oncoprintjs/test/oncoprint-glyphmap.js

A data visualization for cancer genomic data.

$(document).ready(function() {
    var oncoprint = new window.Oncoprint('#oncoprint-glyphmap', 800);
    oncoprint.suppressRendering();

    function geneticComparator() {
        var cna_key = 'disp_cna';
        var cna_order = {
            amp: 0,
            homdel: 1,
            gain: 2,
            hetloss: 3,
            diploid: 4,
            undefined: 5,
        };
        var mut_type_key = 'disp_mut';
        var mut_order = {
            trunc: 0,
            inframe: 1,
            promoter: 2,
            missense: 3,
            undefined: 4,
        };
        var mrna_key = 'disp_mrna';
        var prot_key = 'disp_prot';
        var reg_order = { up: 0, down: 1, undefined: 2 };
        return function(d1, d2) {
            var keys = [cna_key, mut_type_key, mrna_key, prot_key];
            var orders = [cna_order, mut_order, reg_order, reg_order];
            var diff = 0;
            for (var i = 0; i < keys.length; i++) {
                var key = keys[i];
                var order = orders[i];
                if (d1[key] && d2[key]) {
                    diff = order[d1[key]] - order[d2[key]];
                } else if (d1[key]) {
                    diff = -1;
                } else if (d2[key]) {
                    diff = 1;
                }
            }
            return diff;
        };
    }

    var share_id = null;
    for (var i = 0; i < ga_data.length; i++) {
        var track_params = {
            rule_set_params:
                window.geneticrules
                    .genetic_rule_set_different_colors_no_recurrence,
            label: ga_data[i].gene,
            target_group: 0,
            sortCmpFn: geneticComparator(),
            description: ga_data[i].desc,
            na_z: 1.1,
        };
        var new_ga_id = oncoprint.addTracks([track_params])[0];
        ga_data[i].track_id = new_ga_id;
        if (i === 0) {
            share_id = new_ga_id;
        } else {
            oncoprint.shareRuleSet(share_id, new_ga_id);
        }
    }

    oncoprint.hideIds([], true);
    oncoprint.keepSorted(false);

    for (var i = 0; i < ga_data.length; i++) {
        oncoprint.setTrackData(ga_data[i].track_id, ga_data[i].data, 'sample');
        oncoprint.setTrackInfo(ga_data[i].track_id, '');
        oncoprint.setTrackTooltipFn(ga_data[i].track_id, function(data) {
            return '<b>Sample: ' + data.sample + '</b>';
        });
    }

    oncoprint.keepSorted(true);
    oncoprint.releaseRendering();
});