npm - oncoprintjs - Versions diffs - 5.0.3 → 6.0.1 - Mend

oncoprintjs 5.0.3 → 6.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (100) hide show

package/README.md +34 -0
package/dist/index.d.ts +4 -0
package/dist/index.es.js +14746 -0
package/dist/index.es.js.map +1 -0
package/dist/index.js +14760 -0
package/dist/index.js.map +1 -0
package/dist/js/CachedProperty.d.ts +10 -10
package/dist/js/binarysearch.d.ts +1 -1
package/dist/js/bucketsort.d.ts +16 -16
package/dist/js/clustering.d.ts +14 -14
package/dist/js/extractrgba.d.ts +4 -4
package/dist/js/haselementsininterval.d.ts +1 -1
package/dist/js/heatmapcolors.d.ts +5 -4
package/dist/js/makesvgelement.d.ts +1 -1
package/dist/js/modelutils.d.ts +7 -7
package/dist/js/oncoprint.d.ts +168 -170
package/dist/js/oncoprintheaderview.d.ts +23 -22
package/dist/js/oncoprintlabelview.d.ts +79 -78
package/dist/js/oncoprintlegendrenderer.d.ts +32 -31
package/dist/js/oncoprintminimapview.d.ts +69 -68
package/dist/js/oncoprintmodel.d.ts +403 -398
package/dist/js/oncoprintruleset.d.ts +176 -177
package/dist/js/oncoprintshape.d.ts +67 -67
package/dist/js/oncoprintshapetosvg.d.ts +2 -2
package/dist/js/oncoprintshapetovertexes.d.ts +5 -5
package/dist/js/oncoprinttooltip.d.ts +23 -22
package/dist/js/oncoprinttrackinfoview.d.ts +40 -39
package/dist/js/oncoprinttrackoptionsview.d.ts +58 -57
package/dist/js/oncoprintwebglcellview.d.ts +168 -167
package/dist/js/oncoprintzoomslider.d.ts +28 -27
package/dist/js/polyfill.d.ts +4 -4
package/dist/js/precomputedcomparator.d.ts +13 -13
package/dist/js/shaders.d.ts +2 -2
package/dist/js/svgfactory.d.ts +24 -23
package/dist/js/utils.d.ts +16 -16
package/dist/js/workers/clustering-worker.d.ts +19 -20
package/dist/test/gradientCategoricalRuleset.spec.d.ts +1 -1
package/dist/test/monolith.spec.d.ts +1 -1
package/jest.config.ts +2 -0
package/package.json +20 -26
package/rollup.config.ts +14 -0
package/rules/geneticrules.ts +344 -305
package/server.js +11 -0
package/src/img/menudots.svg +9 -9
package/src/img/zoomtofit.svg +12 -12
package/src/index.tsx +13 -0
package/src/js/CachedProperty.ts +6 -7
package/src/js/binarysearch.ts +8 -3
package/src/js/bucketsort.ts +89 -47
package/src/js/clustering.ts +22 -10
package/src/js/extractrgba.ts +16 -12
package/src/js/haselementsininterval.ts +8 -4
package/src/js/heatmapcolors.ts +515 -515
package/src/js/main.js +1 -1
package/src/js/makesvgelement.ts +2 -2
package/src/js/modelutils.ts +11 -8
package/src/js/oncoprint.ts +706 -385
package/src/js/oncoprintheaderview.ts +165 -125
package/src/js/oncoprintlabelview.ts +388 -170
package/src/js/oncoprintlegendrenderer.ts +203 -72
package/src/js/oncoprintminimapview.ts +965 -423
package/src/js/oncoprintmodel.ts +905 -532
package/src/js/oncoprintruleset.ts +694 -379
package/src/js/oncoprintshape.ts +240 -97
package/src/js/oncoprintshapetosvg.ts +77 -26
package/src/js/oncoprintshapetovertexes.ts +153 -48
package/src/js/oncoprinttooltip.ts +58 -27
package/src/js/oncoprinttrackinfoview.ts +115 -59
package/src/js/oncoprinttrackoptionsview.ts +354 -187
package/src/js/oncoprintwebglcellview.ts +951 -415
package/src/js/oncoprintzoomslider.ts +172 -107
package/src/js/polyfill.ts +7 -3
package/src/js/precomputedcomparator.ts +133 -50
package/src/js/shaders.ts +2 -4
package/src/js/svgfactory.ts +128 -73
package/src/js/utils.ts +51 -31
package/src/js/workers/clustering-worker.ts +50 -42
package/src/test/gradientCategoricalRuleset.spec.ts +55 -38
package/src/test/monolith.spec.ts +718 -285
package/test/generate_data.py +108 -0
package/test/glyphmap-data.js +1041 -0
package/test/heatmap-data.js +1027 -0
package/test/index.html +21 -0
package/test/oncoprint-glyphmap.js +79 -0
package/test/oncoprint-heatmap.js +123 -0
package/tsconfig.json +4 -10
package/tsconfig.test.json +11 -0
package/.idea/misc.xml +0 -6
package/.idea/modules.xml +0 -8
package/.idea/oncoprintjs.iml +0 -12
package/.idea/vcs.xml +0 -6
package/.idea/workspace.xml +0 -105
package/dist/.gitkeep +0 -0
package/dist/js/minimaputils.d.ts +0 -0
package/dist/oncoprint.bundle.js +0 -44313
package/jest.config.js +0 -12
package/src/js/minimaputils.ts +0 -0
package/typings/custom.d.ts +0 -7
package/typings/missing.d.ts +0 -7
package/webpack.config.js +0 -43

