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Reduce label noise, omit accessions, fix search bug in Gene Hints #290

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merged 2 commits into from
Jan 5, 2022
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Reduce label noise, omit accessions, fix search bug in Gene Hints #290

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20a0121
Omit paralogs that are raw accessions
eweitz Jan 5, 2022
9a4252e
Reduce padding and # labels, fix search bug in Gene Hints
eweitz Jan 5, 2022
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4 changes: 2 additions & 2 deletions src/js/annotations/labels.js
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ function fillAnnotLabels(sortedAnnots=[]) {
sortedAnnots = ideo.flattenAnnots();
}

const m = 5; // padding
const m = 3; // padding

sortedAnnots.forEach((annot, i) => {
const layout = getAnnotLabelLayout(annot, ideo);
Expand Down Expand Up @@ -265,7 +265,7 @@ function fillAnnotLabels(sortedAnnots=[]) {
});


spacedAnnots = applyRankCutoff(spacedAnnots, 20, ideo);
spacedAnnots = applyRankCutoff(spacedAnnots, 10, ideo);

// Ensure highest-ranked annots are ordered last in SVG,
// to ensure the are written before lower-ranked annots
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11 changes: 10 additions & 1 deletion src/js/kit/related-genes.js
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Expand Up @@ -424,9 +424,16 @@ async function fetchParalogs(annot, ideo) {
const homologs = ensemblHomologs.data[0].homologies;

// Fetch positions of paralogs
const annots =
let annots =
await fetchParalogPositionsFromMyGeneInfo(homologs, annot, ideo);

// Omit genes named like "AC113554.1", which is an "accession.version".
// Such accVers are raw and poorly suited here.
annots = annots.filter(annot => {
const isAccVer = annot.name.match(/^AC[0-9.]+$/);
return !isAccVer;
});

return annots;
}

Expand Down Expand Up @@ -1040,6 +1047,8 @@ function _initGeneHints(config, annotsInList) {

initAnalyzeRelatedGenes(ideogram);

initGeneCache(ideogram.config.organism, ideogram);

return ideogram;
}

Expand Down