Merge pull request #360 from eweitz/fix-annot-filter

Fix `annotsInList` parameter, improve accessibility

examples/vanilla/gene-leads.html

@@ -251,7 +251,8 @@ <h1>Gene Leads<small>Enrich your gene search</small></h1>
       onClickAnnot
     }
 
-    // If you don't want certain genes displayed, do this:
+    const annotsInList = 'all';
+    // If you only want certain genes displayed, do this:
     // annotsInList = ['CDK9', 'CDK19', 'CDK1'];
     //
     // A longer list of genes, from Scanpy / Seurat 3k PBMC tutorial
@@ -260,16 +261,16 @@ <h1>Gene Leads<small>Enrich your gene search</small></h1>
     //   "CORO1C","USP30","GLTP","GIT2","HVCN1","ALDH2","TMEM116","NAA25","RPH3A","OAS1","FBXO21","RFC5","TAOK3","DYNLL1","MLEC","OASL","ORAI1","SETD1B","CLIP1","RILPL2","SNRNP35","EIF2B1","NCOR2","NOC4L","MRP63","GTF3A","MTIF3","FRY-AS1","N4BP2L1","SPG20","ALG5","EXOSC8","MTRF1","DNAJC15","CCDC122","TSC22D1","DLEU7","RNASEH2B","MZT1","DIS3","MYCBP2","RBM26-AS1","UBAC2","GPR183","CLYBL","ARGLU1","ABHD13","TNFSF13B","ARHGEF7","MCF2L","CDC16","RPPH1","METTL3","CMTM5","DHRS4","PSME1","RP11-468E2.4","IRF9","CHMP4A","MDP1","GMPR2","TINF2","CIDEB","LTB4R","GZMH","GZMB","SCFD1","AP4S1","EAPP","PPP2R3C","FBXO33","FKBP3","MIS18BP1","NEMF","ARF6","C14orf166","PTGDR","PSMC6","CGRRF1","MAPK1IP1L","LGALS3","RP11-349A22.5","ARID4A","JKAMP","MNAT1","CTD-2302E22.4","ATP6V1D","EIF2S1","ARG2","VTI1B","RAD51B","DCAF5","ERH","SRSF5","PCNX","RBM25","NUMB","LIN52","NPC2","ISCA2","DLST","RPS6KL1","RP11-950C14.3","C14orf1","RP11-488C13.5","GSTZ1","AHSA1","SNW1","SEL1L","SPATA7","TTC8","TRIP11","ATXN3","IFI27","DICER1","TCL1B","TCL1A","RP11-164H13.1","HSP90AA1","ANKRD9","CDC42BPB","TNFAIP2","EIF5","TRMT61A","BAG5","SIVA1","PLD4","C14orf80","AL928768.3","KIAA0125","UBE3A","ATP10A","KLF13","RP11-1000B6.3","ARHGAP11A","DPH6","THBS1","EIF2AK4","PLCB2","C15orf57","RPUSD2","RMDN3","TMEM87A","ZNF106","TMEM62","ADAL","PDIA3","CASC4","TRIM69","USP8","SPPL2A","RP11-430B1.2","ARPP19","RP11-139H15.1","TCF12","LINC00926","ADAM10","MYO1E","BNIP2","NARG2","RP11-219B17.1","RORA","VPS13C","TPM1","RAB8B","APH1B","FAM96A","KIAA0101","CLPX","AAGAB","C15orf61","FEM1B","EDC3","COMMD4","NEIL1","SIN3A","SCAPER","RCN2","HMG20A","ST20","BCL2A1","MESDC2","IL16","WHAMM","HOMER2","FANCI","IDH2","UNC45A","HDDC3","CHD2","ARRDC4","LYSMD4","TARSL2","POLR3K","HBA1","LUC7L","RAB40C","C16orf13","STUB1","FAM173A","RPUSD1","NME3","HAGH","NDUFB10","GFER","IL32","ZNF263","CORO7","DNAJA3","NUDT16L1","CARHSP1","USP7","ATF7IP2","DEXI","LITAF","TNFRSF17","PDXDC1","FOPNL","COQ7","CCP110","IGSF6","C16orf52","POLR3E","GGA2","EARS2","PRKCB","RBBP6","RABEP2","CD19","SPNS1","SNX29P2","C16orf54","TMEM219","TAOK2","YPEL3","SEPHS2","ZNF747","ZNF688","PHKG2","STX4","FUS","PYCARD","TGFB1I1","C16orf58","RP11-42I10.1","CNEP1R1","SNX20","AKTIP","BBS2","CPNE2","ARL2BP","CIAPIN1","GPR56","KIFC3","C16orf80","GOT2","FAM96B","CES4A","TMEM208","ACD","TANGO6","CYB5B","NFAT5","ST3GAL2","RP11-432I5.1","ATXN1L","HP","PSMD7","RP11-252A24.3","GABARAPL2","KARS","TERF2IP","COTL1","C16orf74","IRF8","BANP","CYBA","MVD","SPG7","ZNF276","TIMM22","YWHAE","PITPNA-AS1","PRPF8","SERPINF1","SMYD4","PAFAH1B1","SHPK-1","P2RX5","ARRB2","PSMB6","GP1BA","SLC25A11","ZNF232","ZNF594","TXNDC17","ALOX12","CLEC10A","ASGR1","ACADVL","ELP5","ACAP1","TMEM102","TNFSF12","AC113189.5","SAT2","C17orf59","ADPRM","UBB","TRPV2","PLD6","NT5M","MED9","RASD1","PEMT","SREBF1","TRIM16L","GRAP","IFT20","POLDIP2","TMEM199","PROCA1","RAB34","NEK8","PHF12","ADAP2","NF1","UTP6","CCL2","SLFN5","SLFN12","CCL5","CCL3","CCL4","CCL4L1","GGNBP2","MRM1","AATF","TADA2A","MLLT6","RARA","CTD-2267D19.2","RP5-1028K7.2","DNAJC7","NKIRAS2","RP11-400F19.6","MLX","TUBG2","VPS25","RUNDC1","IFI35","NBR1","DHX8","RP11-527L4.5","HDAC5","GRN","ITGA2B","HEXIM2","RP11-798G7.6","GOSR2","ITGB3","OSBPL7","ABI3","PDK2","SAMD14","LRRC59","ABCC3","LUC7L3","MMD","NOG","SCPEP1","MRPS23","BZRAP1-AS1","SEPT4","YPEL2","INTS2","CYB561","LIMD2","PSMC5","CD79B","ICAM2","TEX2","NOL11","ARSG","CTD-2006K23.1","NAT9","TMEM104","ATP5H","SLC16A5","ARMC7","NT5C","GGA3","GRB2","SMIM5","GALK1","SPHK1","USP36","RNF213","RP11-1055B8.7","OXLD1","ARL16","ARHGDIA","STRA13","RFNG","GPS1","C17orf62","FN3KRP","YES1","SMCHD1","RP13-270P17.3","RALBP1","VAPA","PSMG2","OSBPL1A","RNF125","ZNF397","INO80C","ATP5A1","CXXC1","NARS","MALT1","RP11-879F14.2","TMX3","NFATC1","RBCK1","RP11-314N13.3","SIRPG","SNRPB","ITPA","C20orf27","PRNP","PCNA","CRLS1","ANKEF1","MKKS","TASP1","SNX5","RIN2","NAA20","CD93","CST3","CST7","ABHD12","PLAGL2","SNTA1","NECAB3","PXMP4","RALY","PIGU","UQCC1","RBM39","AAR2","