Merge pull request #196 from eweitz/dog-centromeres

Dog centromeres and Y chromosome; multi-row layout
eweitz · Apr 14, 2020 · cd77ee0 · cd77ee0
2 parents 63a927b + fa26ba4
commit cd77ee0
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diff --git a/data/bands/native/canis-lupus-familiaris.json b/data/bands/native/canis-lupus-familiaris.json
@@ -0,0 +1,84 @@
+{
+  "chrBands": [
+    "1 p 1 0 1 0 1",
+    "1 q 1 1 122678785 1 122678785",
+    "2 p 1 0 1 0 1",
+    "2 q 1 1 85426708 1 85426708",
+    "3 p 1 0 1 0 1",
+    "3 q 1 1 91889043 1 91889043",
+    "4 p 1 0 1 0 1",
+    "4 q 1 1 88276631 1 88276631",
+    "5 p 1 0 1 0 1",
+    "5 q 1 1 88915250 1 88915250",
+    "6 p 1 0 1 0 1",
+    "6 q 1 1 77573801 1 77573801",
+    "7 p 1 0 1 0 1",
+    "7 q 1 1 80974532 1 80974532",
+    "8 p 1 0 1 0 1",
+    "8 q 1 1 74330416 1 74330416",
+    "9 p 1 0 1 0 1",
+    "9 q 1 1 61074082 1 61074082",
+    "10 p 1 0 1 0 1",
+    "10 q 1 1 69331447 1 69331447",
+    "11 p 1 0 1 0 1",
+    "11 q 1 1 74389097 1 74389097",
+    "12 p 1 0 1 0 1",
+    "12 q 1 1 72498081 1 72498081",
+    "13 p 1 0 1 0 1",
+    "13 q 1 1 63241923 1 63241923",
+    "14 p 1 0 1 0 1",
+    "14 q 1 1 60966679 1 60966679",
+    "15 p 1 0 1 0 1",
+    "15 q 1 1 64190966 1 64190966",
+    "16 p 1 0 1 0 1",
+    "16 q 1 1 59632846 1 59632846",
+    "17 p 1 0 1 0 1",
+    "17 q 1 1 64289059 1 64289059",
+    "18 p 1 0 1 0 1",
+    "18 q 1 1 55844845 1 55844845",
+    "19 p 1 0 1 0 1",
+    "19 q 1 1 53741614 1 53741614",
+    "20 p 1 0 1 0 1",
+    "20 q 1 1 58134056 1 58134056",
+    "21 p 1 0 1 0 1",
+    "21 q 1 1 50858623 1 50858623",
+    "22 p 1 0 1 0 1",
+    "22 q 1 1 61439934 1 61439934",
+    "23 p 1 0 1 0 1",
+    "23 q 1 1 52294480 1 52294480",
+    "24 p 1 0 1 0 1",
+    "24 q 1 1 47698779 1 47698779",
+    "25 p 1 0 1 0 1",
+    "25 q 1 1 51628933 1 51628933",
+    "26 p 1 0 1 0 1",
+    "26 q 1 1 38964690 1 38964690",
+    "27 p 1 0 1 0 1",
+    "27 q 1 1 45876710 1 45876710",
+    "28 p 1 0 1 0 1",
+    "28 q 1 1 41182112 1 41182112",
+    "29 p 1 0 1 0 1",
+    "29 q 1 1 41845238 1 41845238",
+    "30 p 1 0 1 0 1",
+    "30 q 1 1 40214260 1 40214260",
+    "31 p 1 0 1 0 1",
+    "31 q 1 1 39895921 1 39895921",
+    "32 p 1 0 1 0 1",
+    "32 q 1 1 38810281 1 38810281",
+    "33 p 1 0 1 0 1",
+    "33 q 1 1 31377067 1 31377067",
+    "34 p 1 0 1 0 1",
+    "34 q 1 1 42124431 1 42124431",
+    "35 p 1 0 1 0 1",
+    "35 q 1 1 26524999 1 26524999",
+    "36 p 1 0 1 0 1",
+    "36 q 1 1 30810995 1 30810995",
+    "37 p 1 0 1 0 1",
+    "37 q 1 1 30902991 1 30902991",
+    "38 p 1 0 1 0 1",
+    "38 q 1 1 23914537 1 23914537",
+    "X p 1 0 1 0 50000000",
+    "X q 1 50000001 123869142 50000001 123869142",
+    "Y p 1 0 1 0 10000000",
+    "Y q 1 10000001 20000000 10000001 20000000"
+  ]
+}
diff --git a/data/bands/native/felis-catus.json b/data/bands/native/felis-catus.json
@@ -1 +1,42 @@
-{"chrBands": ["A1 p 1 0 3713 0 89880064", "A1 q 1 3714 10000.0 89880064 242100913", "A2 p 1 0 2523 0 61080734", "A2 q 1 2524 7082.655941904689 61080734 171471747", "A3 p 1 0 2142 0 51856977", "A3 q 1 2143 5914.9882264177995 51856977 143202405", "B1 p 1 0 1623 0 39294480", "B1 q 1 1624 8600.25211883443 39294480 208212889", "B2 p 1 0 1246 0 30165856", "B2 q 1 1247 6414.789439476422 30165856 155302638", "B3 p 1 0 1225 0 29663499", "B3 q 1 1226 6185.5119480693575 29663499 149751809", "B4 p 1 0 1851 0 44808485", "B4 q 1 1852 5969.770754230902 44808485 144528695", "C1 p 1 0 4498 0 108907037", "C1 q 1 4499 9202.366865919254 108907037 222790142", "C2 p 1 0 3148 0 76225444", "C2 q 1 3149 6658.097567769189 76225444 161193150", "D1 