react-mutation-mapper 0.8.57 → 0.8.59

package/dist/index.js

@@ -6865,10 +6865,16 @@ var LollipopPlotNoTooltip = /** @class */ (function (_super) {
         writable: true,
         value: function (y, yMax, ticks, placement, groupName, symbol) {
             if (symbol === void 0) { symbol = '#'; }
-            var label = groupName
-                ? symbol + " " + (this.props.hugoGeneSymbol ||
-                    '') + " " + groupName + " Mutations"
-                : symbol + " " + (this.props.hugoGeneSymbol || '') + " Mutations";
+            var label;
+            if (this.props.yAxisLabelFormatter) {
+                label = this.props.yAxisLabelFormatter(symbol, groupName);
+            }
+            else {
+                label = groupName
+                    ? symbol + " " + (this.props.hugoGeneSymbol ||
+                        '') + " " + groupName + " Mutations"
+                    : symbol + " " + (this.props.hugoGeneSymbol || '') + " Mutations";
+            }
             var placeOnBottom = placement === LollipopPlacement.BOTTOM;
             return (React__namespace.createElement(cbioportalFrontendCommons.SVGAxis, { key: "lollipopPlotYAxis_" + (placeOnBottom ? 'bottom' : 'top'), x: this.geneX - this.yAxisPadding, y: y, length: this.yAxisHeight, tickLength: 7, rangeLower: 0, rangeUpper: yMax, ticks: ticks, vertical: true, verticalLabelPadding: this.props.yAxisLabelPadding, reverse: placeOnBottom, label: label }));
         }
@@ -9549,7 +9555,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
         value: function (mutationsAtPosition, countsByPosition) {
             var codon = mutationsAtPosition[0].proteinPosStart;
             var count = countsByPosition[codon];
-            var countInfo = this.props.lollipopTooltipCountInfo ? (this.props.lollipopTooltipCountInfo(count, mutationsAtPosition)) : (React__namespace.createElement("strong", null,
+            var countInfo = this.props.lollipopTooltipCountInfo ? (this.props.lollipopTooltipCountInfo(count, mutationsAtPosition, this.props.axisMode)) : (React__namespace.createElement("strong", null,
                 count,
                 " mutation", "" + (count !== 1 ? 's' : '')));
             var label = lollipopLabelText(mutationsAtPosition);
@@ -10027,7 +10033,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
                     React__namespace.createElement(reactCollapse.Collapse, { isOpened: this.controlsConfig.legendShown }, this.props.legend || React__namespace.createElement(DefaultLollipopPlotLegend, null)),
                     React__namespace.createElement(LollipopPlot, { sequence: this.sequence, lollipops: this.lollipops, domains: this.domains, dataStore: this.props.store.dataStore, vizWidth: this.props.geneWidth, vizHeight: this.props.vizHeight, hugoGeneSymbol: this.hugoGeneSymbol, xMax: this.proteinLength, yMax: this.yMaxInput, yMaxFractionDigits: this.yMaxSliderStep < 1
                             ? this.props.yMaxFractionDigits
-                            : undefined, yMaxLabelPostfix: this.props.yMaxLabelPostfix, yAxisLabelPadding: this.props.yAxisLabelPadding, showYAxis: this.props.showYAxis, bottomYMax: this.bottomYMaxInput, onXAxisOffset: this.onXAxisOffset, topYAxisSymbol: this.props.topYAxisSymbol, bottomYAxisSymbol: this.props.bottomYAxisSymbol, groups: this.groups }),
+                            : undefined, yMaxLabelPostfix: this.props.yMaxLabelPostfix, yAxisLabelPadding: this.props.yAxisLabelPadding, showYAxis: this.props.showYAxis, bottomYMax: this.bottomYMaxInput, onXAxisOffset: this.onXAxisOffset, topYAxisSymbol: this.props.topYAxisSymbol, bottomYAxisSymbol: this.props.bottomYAxisSymbol, groups: this.groups, yAxisLabelFormatter: this.props.yAxisLabelFormatter }),
                     React__namespace.createElement(TrackPanel, { store: this.props.store, geneWidth: this.props.geneWidth, tracks: this.props.tracks, trackVisibility: this.trackVisibility, pubMedCache: this.props.pubMedCache, proteinLength: this.proteinLength, geneXOffset: this.geneXOffset, collapsePtmTrack: this.props.collapsePtmTrack, collapseUniprotTopologyTrack: this.props.collapseUniprotTopologyTrack })));
