a, b);
      });
    } else {
      // Sort by genomic position, in ascending order
      annots[m].annots.sort((a, b) => a[1] - b[1]);
    }

    for (j = 0; j < annots[m].annots.length; j++) {
      annots[m].annots[j].domId = getAnnotDomId(m, j);
    }
  }

  return [annots, omittedAnnots];
}

function warnOfUndefinedChromosome(annotsByChr) {
  console.warn(
    'Chromosome "' + annotsByChr.chr + '" undefined in ideogram; ' +
    annotsByChr.annots.length + ' annotations not shown'
  );
}

function addAnnots(rawAnnots, keys, ideo) {
  var m, i, annotsByChr, chrModel,
    annots = [],
    omittedAnnots = {};

  m = -1;
  for (i = 0; i < rawAnnots.length; i++) {
    annotsByChr = rawAnnots[i];
    chrModel = ideo.chromosomes[ideo.config.taxid][annotsByChr.chr];

    if (typeof chrModel === 'undefined') {
      warnOfUndefinedChromosome(annotsByChr);
      continue;
    }

    m++;
    annots.push({chr: annotsByChr.chr, annots: []});

    if (ideo.config.annotationsLayout !== 'heatmap-2d') {
      [annots, omittedAnnots] =
        addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
          keys, ideo);
    } else {
      [annots, omittedAnnots] =
        add2dAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
          keys, ideo);
    }
  }
  return [annots, omittedAnnots];
}

function sendTrackAndAnnotWarnings(omittedAnnots, ideo) {
  var numOmittedTracks,
    layout = ideo.config.annotationsLayout,
    numTracks = ideo.config.numAnnotTracks;

  if (!/heatmap/.test(layout) && numTracks > 10) {
    console.error(
      'Ideogram only displays up to 10 tracks at a time.  ' +
      'You specified ' + numTracks + ' tracks.  ' +
      'Perhaps consider a different way to visualize your data.'
    );
  }

  numOmittedTracks = Object.keys(omittedAnnots).length;
  if (numOmittedTracks) {
    console.warn(
      'Ideogram configuration specified ' + numTracks + ' tracks, ' +
      'but loaded annotations contain ' + numOmittedTracks + ' ' +
      'extra tracks.'
    );
  }
}

/**
 * Proccesses genome annotation data.
 *
 * This method converts raw annotation data from server, which is structured as
 * an array of arrays, into a more verbose data structure consisting of an
 * array of objects.  It also adds pixel offset information.
 */
function processAnnotData(rawAnnots) {
  var keys, annots, omittedAnnots,
    ideo = this;

  keys = rawAnnots.keys;
  rawAnnots = rawAnnots.annots;

  [annots, omittedAnnots] = addAnnots(rawAnnots, keys, ideo);
  annots = orderAnnotContainers(annots, ideo);

  sendTrackAndAnnotWarnings(omittedAnnots, ideo);

  return annots;
}

export {processAnnotData, getAnnotDomId};