p 1 0 1371 0 33184684", "D1 q 1 1372 4859.462384596625 33184684 117648028", "D2 p 1 0 860 0 20812855", "D2 q 1 861 3725.16810789557 20812855 90186660", "D3 p 1 0 1313 0 31780724", "D3 q 1 1314 4001.8108481895733 31780724 96884206", "D4 p 1 0 1343 0 32525998", "D4 q 1 1344 3986.835522590532 32525998 96521652", "E1 p 1 0 1068 0 25862966", "E1 q 1 1069 2622.6538435235066 25862966 63494689", "E2 p 1 0 1030 0 24929418", "E2 q 1 1031 2657.5816754561347 24929418 64340295", "E3 p 1 0 753 0 18233305", "E3 q 1 754 1844.2013888646509 18233305 44648284", "F1 p 1 0 41 0 1000001", "F1 q 1 42 2960.0980067349024 1000001 71664243", "F2 p 1 0 41 0 1000001", "F2 q 1 42 3542.012912607232 1000001 85752456", "X p 1 0 2128 0 51521357", "X q 1 2129 5392.669006580739 51521357 130557009"]}
+{
+  "chrBands": [
+    "A1 p 1 0 3713 0 89880064",
+    "A1 q 1 3714 10000.0 89880064 242100913",
+    "A2 p 1 0 2523 0 61080734",
+    "A2 q 1 2524 7082.655941904689 61080734 171471747",
+    "A3 p 1 0 2142 0 51856977",
+    "A3 q 1 2143 5914.9882264177995 51856977 143202405",
+    "B1 p 1 0 1623 0 39294480",
+    "B1 q 1 1624 8600.25211883443 39294480 208212889",
+    "B2 p 1 0 1246 0 30165856",
+    "B2 q 1 1247 6414.789439476422 30165856 155302638",
+    "B3 p 1 0 1225 0 29663499",
+    "B3 q 1 1226 6185.5119480693575 29663499 149751809",
+    "B4 p 1 0 1851 0 44808485",
+    "B4 q 1 1852 5969.770754230902 44808485 144528695",
+    "C1 p 1 0 4498 0 108907037",
+    "C1 q 1 4499 9202.366865919254 108907037 222790142",
+    "C2 p 1 0 3148 0 76225444",
+    "C2 q 1 3149 6658.097567769189 76225444 161193150",
+    "D1 p 1 0 1371 0 33184684",
+    "D1 q 1 1372 4859.462384596625 33184684 117648028",
+    "D2 p 1 0 860 0 20812855",
+    "D2 q 1 861 3725.16810789557 20812855 90186660",
+    "D3 p 1 0 1313 0 31780724",
+    "D3 q 1 1314 4001.8108481895733 31780724 96884206",
+    "D4 p 1 0 1343 0 32525998",
+    "D4 q 1 1344 3986.835522590532 32525998 96521652",
+    "E1 p 1 0 1068 0 25862966",
+    "E1 q 1 1069 2622.6538435235066 25862966 63494689",
+    "E2 p 1 0 1030 0 24929418",
+    "E2 q 1 1031 2657.5816754561347 24929418 64340295",
+    "E3 p 1 0 753 0 18233305",
+    "E3 q 1 754 1844.2013888646509 18233305 44648284",
+    "F1 p 1 0 41 0 1000001",
+    "F1 q 1 42 2960.0980067349024 1000001 71664243",
+    "F2 p 1 0 41 0 1000001",
+    "F2 q 1 42 3542.012912607232 1000001 85752456",
+    "X p 1 0 2128 0 51521357",
+    "X q 1 2129 5392.669006580739 51521357 130557009"
+  ]
+}
diff --git a/dist/data/bands/native/canis-lupus-familiaris.json b/dist/data/bands/native/canis-lupus-familiaris.json
@@ -0,0 +1,84 @@
+{
+  "chrBands": [
+    "1 p 1 0 1 0 1",
+    "1 q 1 1 122678785 1 122678785",
+    "2 p 1 0 1 0 1",
+    "2 q 1 1 85426708 1 85426708",
+    "3 p 1 0 1 0 1",
+    "3 q 1 1 91889043 1 91889043",
+    "4 p 1 0 1 0 1",
+    "4 q 1 1 88276631 1 88276631",
+    "5 p 1 0 1 0 1",
+    "5 q 1 1 88915250 1 88915250",
+    "6 p 1 0 1 0 1",
+    "6 q 1 1 77573801 1 77573801",
+    "7 p 1 0 1 0 1",
+    "7 q 1 1 80974532 1 80974532",
+    "8 p 1 0 1 0 1",
+    "8 q 1 1 74330416 1 74330416",
+    "9 p 1 0 1 0 1",
+    "9 q 1 1 61074082 1 61074082",
+    "10 p 1 0 1 0 1",
+    "10 q 1 1 69331447 1 69331447",
+    "11 p 1 0 1 0 1",
+    "11 q 1 1 74389097 1 74389097",
+    "12 p 1 0 1 0 1",
+    "12 q 1 1 72498081 1 72498081",
+    "13 p 1 0 1 0 1",
+    "13 q 1 1 63241923 1 63241923",
+    "14 p 1 0 1 0 1",
+    "14 q 1 1 60966679 1 60966679",
+    "15 p 1 0 1 0 1",
+    "15 q 1 1 64190966 1 64190966",
+    "16 p 1 0 1 0 1",
+    "16 q 1 1 59632846 1 59632846",
+    "17 p 1 0 1 0 1",
+    "17 q 1 1 64289059 1 64289059",
