@genspectrum/dashboard-components 0.11.0 → 0.11.2

package/dist/style.css

@@ -2684,6 +2684,9 @@ input.tab:checked + .tab-content,
   border-end-end-radius: inherit;
   border-start-end-radius: inherit;
 }
+.modal-middle {
+  place-items: center;
+}
 .modal-bottom {
   place-items: end;
 }
@@ -2957,6 +2960,9 @@ input.tab:checked + .tab-content,
 .-top-3 {
   top: -0.75rem;
 }
+.bottom-0 {
+  bottom: 0px;
+}
 .bottom-full {
   bottom: 100%;
 }
@@ -2993,6 +2999,9 @@ input.tab:checked + .tab-content,
 .z-10 {
   z-index: 10;
 }
+.z-\[1001\] {
+  z-index: 1001;
+}
 .float-right {
   float: right;
 }
@@ -3122,6 +3131,9 @@ input.tab:checked + .tab-content,
 .min-w-\[7\.5rem\] {
   min-width: 7.5rem;
 }
+.max-w-3xl {
+  max-width: 48rem;
+}
 .max-w-screen-lg {
   max-width: 1024px;
 }
@@ -3199,6 +3211,9 @@ input.tab:checked + .tab-content,
 .break-words {
   overflow-wrap: break-word;
 }
+.rounded {
+  border-radius: 0.25rem;
+}
 .rounded-lg {
   border-radius: 0.5rem;
 }
@@ -3272,6 +3287,10 @@ input.tab:checked + .tab-content,
 .p-4 {
   padding: 1rem;
 }
+.px-1 {
+  padding-left: 0.25rem;
+  padding-right: 0.25rem;
+}
 .px-4 {
   padding-left: 1rem;
   padding-right: 1rem;

package/dist/util.d.ts

@@ -157,6 +157,22 @@ declare const lapisFilterSchema: default_2.ZodIntersection<default_2.ZodRecord<d
     aminoAcidInsertions?: string[] | undefined;
 }>>;
 
+export declare type MapSource = default_2.infer<typeof mapSourceSchema>;
+
+declare const mapSourceSchema: default_2.ZodObject<{
+    type: default_2.ZodLiteral<"topojson">;
+    url: default_2.ZodString;
+    topologyObjectsKey: default_2.ZodString;
+}, "strip", default_2.ZodTypeAny, {
+    type: "topojson";
+    url: string;
+    topologyObjectsKey: string;
+}, {
+    type: "topojson";
+    url: string;
+    topologyObjectsKey: string;
+}>;
+
 export declare type MutationComparisonProps = default_2.infer<typeof mutationComparisonPropsSchema>;
 
 declare const mutationComparisonPropsSchema: default_2.ZodObject<{
@@ -835,7 +851,7 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-number-sequences-over-time': NumberSequencesOverTimeComponent;
+        'gs-aggregate': AggregateComponent;
     }
 }
 
@@ -843,7 +859,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-number-sequences-over-time': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-aggregate': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }
@@ -851,7 +867,7 @@ declare global {
 
 declare global {
     interface HTMLElementTagNameMap {
-        'gs-aggregate': AggregateComponent;
+        'gs-number-sequences-over-time': NumberSequencesOverTimeComponent;
     }
 }
 
@@ -859,7 +875,7 @@ declare global {
 declare global {
     namespace JSX {
         interface IntrinsicElements {
-            'gs-aggregate': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
+            'gs-number-sequences-over-time': DetailedHTMLProps<HTMLAttributes<HTMLElement>, HTMLElement>;
         }
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@genspectrum/dashboard-components",
-    "version": "0.11.0",
+    "version": "0.11.2",
     "description": "GenSpectrum web components for building dashboards",
     "type": "module",
     "license": "AGPL-3.0-only",

package/src/preact/map/sequences-by-location-map.tsx

@@ -1,10 +1,11 @@
 import type { Feature, FeatureCollection, GeometryObject } from 'geojson';
 import Leaflet, { type Layer, type LayerGroup } from 'leaflet';
 import type { FunctionComponent } from 'preact';
-import { useEffect, useRef } from 'preact/hooks';
+import { useEffect, useMemo, useRef } from 'preact/hooks';
 
 import { type GeoJsonFeatureProperties, type MapSource, useGeoJsonMap } from './useGeoJsonMap';
 import { type AggregateData } from '../../query/queryAggregateData';
+import { InfoHeadline1, InfoParagraph } from '../components/info';
 import { LoadingDisplay } from '../components/loading-display';
 import { formatProportion } from '../shared/table/formatProportion';
 