MYL9","RPN2","BLCAP","CTNNBL1","MAFB","SRSF6","TTPAL","PKIG","YWHAB","DNTTIP1","UBE2C","MMP9","LINC00494","STAU1","CEBPB","KCNG1","ATP9A","FAM210B","RTFDC1","ZBP1","PMEPA1","STX16","TUBB1","PSMA7","DIDO1","GID8","TPD52L2","TCEA2","RGS19","PRSS57","ELANE","POLR2E","ATP5D","C19orf24","MUM1","ATP8B3","PLEKHJ1","GADD45B","SLC39A3","NFIC","DOHH","TBXA2R","SIRT6","CCDC94","FEM1A","SAFB2","DUS3L","VMAC","ALKBH7","DENND1C","PCP2","RETN","MAP2K7","CD320","RAB11B","MARCH2","HNRNPM","ZNF559","ZNF561","CDC37","S1PR5","ILF3-AS1","ILF3","C19orf52","SMARCA4","TMEM205","ZNF653","ECSIT","ELOF1","ZNF69","ZNF799","FBXW9","HOOK2","RAD23A","IL27RA","SAMD1","PRKACA","ZNF333","AC004257.3","AKAP8","TPM4","FAM32A","CHERP","SMIM7","MYO9B","BABAM1","MVB12A","SLC27A1","COLGALT1","INSL3","CCDC124","IFI30","JUND","ELL","CRTC1","RFXANK","NR2C2AP","ZNF682","ZNF493","LINC00662","PLEKHF1","ANKRD27","LSM14A","PDCD2L","ARHGAP33","TYROBP","POLR2I","TBCB","AC092295.7","AC074138.3","ZNF567","PPP1R14A","C19orf33","KCNK6","RASGRP4","ACTN4","CAPN12","HNRNPL","MRPS12","SAMD4B","EID2","PSMC4","TMEM91","ATP5SL","CEACAM4","CD79A","CTC-378H22.1","ETHE1","ZNF404","ZNF45","TOMM40","RELB","PRKD2","BBC3","C5AR1","C5AR2","DHX34","NAPA-AS1","PLA2G4C","CYTH2","GYS1","TRPM4","CD37","FCGRT","PRRG2","IL4I1","SPIB","NKG7","ZNF175","SIGLEC14","FPR1","ZNF350","ZNF615","ZNF841","ZNF836","ZNF528","ZNF468","MYADM","OSCAR","PRPF31","MBOAT7","LILRA4","LAIR1","KIR2DL3","KIR3DL2","FCAR","PPP6R1","SUV420H2","ISOC2","ZNF628","CTD-2537I9.12","EPN1","AURKC","CTC-444N24.11","ZNF587B","ZNF256","CTD-2368P22.1","AC010642.1","EIF1AY","TPTEP1","CECR5","PEX26","MRPL40","CLDN5","SEPT5","ARVCF","PPIL2","IGLL5","DDT","GUCD1","EWSR1","GAS2L1","NEFH","ZMAT5","RFPL2","FBXO7","HMGXB4","EIF3D","PVALB","MPST","LGALS2","SH3BP1","LGALS1","ANKRD54","DDX17","APOBEC3A","APOBEC3B","APOBEC3G","RPS19BP1","ADSL","PHF5A","DESI1","WBP2NL","SMDT1","PACSIN2","PARVB","LDOC1L","PRR5","ATXN10","TTC38","CTA-29F11.1","CRELD2","LMF2","TYMP","RABL2B","SAMSN1","USP25","MAP3K7CL","BACH1","MIS18A","ATP5O","KCNE1","TTC3","DSCR3","BRWD1","BACE2","SIK1","C21orf33","ICOSLG","SUMO3","SLC19A1","S100B","PRMT2"
     // ]
     //
-    // let ideogram = Ideogram.initRelatedGenes(config, annotsInList)
+    let ideogram = Ideogram.initRelatedGenes(config, annotsInList)
 