+    "18 p 1 0 1 0 1",
+    "18 q 1 1 55844845 1 55844845",
+    "19 p 1 0 1 0 1",
+    "19 q 1 1 53741614 1 53741614",
+    "20 p 1 0 1 0 1",
+    "20 q 1 1 58134056 1 58134056",
+    "21 p 1 0 1 0 1",
+    "21 q 1 1 50858623 1 50858623",
+    "22 p 1 0 1 0 1",
+    "22 q 1 1 61439934 1 61439934",
+    "23 p 1 0 1 0 1",
+    "23 q 1 1 52294480 1 52294480",
+    "24 p 1 0 1 0 1",
+    "24 q 1 1 47698779 1 47698779",
+    "25 p 1 0 1 0 1",
+    "25 q 1 1 51628933 1 51628933",
+    "26 p 1 0 1 0 1",
+    "26 q 1 1 38964690 1 38964690",
+    "27 p 1 0 1 0 1",
+    "27 q 1 1 45876710 1 45876710",
+    "28 p 1 0 1 0 1",
+    "28 q 1 1 41182112 1 41182112",
+    "29 p 1 0 1 0 1",
+    "29 q 1 1 41845238 1 41845238",
+    "30 p 1 0 1 0 1",
+    "30 q 1 1 40214260 1 40214260",
+    "31 p 1 0 1 0 1",
+    "31 q 1 1 39895921 1 39895921",
+    "32 p 1 0 1 0 1",
+    "32 q 1 1 38810281 1 38810281",
+    "33 p 1 0 1 0 1",
+    "33 q 1 1 31377067 1 31377067",
+    "34 p 1 0 1 0 1",
+    "34 q 1 1 42124431 1 42124431",
+    "35 p 1 0 1 0 1",
+    "35 q 1 1 26524999 1 26524999",
+    "36 p 1 0 1 0 1",
+    "36 q 1 1 30810995 1 30810995",
+    "37 p 1 0 1 0 1",
+    "37 q 1 1 30902991 1 30902991",
+    "38 p 1 0 1 0 1",
+    "38 q 1 1 23914537 1 23914537",
+    "X p 1 0 1 0 50000000",
+    "X q 1 50000001 123869142 50000001 123869142",
+    "Y p 1 0 1 0 10000000",
+    "Y q 1 10000001 20000000 10000001 20000000"
+  ]
+}
diff --git a/examples/vanilla/eukaryotes.html b/examples/vanilla/eukaryotes.html
@@ -60,9 +60,9 @@ <h1>Eukaryotes | Ideogram</h1>
         <li><label for="pan-troglodytes"><input type="radio" name="org" value="pan-troglodytes" id="pan-troglodytes">Chimpanzee (Pan troglodytes)</label></li>
         <li><label for="macaca-mulatta"><input type="radio" name="org" value="macaca-mulatta" id="macaca-mulatta">Macaque (Macaca mulatta)</label></li>
         <li><label for="felis-catus"><input type="radio" name="org" value="felis-catus" id="felis-catus">Cat (Felis catus)</label></li>
-        <!-- <li><label for="canis-lupus-familiaris"><input type="radio" name="org" value="canis-lupus-familiaris" id="canis-lupus-familiaris">Dog (Canis lupus familiaris)</label></li> -->
+        <li><label for="canis-lupus-familiaris"><input type="radio" name="org" value="canis-lupus-familiaris" id="canis-lupus-familiaris">Dog (Canis lupus familiaris)</label></li>
         <!-- <li><label for="gallus-gallus"><input type="radio" name="org" value="gallus-gallus" id="gallus-gallus">Chicken (Gallus gallus)</label></li> -->
-        <!-- <li><label for="bos-taurus"><input type="radio" name="org" value="bos-taurus" id="bos-taurus">Cow (Bos taurus)</label></li> -->
+        <li><label for="bos-taurus"><input type="radio" name="org" value="bos-taurus" id="bos-taurus">Cow (Bos taurus)</label></li>
         <li><label for="sus-scrofa"><input type="radio" name="org" value="sus-scrofa" id="sus-scrofa">Pig (Sus scrofa)</label></li>
       </ul>
     </li>
@@ -88,7 +88,7 @@ <h1>Eukaryotes | Ideogram</h1>
       Protozoa
       <ul>
         <li><label for="plasmodium-falciparum"><input type="radio" name="org" value="plasmodium-falciparum" id="plasmodium-falciparum">Malaria parasite (Plasmodium falciparum)</label></li>
-        <!-- <li><label for="leishmania-donovani"><input type="radio" name="org" value="leishmania-donovani" id="leishmania-donovani">Leishmania parasite (Leishmania donovani)</label></li> -->
+        <li><label for="leishmania-donovani"><input type="radio" name="org" value="leishmania-donovani" id="leishmania-donovani">Leishmania parasite (Leishmania donovani)</label></li>
       </ul>
     </li>
   </ul>