@@ -22,6 +23,7 @@ type SequencesByLocationMapProps = {
     zoom: number;
     offsetX: number;
     offsetY: number;
+    hasTableView: boolean;
 };
 
 export const SequencesByLocationMap: FunctionComponent<SequencesByLocationMapProps> = ({
@@ -49,21 +51,31 @@ export const SequencesByLocationMapInner: FunctionComponent<SequencesByLocationM
     zoom,
     offsetX,
     offsetY,
+    hasTableView,
 }) => {
     const ref = useRef<HTMLDivElement>(null);
 
-    useEffect(() => {
-        if (!ref.current || geojsonData === undefined || locationData === undefined) {
-            return;
-        }
-
+    const { locations, totalCount, countOfMatchedLocationData, unmatchedLocations } = useMemo(() => {
         const countAndProportionByCountry = buildLookupByLocationField(locationData, lapisLocationField);
-        const locations = matchLocationDataAndGeoJsonFeatures(
+        const { locations, unmatchedLocations } = matchLocationDataAndGeoJsonFeatures(
             geojsonData,
             countAndProportionByCountry,
             lapisLocationField,
         );
 
+        const totalCount = locationData.map((value) => value.count).reduce((sum, b) => sum + b, 0);
+        const countOfMatchedLocationData = locations
+            .map((location) => location.properties.data?.count ?? 0)
+            .reduce((sum, b) => sum + b, 0);
+
+        return { locations, totalCount, countOfMatchedLocationData, unmatchedLocations };
+    }, [geojsonData, locationData, lapisLocationField]);
+
+    useEffect(() => {
+        if (!ref.current) {
+            return;
+        }
+
         const leafletMap = Leaflet.map(ref.current, {
             scrollWheelZoom: enableMapNavigation,
             zoomControl: enableMapNavigation,
@@ -88,9 +100,85 @@ export const SequencesByLocationMapInner: FunctionComponent<SequencesByLocationM
         return () => {
             leafletMap.remove();
         };
-    }, [ref, locationData, geojsonData, enableMapNavigation, lapisLocationField, zoom, offsetX, offsetY]);
+    }, [ref, locations, enableMapNavigation, lapisLocationField, zoom, offsetX, offsetY]);
 
-    return <div ref={ref} className='h-full' />;
+    const nullCount = locationData.find((row) => row[lapisLocationField] === null)?.count ?? 0;
+
+    return (
+        <div className='h-full'>
+            <div ref={ref} className='h-full' />
+            <div className='relative'>
+                <DataMatchInformation
+                    totalCount={totalCount}
+                    countOfMatchedLocationData={countOfMatchedLocationData}
+                    unmatchedLocations={unmatchedLocations}
+                    nullCount={nullCount}
+                    hasTableView={hasTableView}
+                />
+            </div>
+        </div>
+    );
+};
+
+type DataMatchInformationProps = {
+    totalCount: number;
+    countOfMatchedLocationData: number;
+    unmatchedLocations: string[];
+    nullCount: number;
+    hasTableView: boolean;
+};
+
+const DataMatchInformation: FunctionComponent<DataMatchInformationProps> = ({
+    totalCount,
+    countOfMatchedLocationData,
+    unmatchedLocations,
+    nullCount,
+    hasTableView,
+}) => {
+    const dialogRef = useRef<HTMLDialogElement>(null);
+
+    const proportion = formatProportion(countOfMatchedLocationData / totalCount);
+
+    return (
+        <>
+            <button
+                onClick={() => dialogRef.current?.showModal()}
+                className='text-sm absolute bottom-0 px-1 z-[1001] bg-white rounded border cursor-pointer tooltip'
+                data-tip='Click for detailed information'
+            >
+                This map shows {proportion} of the data.
+            </button>
+            <dialog ref={dialogRef} className={'modal modal-middle'}>
+                <div className='modal-box max-w-3xl'>
+                    <InfoHeadline1>Sequences By Location - Map View</InfoHeadline1>
+                    <InfoParagraph>
+                        The current filter has matched {totalCount.toLocaleString('en-us')} sequences. From these
+                        sequences, we were able to match {countOfMatchedLocationData.toLocaleString('en-us')} (
+                        {proportion}) on locations on the map.
+                    </InfoParagraph>
+                    <InfoParagraph>
+                        {unmatchedLocations.length > 0 && (
+                            <>
+                                The following locations from the data could not be matched on the map:{' '}
+                                {unmatchedLocations.map((it) => `"${it}"`).join(', ')}.{' '}
+                            </>
+                        )}
+                        {nullCount > 0 &&
+                            `${nullCount.toLocaleString('en-us')} matching sequences have no location information. `}
+                        {hasTableView && 'You can check the table view for more detailed information.'}
+                    </InfoParagraph>
+                    <div className='modal-action'>
+                        <form method='dialog'>
+                            <button className={'float-right underline text-sm hover:text-blue-700 mr-2'}>Close</button>
+                        </form>
+                    </div>
+                </div>
+                <form method='dialog' className='modal-backdrop'>
+                    <button>Helper to close when clicked outside</button>
+                </form>
+            </dialog>
+        </>
+    );
 };
 