-    let ideogram;
+    // let ideogram;
 
     // A switch to expose internal timing data, to aid performance engineering
     if ('debug' in urlParams) config.debug = true;
 
     if ('cold' in urlParams === false) {
       if ('q' in urlParams) {
-        ideogram = Ideogram.initRelatedGenes(config);
+        ideogram = Ideogram.initRelatedGenes(config, annotsInList);
       } else {
         config.legendName = 'Gene leads'
         // config.legendContent = ''
@@ -289,7 +290,7 @@ <h1>Gene Leads<small>Enrich your gene search</small></h1>
             ideogram = Ideogram.initGeneLeads(config);
             }
           } else {
-            ideogram = Ideogram.initRelatedGenes(config);
+            ideogram = Ideogram.initRelatedGenes(config, annotsInList);
           }
 
         } else {

src/js/annotations/draw.js

@@ -46,6 +46,11 @@ function drawAnnots(friendlyAnnots, layout, keep=false, isOtherLayout=false) {
     ideo = this,
     chrs = ideo.chromosomes[ideo.config.taxid]; // TODO: multiorganism
 
+  if (friendlyAnnots.length === 0) {
+    ideo.annots = [];
+    return;
+  }
+
   if (
     'annots' in friendlyAnnots[0] || // When filtering
     'values' in friendlyAnnots[0] // When drawing cached expression matrices

src/js/annotations/legend.js

@@ -52,7 +52,7 @@ function getListItems(labels, svg, list, nameHeight, ideo) {
 
   for (i = 0; i < list.rows.length; i++) {
     row = list.rows[i];
-    labels += '<li>' + row.name + '</li>';
+    labels += '<li class="_ideoLegendEntry">' + row.name + '</li>';
     y = lineHeight * (i - 1) + nameHeight + 1;
     if ('name' in list) y += lineHeight;
     icon = getIcon(row, ideo);
@@ -94,7 +94,8 @@ function writeLegend(ideo) {
         `left: -${nameHeight - 5}px;"`;
     }
     if ('name' in list) {
-      labels = `<div ${nameStyle}>` + list.name + `</div>`;
+      labels =
+        `<li class="_ideoLegendName" ${nameStyle}>` + list.name + `</li>`;
     }
     svg = '<svg id="_ideogramLegendSvg" width="' + lineHeight + '">';
     [labels, svg] = getListItems(labels, svg, list, nameHeight, ideo);

src/js/kit/protein-color.js

@@ -194,6 +194,7 @@ export function getColors(domainType) {
     domainType.includes('(G-protein), alpha subunit') ||
     domainType === 'SCAN domain' ||
     domainType === 'Apolipoprotein A/E' ||
+    domainType.includes('Clusterin') || // a.k.a. apolipoprotein J, e.g. CLU
     domainType.includes('SMAD domain') ||
     domainType === 'PLAC' ||
     domainType.endsWith('tripeptidyl peptidase II') ||
@@ -366,6 +367,7 @@ export function getColors(domainType) {
     domainType === 'Phosphopantetheine binding ACP domain' ||
     domainType === 'Multicopper oxidase, second cupredoxin domain' ||
     domainType === 'Helicase, C-terminal' ||
+    domainType.includes('Carboxylesterase') || // e.g. ACHE
     domainType.includes('presequence') || // e.g. ALAS2
     domainType.endsWith('CC3') // e.g. PRKDC
   ) {
@@ -588,6 +590,7 @@ export function getColors(domainType) {
     domainType.includes('TATA') ||
     domainType.includes('Citron') ||
     domainType === 'RIH domain' ||
+    domainType.toLowerCase().includes('sclerostin') || // e.g. SOSTDC1
     domainType === 'ZU5 domain' // e.g. TJP1
   ) {
     return [yellow, yellowLine];
@@ -601,6 +604,7 @@ export function getColors(domainType) {
     domainType === 'DIX domain' ||
     domainType === 'Ferritin-like diiron domain' ||
     domainType === '4Fe-4S dicluster domain' ||
+    domainType === 'Transferrin-like domain' || // iron-related, e.g. MELTF
     domainType === 'PAS domain' ||
     domainType === 'PAS fold' ||
     domainType === 'Polyketide synthase, dehydratase domain' ||
@@ -646,6 +650,7 @@ export function getColors(domainType) {
     domainType ===
       'VWF/SSPO/Zonadhesin-like, cysteine-rich domain' || // E.g. VWF
     domainType === 'Kappa casein' ||
+    domainType === 'Casein, alpha/beta' ||
     domainType === 'Natriuretic peptide' ||
     domainType === 'EMI domain' ||
     domainType === 'Neurohypophysial hormone' ||
@@ -696,6 +701,7 @@ export function getColors(domainType) {
     domainType.includes('Shisa') ||
     domainType === 'ABC-2 family transporter protein' ||
     domainType === 'Anoctamin' ||
+    domainType === 'Sodium-dependent phosphate transport protein' || // SLC34A2
     domainType.includes('MHC II-interacting') // e.g. CD74
   ) {
     return [darkBrown, darkBrownLine];
@@ -775,10 +781,12 @@ export function getColors(domainType) {
     domainType.endsWith('coiled-coil region') ||
     domainType.includes('zinc ribbon fold') ||
     domainType.includes('zinc-ribbon') ||
+    domainType.toLowerCase().includes('anhydrase') || // e.g. CA6
     domainType === 'Macroglobulin domain' ||
     domainType.includes('KH0') ||
     domainType.includes('EGF') ||
-    domainType.toLowerCase().includes('olfact')
+    domainType.toLowerCase().includes('olfact') ||
+    domainType.toLowerCase().includes('mucin') // e.g. CEL
   ) {
     return [seafoam, seafoamLine];
   } else if (
@@ -911,7 +919,8 @@ export function getColors(domainType) {
     domainType.toLowerCase().includes('decarboxylase') ||
     domainType.toLowerCase().includes('hydrolase') ||
     domainType.includes('PH domain') ||
-    domainType.includes('cytosolic')
+    domainType.includes('cytosolic') ||
+    domainType.toLowerCase().includes('homeobox')
   ) {
     return [lightBlue, lightBlueLine];
   }