diff --git a/examples/vanilla/orthologs.html b/examples/vanilla/orthologs.html
@@ -35,8 +35,8 @@ <h1>Orthologs | Ideogram</h1>
   </label>
   <div style="font-size: 12px; position: relative; top: -7px;">
     Examples:
-    <a href="?genes=MTOR&org=homo-sapiens&org2=mus-musculus&backend=oma">MTOR</a> |
-    <a href="?genes=MTOR,BRCA1&org=homo-sapiens&org2=mus-musculus&backend=oma">MTOR, BRCA1</a> |
+    <a href="?genes=MTOR&org=homo-sapiens&org2=mus-musculus&backend=orthodb">MTOR</a> |
+    <a href="?genes=MTOR,BRCA1&org=homo-sapiens&org2=mus-musculus&backend=orthodb">MTOR, BRCA1</a> |
     <a href="?loci=2:150000000,5:20000000&org=homo-sapiens&org2=mus-musculus">2:150000000, 5:200000000</a>
   </div>
   <label for="org">
@@ -80,8 +80,8 @@ <h1>Orthologs | Ideogram</h1>
   <label for="backend">
     Orthology backend:
     <select class="left-select backend-select" id="backend">
-      <option id="oma" selected>OMA Browser</option>
-      <option id="orthodb">OrthoDB</option>
+      <option id="orthodb" selected>OrthoDB</option>
+      <option id="oma">OMA Browser</option>
     </select>
   </label>
   </div>
@@ -293,7 +293,7 @@ <h1>Orthologs | Ideogram</h1>
         }
         urlParams['org'] = 'homo-sapiens';
         urlParams['org2'] = 'mus-musculus';
-        urlParams['backend'] = 'oma';
+        urlParams['backend'] = 'orthodb';
         // urlParams['loci'] = '1:11106531-11262557,4:148448582-148557685';
       }
 