 function buildLookupByLocationField(locationData: AggregateData, lapisLocationField: string) {
@@ -139,7 +227,7 @@ function matchLocationDataAndGeoJsonFeatures(
         console.warn(unmatchedLocationsWarning); // eslint-disable-line no-console -- We should give some feedback about unmatched location data.
     }
 
-    return locations;
+    return { locations, unmatchedLocations };
 }
 
 function getColor(value: number | undefined): string {

package/src/preact/map/sequences-by-location.tsx

@@ -98,6 +98,7 @@ const SequencesByLocationMapTabs: FunctionComponent<SequencesByLocationMapTabsPr
                             zoom={originalComponentProps.zoom}
                             offsetX={originalComponentProps.offsetX}
                             offsetY={originalComponentProps.offsetY}
+                            hasTableView={originalComponentProps.views.includes(views.table)}
                         />
                     ),
                 };

package/src/utilEntrypoint.ts

@@ -27,6 +27,7 @@ export type {
     RelativeGrowthAdvantageProps,
 } from './preact/relativeGrowthAdvantage/relative-growth-advantage';
 export type { StatisticsProps } from './preact/statistic/statistics';
+export type { MapSource } from './preact/map/useGeoJsonMap';
 
 export type { ConfidenceIntervalMethod } from './preact/shared/charts/confideceInterval';
 

package/src/web-components/visualization/gs-sequences-by-location.stories.ts

@@ -17,7 +17,7 @@ const codeExample = `<gs-sequences-by-location
     lapisFilter='{"dateFrom":"2022-01-01","dateTo":"2022-04-01"}'
     lapisLocationField='country'
     mapSource='{"type":"topojson","url":"https://mock.map.data/topo.json","topologyObjectsKey":"countries"}'
-    enableMapNavigation='false'
+    enableMapNavigation
     width='1100px'
     height='800px'
     views='["map"]'
@@ -25,7 +25,7 @@ const codeExample = `<gs-sequences-by-location
     offsetX='0'
     offsetY='10'
     pageSize='5'
-/>`;
+></gs-sequences-by-location>`;
 
 const meta: Meta<Required<SequencesByLocationProps>> = {
     title: 'Visualization/Sequences by location',
@@ -84,7 +84,7 @@ const Template: StoryObj<SequencesByLocationProps> = {
     args: {
         enableMapNavigation: false,
         width: '1100px',
-        height: '800px',
+        height: '700px',
         views: ['map', 'table'],
         pageSize: 10,
     },
@@ -150,7 +150,7 @@ export const Germany: StoryObj<SequencesByLocationProps> = {
             topologyObjectsKey: 'deu',
         },
         views: ['map', 'table'],
-        zoom: 6.3,
+        zoom: 6,
         offsetX: 10,
         offsetY: 51.4,
     },

package/src/web-components/visualization/gs-sequences-by-location.tsx

@@ -130,7 +130,7 @@ export class SequencesByLocationComponent extends PreactLitAdapterWithGridJsStyl
      * Enable map navigation (dragging, keyboard navigation, zooming).
      */
     @property({ type: Boolean })
-    enableMapNavigation: boolean = true;
+    enableMapNavigation: boolean = false;
 
     /**
      * The width of the component.