react-mutation-mapper 0.8.57 → 0.8.58

package/dist/component/lollipopMutationPlot/AxisScaleSwitch.d.ts

@@ -0,0 +1,19 @@
+import * as React from 'react';
+interface IAxisScaleSwitchProps {
+    onChange: (selectedScale: AxisScale) => void;
+    selectedScale: AxisScale;
+}
+export declare enum AxisScale {
+    PERCENT = "%",
+    COUNT = "#"
+}
+export declare class AxisScaleSwitch extends React.Component<IAxisScaleSwitchProps, {}> {
+    static defaultProps: Partial<IAxisScaleSwitchProps>;
+    private selectedScale;
+    constructor(props: IAxisScaleSwitchProps);
+    toggleButton(scale: AxisScale, onClick: () => void): JSX.Element;
+    render(): JSX.Element;
+    private handlePercentClick;
+    private handleCountClick;
+}
+export {};

package/dist/component/lollipopMutationPlot/LollipopMutationPlot.d.ts

@@ -5,6 +5,7 @@ import { LollipopPlacement, LollipopSpec } from '../../model/LollipopSpec';
 import { MutationMapperStore } from '../../model/MutationMapperStore';
 import { TrackDataStatus, TrackName, TrackVisibility } from '../track/TrackSelector';
 import './lollipopMutationPlot.scss';
+import { AxisScale } from './AxisScaleSwitch';
 export declare type LollipopMutationPlotProps<T extends Mutation> = {
     store: MutationMapperStore<T>;
     controlsConfig?: LollipopPlotControlsConfig;
@@ -24,7 +25,9 @@ export declare type LollipopMutationPlotProps<T extends Mutation> = {
     bottomYAxisDefaultMax?: number;
     bottomYAxisDefaultMin?: number;
     yAxisLabelPadding?: number;
-    lollipopTooltipCountInfo?: (count: number, mutations?: Partial<T>[]) => JSX.Element;
+    lollipopTooltipCountInfo?: (count: number, mutations?: Partial<T>[], axisMode?: AxisScale) => JSX.Element;
+    yAxisLabelFormatter?: (symbol?: string, groupName?: string) => string;
+    axisMode?: AxisScale;
     customControls?: JSX.Element;
     onXAxisOffset?: (offset: number) => void;
     geneWidth: number;

package/dist/component/lollipopMutationPlot/LollipopTooltipCountInfo.d.ts

@@ -0,0 +1,10 @@
+import { Mutation } from 'cbioportal-ts-api-client';
+import * as React from 'react';
+import { AxisScale } from './AxisScaleSwitch';
+interface ILollipopTooltipCountInfoProps {
+    count: number;
+    mutations?: Mutation[];
+    axisMode?: AxisScale;
+}
+export declare const LollipopTooltipCountInfo: React.FC<ILollipopTooltipCountInfoProps>;
+export {};

package/dist/component/lollipopMutationPlot/PercentToggle.d.ts

@@ -0,0 +1,11 @@
+import * as React from 'react';
+import { AxisScale } from './AxisScaleSwitch';
+interface IPercentToggleProps {
+    axisMode?: AxisScale;
+    onScaleToggle?: (selectedScale: AxisScale) => void;
+}
+export declare class PercentToggle extends React.Component<IPercentToggleProps, {}> {
+    constructor(props: IPercentToggleProps);
+    render(): JSX.Element;
+}
+export {};

package/dist/component/lollipopPlot/LollipopPlot.d.ts

@@ -25,6 +25,7 @@ export declare type LollipopPlotProps = {
     hugoGeneSymbol?: string;
     dataStore?: DataStore;
     onXAxisOffset?: (offset: number) => void;
+    yAxisLabelFormatter?: (symbol?: string, groupName?: string) => string;
 };
 export default class LollipopPlot extends React.Component<LollipopPlotProps, {}> {
     private hitZoneConfig;

package/dist/index.d.ts

@@ -42,6 +42,9 @@ export { default as Domain } from './component/lollipopPlot/Domain';
 export { HotspotInfo } from './component/hotspot/HotspotInfo';
 export { default as Lollipop } from './component/lollipopPlot/Lollipop';
 export { default as LollipopMutationPlot } from './component/lollipopMutationPlot/LollipopMutationPlot';
+export * from './component/lollipopMutationPlot/PercentToggle';
+export * from './component/lollipopMutationPlot/AxisScaleSwitch';
+export * from './component/lollipopMutationPlot/LollipopTooltipCountInfo';
 export { default as LollipopPlot } from './component/lollipopPlot/LollipopPlot';
 export { default as LollipopPlotNoTooltip } from './component/lollipopPlot/LollipopPlotNoTooltip';
 export { default as Sequence } from './component/lollipopPlot/LollipopPlot';