package/test/index.html ADDED Viewed

@@ -0,0 +1,21 @@
+<html>
+    <head>
+        <script
+            type="text/javascript"
+            src="https://code.jquery.com/jquery-1.11.3.js"
+        ></script>
+        <script type="text/javascript" src="./oncoprint-bundle.js"></script>
+        <script type="text/javascript" src="./geneticrules.js"></script>
+    </head>
+    <body>
+        <h2>Oncoprint Genomic Alterations</h2>
+        <div id="oncoprint-glyphmap"></div>
+        <h2>Oncoprint Heatmap</h2>
+        <div id="oncoprint-heatmap"></div>
+        <script type="text/javascript" src="./glyphmap-data.js"></script>
+        <script type="text/javascript" src="./oncoprint-glyphmap.js"></script>
+        <script type="text/javascript" src="./heatmap-data.js"></script>
+        <script type="text/javascript" src="./oncoprint-heatmap.js"></script>
+    </body>
+</html>

package/test/oncoprint-glyphmap.js ADDED Viewed

@@ -0,0 +1,79 @@
+$(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();
+});

package/test/oncoprint-heatmap.js ADDED Viewed

@@ -0,0 +1,123 @@
+$(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();
+});

package/tsconfig.json CHANGED Viewed

@@ -1,16 +1,10 @@
 {
+  "extends": "../config/tsconfig.json",
   "compilerOptions": {
-    "outDir": "./dist/",
-    "allowSyntheticDefaultImports": true,
-    "noImplicitAny": true,
-    "module": "es6",
-    "target": "es2015",
-    "declaration":true
+    "strictNullChecks": false
   },
-  "exclude": ["./node_modules/*"],
   "include": [
-    "./node_modules/@types/**/*",
-    "./typings/**/*",
-    "./src/**/*"
+    "src",
+    "../typings/**/*"
   ]
 }

package/tsconfig.test.json ADDED Viewed

@@ -0,0 +1,11 @@
+{
+  "extends": "../config/tsconfig.test.json",
+  "compilerOptions": {
+    "strictNullChecks": false
+  },
+  "include": [
+    "../typings/file.d.ts",
+    "../typings/missing.d.ts",
+    "../typings/worker.d.ts"
+  ]
+}

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@@ -1,6 +0,0 @@
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package/dist/js/minimaputils.d.ts DELETED Viewed

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