             }
             else if (this.props.store.canonicalTranscript.isComplete &&
@@ -10135,6 +10141,128 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
     return LollipopMutationPlot;
 }(React__namespace.Component));
 
+exports.AxisScale = void 0;
+(function (AxisScale) {
+    AxisScale["PERCENT"] = "%";
+    AxisScale["COUNT"] = "#";
+})(exports.AxisScale || (exports.AxisScale = {}));
+var AxisScaleSwitch = /** @class */ (function (_super) {
+    tslib.__extends(AxisScaleSwitch, _super);
+    function AxisScaleSwitch(props) {
+        var _this = _super.call(this, props) || this;
+        Object.defineProperty(_this, "selectedScale", {
+            enumerable: true,
+            configurable: true,
+            writable: true,
+            value: void 0
+        });
+        _this.selectedScale = props.selectedScale;
+        mobx.makeObservable(_this);
+        return _this;
+    }
+    Object.defineProperty(AxisScaleSwitch.prototype, "toggleButton", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function (scale, onClick) {
+            return (React__namespace.createElement("button", { className: classnames__default["default"]({
+                    'btn-secondary': this.props.selectedScale === scale,
+                    'btn-outline-secondary': this.props.selectedScale !== scale,
+                }, 'btn', 'btn-sm', 'btn-axis-switch'), style: {
+                    lineHeight: 1,
+                    cursor: this.props.selectedScale === scale
+                        ? 'default'
+                        : 'pointer',
+                    fontWeight: this.props.selectedScale === scale
+                        ? 'bolder'
+                        : 'normal',
+                }, onClick: onClick }, scale));
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch.prototype, "render", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            return (React__namespace.createElement(reactBootstrap.ButtonGroup, { "aria-label": "" },
+                this.toggleButton(exports.AxisScale.PERCENT, this.handlePercentClick),
+                this.toggleButton(exports.AxisScale.COUNT, this.handleCountClick)));
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch.prototype, "handlePercentClick", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            this.selectedScale = exports.AxisScale.PERCENT;
+            this.props.onChange(this.selectedScale);
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch.prototype, "handleCountClick", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            this.selectedScale = exports.AxisScale.COUNT;
+            this.props.onChange(this.selectedScale);
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch, "defaultProps", {
+        enumerable: true,
+        configurable: true,
+        writable: true,
+        value: {
+            selectedScale: exports.AxisScale.COUNT,
+        }
+    });
+    tslib.__decorate([
+        mobx.observable
+    ], AxisScaleSwitch.prototype, "selectedScale", void 0);
+    tslib.__decorate([
+        mobx.action.bound
+    ], AxisScaleSwitch.prototype, "handlePercentClick", null);
+    tslib.__decorate([
+        mobx.action.bound
+    ], AxisScaleSwitch.prototype, "handleCountClick", null);
+    AxisScaleSwitch = tslib.__decorate([
+        mobxReact.observer
+    ], AxisScaleSwitch);
+    return AxisScaleSwitch;
+}(React__namespace.Component));
+
+var PercentToggle = /** @class */ (function (_super) {
+    tslib.__extends(PercentToggle, _super);
+    function PercentToggle(props) {
+        return _super.call(this, props) || this;
+    }
+    Object.defineProperty(PercentToggle.prototype, "render", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            return (React__namespace.createElement("div", { className: "small", style: { display: 'flex', alignItems: 'center' } },
+                React__namespace.createElement("span", { style: { marginLeft: 10, marginRight: 10 } },
+                    "Y-Axis:",
