oncoprintjs 6.0.0 → 6.0.2

package/dist/js/oncoprintmodel.d.ts

@@ -42,6 +42,7 @@ export declare type ActiveRulesCount = {
     [ruleId: number]: number;
 };
 export declare type TrackSortDirectionChangeCallback = (track_id: TrackId, dir: number) => void;
+export declare type TrackGapChangeCallBack = (track_id: TrackId, on: boolean) => void;
 export declare type CustomTrackOption = {
     label?: string;
     separator?: boolean;
@@ -80,6 +81,7 @@ export declare type UserTrackSpec<D> = {
     sortCmpFn: TrackSortSpecification<D>;
     sort_direction_changeable?: boolean;
     onSortDirectionChange?: TrackSortDirectionChangeCallback;
+    onGapChange?: TrackGapChangeCallBack;
     init_sort_direction?: TrackSortDirection;
     data?: D[];
     rule_set_params?: RuleSetParams;
@@ -187,6 +189,7 @@ export default class OncoprintModel {
     private track_sort_direction_changeable;
     private track_sort_direction;
     private track_sort_direction_change_callback;
+    private track_gap_change_callback;
     private track_data;
     private track_rule_set_id;
     private track_active_rules;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "oncoprintjs",
-  "version": "6.0.0",
+  "version": "6.0.2",
   "description": "A data visualization for cancer genomic data.",
   "types": "./dist/js/oncoprint.d.ts",
   "main": "dist/index.js",
@@ -60,5 +60,5 @@
     "tayden-clusterfck": "^0.7.0",
     "typescript": "4.0.3"
   },
-  "gitHead": "acc9cbdbb6f3c83f854679e84c03555be10769d3"
+  "gitHead": "015e5bda995b7f5db563416c53b9320e0c9da3a8"
 }

package/rules/geneticrules.ts

@@ -15,7 +15,9 @@ export const MUT_COLOR_TRUNC = '#000000';
 export const MUT_COLOR_TRUNC_PASSENGER = '#708090';
 export const MUT_COLOR_FUSION = '#8B00C9';
 export const MUT_COLOR_PROMOTER = '#00B7CE';
+export const MUT_COLOR_PROMOTER_PASSENGER = '#8cedf9';
 export const MUT_COLOR_OTHER = '#cf58bc'; //'#cfb537';
+export const MUT_COLOR_OTHER_PASSENGER = '#f96ae3';
 
 export const MRNA_COLOR_HIGH = '#ff9999';
 export const MRNA_COLOR_LOW = '#6699cc';
@@ -63,8 +65,10 @@ enum ShapeId {
 