src/js/kit/related-genes.js

@@ -75,10 +75,6 @@ function setRelatedAnnotDomIds(ideo) {
   // Arrange related annots by chromosome
   const annotsByChr = {};
   ideo.annots.forEach((annot) => {
-    // if (annot.chr in annotsByChr) {
-      // annotsByChr[annot.chr].push(annot);
-    // } else {
-
     const relevanceSortedAnnots = annot.annots.sort((a, b) => {
       return -ideo.annotSortFunction(a, b);
     });
@@ -110,6 +106,7 @@ function setRelatedAnnotDomIds(ideo) {
   Object.entries(annotsByChr).forEach(([chr, annots]) => {
     updatedAnnots[chr] = {chr, annots: []};
     annots.forEach((annot, annotIndex) => {
+
       // Annots have DOM IDs keyed by chromosome index and annotation index.
       // We reconstruct those here using structures built in two blocks above.
       const chrIndex = sortedChrNames.indexOf(chr);
@@ -666,6 +663,7 @@ async function fetchParalogPositionsFromMyGeneInfo(
 }
 
 function drawNeighborhoods(neighborhoodAnnots, ideo) {
+  neighborhoodAnnots = applyAnnotsIncludeList(neighborhoodAnnots, ideo);
   ideo.drawAnnots(neighborhoodAnnots, 'overlay', true, true);
   moveLegend(ideo);
 }
@@ -983,7 +981,8 @@ function initInteractiveLegend(ideo) {
   function dehighlight() {
     dehighlightAll(ideo);
   }
-  document.querySelectorAll('#_ideogramLegend li').forEach(li => {
+  const entrySelector = '#_ideogramLegend li._ideoLegendEntry';
+  document.querySelectorAll(entrySelector).forEach(li => {
     // li.addEventListener('click', toggleHighlight);
     // WIP: 14373b18319e99febd91816fbc0c1b2e0f20f277
     li.addEventListener('mouseenter', highlight);
@@ -1058,9 +1057,12 @@ function moveLegend(ideo, extraPad=0) {
   initInteractiveLegend(ideo);
 }
 
-/** Filter annotations to only include those in configured list */
+/**
+ * Filter annotations to only include those in configured list
+ *
+ * @return {List<Object>} includedAnnots List of filtered annots objects
+ */
 function applyAnnotsIncludeList(annots, ideo) {
-
   if (ideo.config.annotsInList === 'all') return annots;
 
   const includedAnnots = [];
@@ -1072,6 +1074,33 @@ function applyAnnotsIncludeList(annots, ideo) {
   return includedAnnots;
 }
 
+function filterByAnnotsIncludeList(annots, ideo) {
+  if (ideo.config.annotsInList === 'all') return annots;
+
+  const annotsInList = ideo.config.annotsInList;
+
+  const updated = [];
+  const updatedAnnots = {};
+  ideo.annots.forEach(chrAnnots => {
+    const {chr, annots} = chrAnnots;
+    updatedAnnots[chr] = {chr, annots: []};
+    annots.forEach((annot) => {
+
+      const lcAnnotName = annot.name.toLowerCase();
+      if (
+        'relatedAnnots' in ideo &&
+        !annotsInList.includes(lcAnnotName)
+      ) {
+        return;
+      }
+
+      updatedAnnots[chr].annots.push(annot);
+    });
+    updated.push(updatedAnnots[chr]);
+  });
+  return updated;
+}
+
 /** Fetch and draw interacting genes, return Promise for annots */
 function processInteractions(annot, ideo) {
   return new Promise(async (resolve) => {
@@ -1199,8 +1228,8 @@ function onBeforeDrawAnnots() {
   const ideo = this;
   setRelatedAnnotDomIds(ideo);
 
+  // Handle differential expression extension
   const chrAnnots = ideo.annots;
-
   for (let i = 0; i < chrAnnots.length; i++) {
     const annots = chrAnnots[i].annots;
 
