oncoprintjs/test/oncoprint-heatmap.js

A data visualization for cancer genomic data.

$(document).ready(function() {
    var oncoprint = new window.Oncoprint('#oncoprint-heatmap', 800);
    var TRACK_GROUP = 1;

    // hm_data is in heatmap-data.js

    var current_expansion_tracks = [];
    function makeExpandCallback(gene_id) {
        return function(parent_track_id) {
            oncoprint.suppressRendering();
            try {
                for (var i = 0; i < 3; i++) {
                    var track_params = {
                        rule_set_params: {
                            type: 'gradient',
                            legend_label: 'Expansion',
                            value_key: 'vaf',
                            value_range: [-3, 3],
                            colors: [
                                [0, 255, 255, 1],
                                [0, 0, 0, 1],
                                [255, 255, 0, 1],
                            ],
                            value_stop_points: [-3, 0, 3],
                            null_color: 'rgba(224,224,224,1)',
                        },
                        has_column_spacing: true,
                        track_padding: 5,
                        label: gene_id + 'abc'[i],
                        track_label_color: 'teal',
                        sortCmpFn: function(d1, d2) {
                            return 0;
                        },
                        target_group: TRACK_GROUP,
                        expansion_of: parent_track_id,
                        removable: true,
                        removeCallback: function(track_id) {
                            current_expansion_tracks.splice(
                                current_expansion_tracks.indexOf(track_id),
                                1
                            );
                        },
                    };
                    var new_track_id = oncoprint.addTracks([track_params])[0];
                    if (current_expansion_tracks.length > 0) {
                        oncoprint.shareRuleSet(
                            current_expansion_tracks[0],
                            new_track_id
                        );
                    }
                    current_expansion_tracks.push(new_track_id);
                    var data_record = hm_data.filter(function(record) {
                        return record.gene === gene_id;
                    })[0];
                    oncoprint.setTrackData(
                        new_track_id,
                        data_record.data,
                        'sample'
                    );
                }
            } finally {
                oncoprint.releaseRendering();
            }
        };
    }

    oncoprint.suppressRendering();

    var share_id = null;
    for (var i = 0; i < hm_data.length; i++) {
        var track_params = {
            rule_set_params: {
                type: 'gradient',
                legend_label: 'Heatmap',
                value_key: 'vaf',
                value_range: [-3, 3],
                colors: [
                    [255, 0, 0, 1],
                    [0, 0, 0, 1],
                    [0, 0, 255, 1],
                ],
                value_stop_points: [-3, 0, 3],
                null_color: 'rgba(224,224,224,1)',
            },
            has_column_spacing: true,
            track_padding: 5,
            label: hm_data[i].gene,
            sortCmpFn: function(d1, d2) {
                return 0;
            },
            target_group: TRACK_GROUP,
            expandCallback: makeExpandCallback(hm_data[i].gene),
            removable: true,
        };
        var new_hm_id = oncoprint.addTracks([track_params])[0];
        hm_data[i].track_id = new_hm_id;
        if (i === 0) {
            share_id = new_hm_id;
        } else {
            oncoprint.shareRuleSet(share_id, new_hm_id);
        }
    }

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

    for (var i = 0; i < hm_data.length; i++) {
        oncoprint.setTrackData(hm_data[i].track_id, hm_data[i].data, 'sample');
        oncoprint.setTrackInfo(hm_data[i].track_id, 'VAF');
        oncoprint.setTrackTooltipFn(hm_data[i].track_id, function(data) {
            return (
                '<b>Sample: ' +
                data.sample +
                '<br/>VAF: ' +
                data.vaf.toString().slice(0, 4) +
                '</b>'
            );
        });
    }

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