     missenseMutationDriverRectangle = 'missenseMutationDriverRectangle',
     missenseMutationVUSRectangle = 'missenseMutationVUSRectangle',
-    otherMutationRectangle = 'otherMutationRectangle',
-    promoterMutationRectangle = 'promoterMutationRectangle',
+    otherMutationDriverRectangle = 'otherMutationDriverRectangle',
+    otherMutationVUSRectangle = 'otherMutationVUSRectangle',
+    promoterMutationDriverRectangle = 'promoterMutationDriverRectangle',
+    promoterMutationVUSRectangle = 'promoterMutationVUSRectangle',
     truncatingMutationDriverRectangle = 'truncatingMutationDriverRectangle',
     truncatingMutationVUSRectangle = 'truncatingMutationVUSRectangle',
     inframeMutationDriverRectangle = 'inframeMutationDriverRectangle',
@@ -189,7 +193,7 @@ const shapeBank = {
         height: 33.33,
         z: 6,
     },
-    [ShapeId.otherMutationRectangle]: {
+    [ShapeId.otherMutationDriverRectangle]: {
         type: 'rectangle',
         fill: MUT_COLOR_OTHER,
         x: 0,
@@ -198,7 +202,16 @@ const shapeBank = {
         height: 33.33,
         z: 6,
     },
-    [ShapeId.promoterMutationRectangle]: {
+    [ShapeId.otherMutationVUSRectangle]: {
+        type: 'rectangle',
+        fill: MUT_COLOR_OTHER_PASSENGER,
+        x: 0,
+        y: 33.33,
+        width: 100,
+        height: 33.33,
+        z: 6,
+    },
+    [ShapeId.promoterMutationDriverRectangle]: {
         type: 'rectangle',
         fill: MUT_COLOR_PROMOTER,
         x: 0,
@@ -207,6 +220,15 @@ const shapeBank = {
         height: 33.33,
         z: 6,
     },
+    [ShapeId.promoterMutationVUSRectangle]: {
+        type: 'rectangle',
+        fill: MUT_COLOR_PROMOTER_PASSENGER,
+        x: 0,
+        y: 33.33,
+        width: 100,
+        height: 33.33,
+        z: 6,
+    },
     [ShapeId.truncatingMutationDriverRectangle]: {
         type: 'rectangle',
         fill: MUT_COLOR_TRUNC,
@@ -406,12 +428,16 @@ export const genetic_rule_set_different_colors_no_recurrence: IGeneticAlteration
             conditional: shallowExtend(non_mutation_rule_params.conditional, {
                 disp_mut: {
                     'other,other_rec': {
-                        shapes: [shapeBank[ShapeId.otherMutationRectangle]],
+                        shapes: [
+                            shapeBank[ShapeId.otherMutationDriverRectangle],
+                        ],
                         legend_label: 'Other Mutation',
                         legend_order: MUTATION_LEGEND_ORDER,
                     },
                     'promoter,promoter_rec': {
-                        shapes: [shapeBank[ShapeId.promoterMutationRectangle]],
+                        shapes: [
+                            shapeBank[ShapeId.promoterMutationDriverRectangle],
+                        ],
                         legend_label: 'Promoter Mutation',
                         legend_order: MUTATION_LEGEND_ORDER,
                     },
@@ -451,14 +477,31 @@ export const genetic_rule_set_different_colors_recurrence: IGeneticAlterationRul
             always: non_mutation_rule_params.always,
             conditional: shallowExtend(non_mutation_rule_params.conditional, {
                 disp_mut: {
-                    'other,other_rec': {
-                        shapes: [shapeBank[ShapeId.otherMutationRectangle]],
-                        legend_label: 'Other Mutation',
+                    other_rec: {
+                        shapes: [
+                            shapeBank[ShapeId.otherMutationDriverRectangle],
+                        ],
+                        legend_label: 'Other Mutation (putative driver)',
                         legend_order: MUTATION_LEGEND_ORDER,
                     },
-                    'promoter,promoter_rec': {
-                        shapes: [shapeBank[ShapeId.promoterMutationRectangle]],
-                        legend_label: 'Promoter Mutation',
+                    other: {
+                        shapes: [shapeBank[ShapeId.otherMutationVUSRectangle]],
+                        legend_label: 'Other Mutation (unknown significance)',
+                        legend_order: MUTATION_LEGEND_ORDER,
+                    },
+                    promoter_rec: {
+                        shapes: [
+                            shapeBank[ShapeId.promoterMutationDriverRectangle],
+                        ],
+                        legend_label: 'Promoter Mutation (putative driver)',
+                        legend_order: MUTATION_LEGEND_ORDER,
+                    },
+                    promoter: {
+                        shapes: [
+                            shapeBank[ShapeId.promoterMutationVUSRectangle],
+                        ],
+                        legend_label:
+                            'Promoter Mutation (unknown significance)',
                         legend_order: MUTATION_LEGEND_ORDER,
                     },
                     trunc_rec: {