@@ -304,7 +304,7 @@ <h1>Orthologs | Ideogram</h1>
       }
 
       if ('backend' in urlParams === false) {
-        urlParams['backend'] = 'oma';
+        urlParams['backend'] = 'orthodb';
       }
 
       org1 = urlParams['org'].replace(/-/g, ' ');

diff --git a/src/js/init/organism-metadata.js b/src/js/init/organism-metadata.js
@@ -177,6 +177,13 @@ var organismMetadata = {
     assemblies: {
       default: ''
     }
+  },
+  9615: {
+    commonName: 'Dog',
+    scientificName: 'Canis lupus familiaris',
+    assemblies: {
+      default: ''
+    }
   }
 };
 

diff --git a/src/js/layouts/small-layout.js b/src/js/layouts/small-layout.js
@@ -11,6 +11,14 @@ class SmallLayout extends Layout {
       left: 36.5,
       top: 10
     };
+
+    var taxid = this._ideo.getTaxid(this._ideo.config.organism);
+
+    this.chrs = config.chromosomes[taxid];
+    var numChrs = this.chrs.length;
+
+    // Number of chromosomes per row
+    this.chrsPerRow = Math.ceil(numChrs / config.rows);
   }
 
   // rotateForward(setIndex, chrIndex, chrElement, callback) {
@@ -37,11 +45,57 @@ class SmallLayout extends Layout {
   //     .on('end', callback);
   // }
 
+  /**
+   * eweitz 2020-04-13:
+   * This height metric is crude because it is calculated before
+   * the height ("width") of each chromosome is calculated.
+   *
+   * It calculates height by multiplying the max height of all chromosomes
+   * (specified in the Ideogram configuration object) by the number of rows.
+   * This ensures the ideogram height doesn't truncate in cases like dog
+   * (where chrX on the second row is longer than chr1 on the first), but it
+   * often leaves too much space on the second row, e.g. for human.
+   *
+   * Ideally, ideogram height would be cumulative height per row, plus top
+   * margin.  This would require calling getHeight _after_ all chromosomes
+   * have had their height (technically, chr.width) assigned.  See draft new
+   * getHeight method below this getHeight method.
+  */
   getHeight() {
-    var chrHeight = this._config.chrHeight;
-    return this._config.rows * (chrHeight + this.margin.top * 1.5);
+    var config = this._config;
+    var chrHeight = config.chrHeight * 1.25;
+    return this._config.rows * (chrHeight + this.margin.top);
   }
 
+  /**
+   * eweitz 2020-04-13:
+   * Draft refinement of getHeight.  See note in classic version above.
+   *
+   * Total height is cumulative height per row, plus top margin
+   */
+  // getHeight() {
+  //   let height = 0;
+  //   const rows = this._config.rows;
+  //   const chrEntries = Object.entries(this.chrs);
+
+  //   for (let i = 0; i < rows; i++) {
+  //     let rowHeight = 0;
+  //     // Starting and ending indexes of chromosomes of this row
+  //     const startIndex = this.chrsPerRow * i;
+  //     const endIndex = this.chrsPerRow * (i + 1) - 1;
+
+  //     for (let j = startIndex; j < endIndex; j++) {
+  //       const thisChrHeight = chrEntries[j][1].width;
+  //       if (thisChrHeight > rowHeight) {
+  //         rowHeight = thisChrHeight;
+  //       }
+  //     }
+  //     height += rowHeight + this.margin.top;
+  //   }
+
+  //   return height;
+  // }
+
   getWidth() {
     return '97%';
   }
@@ -55,20 +109,11 @@ class SmallLayout extends Layout {
   }
 
   getChromosomeSetTranslate(setIndex) {
-    var taxid = this._ideo.getTaxid(this._ideo.config.organism);
-
-    // Get first organism chromosomes amount
-    var numChrs = this._ideo.config.chromosomes[taxid].length;
-
-    // Number of chromosomes per row
-    var chrsPerRow = numChrs / this._config.rows;
-
-    var xOffset;
-    var yOffset;
+    var xOffset, yOffset;
 
-    if (setIndex > chrsPerRow - 1) {
-      xOffset = this.margin.left + this._config.chrHeight * 1.4;
-      yOffset = this.getChromosomeSetYTranslate(setIndex - chrsPerRow);
+    if (setIndex > this.chrsPerRow - 1) {
+      xOffset = this.margin.left + this._config.chrHeight * 1.3;
+      yOffset = this.getChromosomeSetYTranslate(setIndex - this.chrsPerRow);
     } else {
       xOffset = this.margin.left;
       yOffset = this.getChromosomeSetYTranslate(setIndex);