+                    ' '),
+                React__namespace.createElement(AxisScaleSwitch, { selectedScale: this.props.axisMode, onChange: this.props.onScaleToggle })));
+        }
+    });
+    return PercentToggle;
+}(React__namespace.Component));
+
+var LollipopTooltipCountInfo = function (_a) {
+    var count = _a.count, mutations = _a.mutations, axisMode = _a.axisMode;
+    var decimalZeros = cbioportalUtils.numberOfLeadingDecimalZeros(count);
+    var fractionDigits = decimalZeros < 0 ? 1 : decimalZeros + 2;
+    return mutations &&
+        mutations.length > 0 &&
+        axisMode === exports.AxisScale.PERCENT ? (React__namespace.createElement("strong", null,
+        cbioportalUtils.formatPercentValue(count, fractionDigits),
+        "% mutation rate")) : (React__namespace.createElement("strong", null,
+        count,
+        " mutation", "" + (count !== 1 ? 's' : '')));
+};
+
 var DefaultStringQueryCache = /** @class */ (function () {
     function DefaultStringQueryCache() {
         Object.defineProperty(this, "_cache", {
@@ -11968,7 +12096,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
             var _this = this;
             return this.groupedMutationsByPosition.map(function (groupedMutations) { return ({
                 group: groupedMutations.group,
-                counts: _this.countUniqueMutationsByPosition(groupedMutations.mutations),
+                counts: _this.countUniqueMutationsByPosition(groupedMutations.mutations, groupedMutations.group),
             }); });
         },
         enumerable: false,
@@ -11985,7 +12113,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
         enumerable: false,
         configurable: true,
         writable: true,
-        value: function (mutationsByPosition) {
+        value: function (mutationsByPosition, group) {
             var _this = this;
             var map = {};
             Object.keys(mutationsByPosition).forEach(function (pos) {
@@ -11993,7 +12121,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
                 // for each position multiple mutations for the same patient is counted only once
                 var mutations = mutationsByPosition[position];
                 if (mutations) {
-                    map[position] = _this.countUniqueMutations(mutations);
+                    map[position] = _this.countUniqueMutations(mutations, group);
                 }
             });
             return map;
@@ -12003,7 +12131,7 @@ var DefaultMutationMapperStore = /** @class */ (function () {
         enumerable: false,
         configurable: true,
         writable: true,
-        value: function (mutations) {
+        value: function (mutations, group) {
             // assume by default all mutations are unique
             // child classes need to override this method to have a custom way of counting unique mutations
             return this.config.getMutationCount
@@ -12881,6 +13009,7 @@ var MutationMapper = /** @class */ (function (_super) {
 }(React__namespace.Component));
 
 exports.Annotation = Annotation;
+exports.AxisScaleSwitch = AxisScaleSwitch;
 exports.BadgeLabel = BadgeLabel;
 exports.BadgeSelector = BadgeSelector;
 exports.Civic = Civic;
@@ -12922,6 +13051,7 @@ exports.Lollipop = Lollipop;
 exports.LollipopMutationPlot = LollipopMutationPlot;
 exports.LollipopPlot = LollipopPlot;
 exports.LollipopPlotNoTooltip = LollipopPlotNoTooltip;
+exports.LollipopTooltipCountInfo = LollipopTooltipCountInfo;
 exports.MSI_H_NAME = MSI_H_NAME;
 exports.MUTATION_COLUMNS_DEFINITION = MUTATION_COLUMNS_DEFINITION;
 exports.MUTATION_COLUMN_HEADERS = MUTATION_COLUMN_HEADERS;
@@ -12941,6 +13071,7 @@ exports.OncoKbFeedback = OncoKbFeedback;
 exports.OncoKbHelper = OncoKbHelper;
 exports.OncoKbTooltip = OncoKbTooltip;
 exports.OncoKbTreatmentTable = OncoKbTreatmentTable;
+exports.PercentToggle = PercentToggle;
 exports.ProteinChange = ProteinChange;
 exports.ProteinImpactTypeBadgeSelector = ProteinImpactTypeBadgeSelector;
 exports.ProteinImpactTypeDropdownSelector = ProteinImpactTypeDropdownSelector;