package/src/js/oncoprintmodel.ts

@@ -61,6 +61,7 @@ export type TrackSortDirectionChangeCallback = (
     track_id: TrackId,
     dir: number
 ) => void;
+export type TrackGapChangeCallBack = (track_id: TrackId, on: boolean) => void;
 export type CustomTrackOption = {
     label?: string;
     separator?: boolean;
@@ -99,6 +100,7 @@ export type UserTrackSpec<D> = {
     sortCmpFn: TrackSortSpecification<D>;
     sort_direction_changeable?: boolean;
     onSortDirectionChange?: TrackSortDirectionChangeCallback;
+    onGapChange?: TrackGapChangeCallBack;
     init_sort_direction?: TrackSortDirection;
     data?: D[];
     rule_set_params?: RuleSetParams;
@@ -288,6 +290,7 @@ export default class OncoprintModel {
     private track_sort_direction_change_callback: TrackProp<
         TrackSortDirectionChangeCallback
     >;
+    private track_gap_change_callback: TrackProp<TrackGapChangeCallBack>;
     private track_data: TrackProp<Datum[]>;
     private track_rule_set_id: TrackProp<RuleSetId>;
     private track_active_rules: TrackProp<ActiveRules>;
@@ -391,6 +394,7 @@ export default class OncoprintModel {
         this.track_sort_direction_changeable = {};
         this.track_sort_direction = {}; // 1: ascending, -1: descending, 0: not
         this.track_sort_direction_change_callback = {};
+        this.track_gap_change_callback = {};
         this.track_data = {};
         this.track_rule_set_id = {}; // track id -> rule set id
         this.track_active_rules = {}; // from track id to active rule map (map with rule ids as keys)
@@ -662,7 +666,7 @@ export default class OncoprintModel {
 
     public setTrackShowGaps(trackId: TrackId, show: boolean) {
         this.track_show_gaps[trackId] = show;
-
+        this.track_gap_change_callback[trackId](trackId, show);
         this.ids_after_a_gap.update(this);
     }
 
@@ -1334,14 +1338,22 @@ export default class OncoprintModel {
                 params.expandButtonTextGetter;
         }
 
+        this.track_sort_direction[track_id] = ifndef(
+            params.init_sort_direction,
+            1
+        );
+
         this.track_can_show_gaps[track_id] = ifndef(
             params.track_can_show_gaps,
             false
         );
-        this.track_show_gaps[track_id] = ifndef(
-            params.show_gaps_on_init,
-            false
-        );
+
+        const trackShowGaps = ifndef(params.show_gaps_on_init, false);
+        this.track_show_gaps[track_id] = trackShowGaps;
+        const trackNotSorted = this.track_sort_direction[track_id] === 0;
+        if (trackShowGaps && trackNotSorted) {
+            this.track_sort_direction[track_id] = 1;
+        }
 
         this.track_sort_cmp_fn[track_id] = params.sortCmpFn;
 
@@ -1352,6 +1364,10 @@ export default class OncoprintModel {
         this.track_sort_direction_change_callback[
             track_id
         ] = ifndef(params.onSortDirectionChange, function() {});
+        this.track_gap_change_callback[track_id] = ifndef(
+            params.onGapChange,
+            function() {}
+        );
         this.track_data[track_id] = ifndef(params.data, []);
         this.track_data_id_key[track_id] = ifndef(params.data_id_key, 'id');
 
@@ -1372,11 +1388,6 @@ export default class OncoprintModel {
             this.setTrackImportantIds(track_id, params.important_ids);
         }
 
-        this.track_sort_direction[track_id] = ifndef(
-            params.init_sort_direction,
-            1
-        );
-
         params.target_group = ifndef(params.target_group, 0);
         this.ensureTrackGroupExists(params.target_group);
 

package/src/js/oncoprinttrackoptionsview.ts

@@ -571,6 +571,7 @@ export default class OncoprintTrackOptionsView {
         this.resize(model, getCellViewHeight);
     }
     public addTracks(model: OncoprintModel, getCellViewHeight: () => number) {
+        this.setTrackShowGaps(model, getCellViewHeight);
         this.renderAllOptions(model);
         this.resize(model, getCellViewHeight);
     }