@@ -1217,6 +1246,11 @@ function onBeforeDrawAnnots() {
   }
 }
 
+function filterAndDrawAnnots(annots, ideo) {
+  annots = applyAnnotsIncludeList(annots, ideo);
+  ideo.drawAnnots(annots);
+}
+
 /** Filter, sort, draw annots.  Move legend. */
 function finishPlotRelatedGenes(type, ideo) {
 
@@ -1228,7 +1262,7 @@ function finishPlotRelatedGenes(type, ideo) {
 
   annots = mergeAnnots(annots);
 
-  ideo.drawAnnots(annots);
+  filterAndDrawAnnots(annots, ideo);
 
   if (ideo.config.showAnnotLabels) {
     const sortedAnnots = ideo.flattenAnnots().sort((a, b) => {
@@ -1929,7 +1963,7 @@ function initSearchIdeogram(kitDefaults, config, annotsInList) {
   if (annotsInList !== 'all') {
     annotsInList = annotsInList.map(name => name.toLowerCase());
   }
-  kitDefaults.annotsInList = annotsInList;
+  config.annotsInList = annotsInList;
 
   kitDefaults.legendPad = kitDefaults.showAnnotLabels ? 80 : 30;
 
@@ -1998,7 +2032,7 @@ function initSearchIdeogram(kitDefaults, config, annotsInList) {
     ideogram.onPlotFoundGenesCallback = config.onPlotFoundGenes;
   }
 
-  // Called upon completing last plot, including all related genes
+  // Called upon hovering over a legend entry, e.g. "Interacting genes"
   if (config.onHoverLegend) {
     ideogram.onHoverLegendCallback = config.onHoverLegend;
   }

test/offline/core.test.js

@@ -166,10 +166,10 @@ describe('Ideogram', function() {
     function callback() {
       var numAnnots = document.getElementsByClassName('annot').length;
       assert.equal(numAnnots, 1000);
-      var numLegendRows = document.querySelectorAll('#_ideogramLegend li').length;
+      var numLegendRows = document.querySelectorAll('._ideoLegendEntry').length;
       assert.equal(numLegendRows, 3);
 
-      var legendNameDom = document.querySelector('#_ideogramLegend div');
+      var legendNameDom = document.querySelector('._ideoLegendName');
       const height = parseFloat(legendNameDom.style.height.replace('px', ''));
       const expectedHeight = 19.12;
       const heightDiff = Math.abs(expectedHeight - height);

test/offline/synteny.test.js

@@ -197,8 +197,8 @@ describe('Ideogram synteny support', function() {
       var numSyntenicRegions = document.getElementsByClassName('syntenicRegion').length;
       assert.equal(numSyntenicRegions, 25);
 
-      var srID = '#chr1-10090_54961724_56447175___chr2-10090_6000000_6500000';
-      var otherSrID = '#chr1-10090_54961724_56447175___chr2-10090_12000000_13000000';
+      var srID = '#chr1-10090_54516053_55989459___chr2-10090_6000000_6500000';
+      var otherSrID = '#chr1-10090_54516053_55989459___chr2-10090_12000000_13000000';
 
       var sr = d3.select(srID);
       var otherSr = d3.select(otherSrID);
@@ -209,6 +209,7 @@ describe('Ideogram synteny support', function() {
 
       sr.dispatch('click');
       var otherSrIsHidden = /hidden/.test(otherSr.nodes()[0].classList.value);
+
       assert.equal(otherSrIsHidden, true);
 
       done();

test/online/related-genes.test.js

@@ -357,6 +357,28 @@ describe('Ideogram related genes kit', function() {
     const ideogram = Ideogram.initRelatedGenes(config);
   });
 
+  // If an app only wants to render specific genes (per `annotsInList`),
+  // and more than those specific genes are found interacting or paralogous,
+  // then ensure Ideogram doesn't display the unspecified genes
+  it('can omit genes not in specified list', done => {
+
+    async function callback() {
+      await ideogram.plotRelatedGenes('CDK9');
+      const annots = document.querySelectorAll('.annot');
+      assert.equal(annots.length, 3);
+      done();
+    }
+
+    var config = {
+      organism: 'Homo sapiens',
+      onLoad: callback,
+      dataDir: '/dist/data/bands/native/'
+    };
+
+    const annotsInList = ['CDK9', 'CDK19', 'CDK1'];
+    const ideogram = Ideogram.initRelatedGenes(config, annotsInList);
+  });
+
   it('handles default display of highly cited genes', done => {
 
     function callback() {