package/dist/index.es.js

@@ -10,7 +10,7 @@ import { CIVIC_NA_VALUE, deriveStructuralVariantType, generateQueryStructuralVar
 import classnames from 'classnames';
 import autobind from 'autobind-decorator';
 import oncoKbLogoImgSrc from 'oncokb-styles/dist/images/logo/oncokb.svg';
-import { Tabs, Tab, Modal } from 'react-bootstrap';
+import { Tabs, Tab, Modal, ButtonGroup } from 'react-bootstrap';
 import { Collapse } from 'react-collapse';
 import ReactTable from 'react-table';
 import { If, Then, Else } from 'react-if';
@@ -6828,10 +6828,16 @@ 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.createElement(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 }));
         }
@@ -9512,7 +9518,7 @@ 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.createElement("strong", null,
+            var countInfo = this.props.lollipopTooltipCountInfo ? (this.props.lollipopTooltipCountInfo(count, mutationsAtPosition, this.props.axisMode)) : (React.createElement("strong", null,
                 count,
                 " mutation", "" + (count !== 1 ? 's' : '')));
             var label = lollipopLabelText(mutationsAtPosition);
@@ -9990,7 +9996,7 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
                     React.createElement(Collapse, { isOpened: this.controlsConfig.legendShown }, this.props.legend || React.createElement(DefaultLollipopPlotLegend, null)),
                     React.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.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 &&
@@ -10098,6 +10104,128 @@ var LollipopMutationPlot = /** @class */ (function (_super) {
     return LollipopMutationPlot;
 }(React.Component));
 
+var AxisScale;
+(function (AxisScale) {
+    AxisScale["PERCENT"] = "%";
+    AxisScale["COUNT"] = "#";
+})(AxisScale || (AxisScale = {}));
+var AxisScaleSwitch = /** @class */ (function (_super) {
+    __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;
+        makeObservable(_this);
+        return _this;
+    }
+    Object.defineProperty(AxisScaleSwitch.prototype, "toggleButton", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function (scale, onClick) {
+            return (React.createElement("button", { className: classnames({
+                    '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.createElement(ButtonGroup, { "aria-label": "" },
+                this.toggleButton(AxisScale.PERCENT, this.handlePercentClick),
+                this.toggleButton(AxisScale.COUNT, this.handleCountClick)));
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch.prototype, "handlePercentClick", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            this.selectedScale = AxisScale.PERCENT;
+            this.props.onChange(this.selectedScale);
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch.prototype, "handleCountClick", {
+        enumerable: false,
+        configurable: true,
+        writable: true,
+        value: function () {
+            this.selectedScale = AxisScale.COUNT;
+            this.props.onChange(this.selectedScale);
+        }
+    });
+    Object.defineProperty(AxisScaleSwitch, "defaultProps", {
+        enumerable: true,
+        configurable: true,
+        writable: true,
+        value: {
+            selectedScale: AxisScale.COUNT,
+        }
+    });
+    __decorate([
+        observable
+    ], AxisScaleSwitch.prototype, "selectedScale", void 0);
+    __decorate([
+        action.bound
+    ], AxisScaleSwitch.prototype, "handlePercentClick", null);
+    __decorate([
+        action.bound
+    ], AxisScaleSwitch.prototype, "handleCountClick", null);
+    AxisScaleSwitch = __decorate([
+        observer
+    ], AxisScaleSwitch);
+    return AxisScaleSwitch;
+}(React.Component));
+
+var PercentToggle = /** @class */ (function (_super) {
+    __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.createElement("div", { className: "small", style: { display: 'flex', alignItems: 'center' } },
+                React.createElement("span", { style: { marginLeft: 10, marginRight: 10 } },
+                    "Y-Axis:",
+                    ' '),
+                React.createElement(AxisScaleSwitch, { selectedScale: this.props.axisMode, onChange: this.props.onScaleToggle })));
+        }
+    });
+    return PercentToggle;
+}(React.Component));
+
+var LollipopTooltipCountInfo = function (_a) {
+    var count = _a.count, mutations = _a.mutations, axisMode = _a.axisMode;
+    var decimalZeros = numberOfLeadingDecimalZeros(count);
+    var fractionDigits = decimalZeros < 0 ? 1 : decimalZeros + 2;
+    return mutations &&
+        mutations.length > 0 &&
+        axisMode === AxisScale.PERCENT ? (React.createElement("strong", null,
+        formatPercentValue(count, fractionDigits),
+        "% mutation rate")) : (React.createElement("strong", null,
+        count,
+        " mutation", "" + (count !== 1 ? 's' : '')));
+};
+
 var DefaultStringQueryCache = /** @class */ (function () {
     function DefaultStringQueryCache() {
         Object.defineProperty(this, "_cache", {
@@ -12843,5 +12971,5 @@ var MutationMapper = /** @class */ (function (_super) {
     return MutationMapper;
 }(React.Component));
 
-export { Annotation, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download$7 as civicDownload, sortValue$8 as civicSortValue, download$4 as clinvarDownload, sortValue$3 as clinvarSortValue, download$3 as dbsnpDownload, sortValue$2 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSingleSignalValue, getTumorTypeNameWithExclusionInfo, getUrl, download$2 as gnomadDownload, sortValue$1 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$1 as hgvscDownload, sortValue as hgvscSortValue, sortValue$5 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$6 as myCancerGenomeDownload, sortValue$7 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$5 as oncoKbAnnotationDownload, sortValue$6 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
+export { Annotation, AxisScale, AxisScaleSwitch, BadgeLabel, BadgeSelector, Civic, ClinvarInterpretation, ClinvarSummary, ColumnHeader, ColumnSelector, ColumnSortDirection, DEFAULT_ANNOTATION_DATA, DEFAULT_GENOME_NEXUS_URL, DEFAULT_MUTATION_ALIGNER_PROXY_URL_TEMPLATE, DEFAULT_MUTATION_ALIGNER_URL_TEMPLATE, DEFAULT_MUTATION_COLUMNS, DEFAULT_MY_GENE_URL_TEMPLATE, DEFAULT_ONCO_KB_URL, DEFAULT_PROTEIN_IMPACT_TYPE_COLORS, DEFAULT_UNIPROT_ID_URL_TEMPLATE, DataFilterType, DataTable, Dbsnp, DbsnpId, DefaultMutationMapperDataFetcher, DefaultMutationMapperDataStore, DefaultMutationMapperFilterApplier, DefaultMutationMapperStore, DefaultMutationTable, Domain, DropdownSelector, FilterResetPanel, GenericAnnotation, Gnomad, GnomadFrequency, GnomadFrequencyBreakdown, GnomadFrequencyTable, GnomadFrequencyValue, Hgvsc, Hgvsg, HotspotAnnotation, HotspotInfo, Lollipop, LollipopMutationPlot, LollipopPlot, LollipopPlotNoTooltip, LollipopTooltipCountInfo, MSI_H_NAME, MUTATION_COLUMNS_DEFINITION, MUTATION_COLUMN_HEADERS, MUTATION_STATUS_BADGE_STYLE_OVERRIDE, MUTATION_TYPE_PRIORITY, MutationColumn, MutationColumnName, MutationMapper, MutationStatus, MutationStatusBadgeSelector, MyCancerGenome, ONCOKB_DEFAULT_DATA, ONCOKB_DEFAULT_INFO, OTHER_BIOMARKER_HUGO_SYMBOL, OTHER_BIOMARKER_NAME, OncoKB, OncoKBSuggestAnnotationLinkout, OncoKbFeedback, OncoKbHelper, OncoKbTooltip, OncoKbTreatmentTable, OtherBiomarkersQueryType, PercentToggle, ProteinChange, ProteinImpactTypeBadgeSelector, ProteinImpactTypeDropdownSelector, RefComponent, ReferenceList, LollipopPlot as Sequence, Signal, SignalTable, SummaryWithRefs, TEXT_INPUT_FILTER_ID, TMB_H_NAME, TrackName, TrackSelector, USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB, sortValue$4 as annotationSortValue, applyDataFilters, applyDataFiltersOnDatum, applyDefaultMutationFilter, applyDefaultMutationStatusFilter, applyDefaultPositionFilter, applyDefaultProteinImpactTypeFilter, calculateGnomadAlleleFrequency, download$7 as civicDownload, sortValue$8 as civicSortValue, download$4 as clinvarDownload, sortValue$3 as clinvarSortValue, download$3 as dbsnpDownload, sortValue$2 as dbsnpSortValue, defaultOncoKbFilter, errorIcon, fetchVariantAnnotationsByMutation, fetchVariantAnnotationsIndexedByGenomicLocation, findAllUniquePositions, findNonTextInputFilters, findOneMutationFilterValue, findTextInputFilter, getAllOptionValues, getAnnotationData, getClinvarData, getColorForProteinImpactType, getGnomadData, getHgvscColumnData, getHgvsgColumnData, getProteinImpactTypeBadgeLabel, getProteinImpactTypeOptionLabel, getSelectedOptionValues, getSignalData, getSingleSignalValue, getTumorTypeNameWithExclusionInfo, getUrl, download$2 as gnomadDownload, sortValue$1 as gnomadSortValue, groupDataByGroupFilters, groupDataByProteinImpactType, groupOncoKbIndicatorDataByMutations, handleOptionSelect, download$1 as hgvscDownload, sortValue as hgvscSortValue, sortValue$5 as hotspotAnnotationSortValue, includesSearchTextIgnoreCase, indexPositions, initDefaultMutationMapperStore, initDefaultTrackVisibility, initGenomeNexusClient, initGenomeNexusInternalClient, initOncoKbClient, levelIconClassNames, loaderIcon, mergeColumns, mutationTypeSort, download$6 as myCancerGenomeDownload, sortValue$7 as myCancerGenomeSortValue, normalizeLevel, onFilterOptionSelect, download$5 as oncoKbAnnotationDownload, sortValue$6 as oncoKbAnnotationSortValue, oncogenicityIconClassNames, proteinChangeSortMethod, rightAlignedCell, download as signalDownload, getSortValue as signalSortValue, updatePositionHighlightFilters, updatePositionRangeHighlightFilters, updatePositionSelectionFilters };
 //# sourceMappingURL=index.es.js.map