@genspectrum/dashboard-components 0.1.3 → 0.1.4
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.
- package/custom-elements.json +311 -75
- package/dist/dashboard-components.js +622 -434
- package/dist/dashboard-components.js.map +1 -1
- package/dist/genspectrum-components.d.ts +229 -42
- package/dist/style.css +132 -139
- package/package.json +9 -5
- package/src/preact/aggregatedData/aggregate.stories.tsx +5 -5
- package/src/preact/aggregatedData/aggregate.tsx +8 -4
- package/src/preact/components/ReferenceGenomesAwaiter.tsx +25 -0
- package/src/preact/components/csv-download-button.tsx +8 -2
- package/src/preact/components/headline.tsx +16 -4
- package/src/preact/components/min-max-range-slider.tsx +4 -4
- package/src/preact/components/percent-intput.tsx +2 -3
- package/src/preact/components/resize-container.tsx +23 -0
- package/src/preact/components/table.tsx +1 -0
- package/src/preact/components/tabs.stories.tsx +2 -2
- package/src/preact/components/tabs.tsx +47 -24
- package/src/preact/dateRangeSelector/date-range-selector.stories.tsx +36 -4
- package/src/preact/dateRangeSelector/date-range-selector.tsx +57 -43
- package/src/preact/locationFilter/location-filter.tsx +2 -2
- package/src/preact/mutationComparison/getMutationComparisonTableData.spec.ts +5 -5
- package/src/preact/mutationComparison/getMutationComparisonTableData.ts +45 -10
- package/src/preact/mutationComparison/mutation-comparison-table.tsx +20 -22
- package/src/preact/mutationComparison/mutation-comparison-venn.tsx +6 -3
- package/src/preact/mutationComparison/mutation-comparison.stories.tsx +8 -1
- package/src/preact/mutationComparison/mutation-comparison.tsx +13 -4
- package/src/preact/mutationFilter/mutation-filter.stories.tsx +70 -31
- package/src/preact/mutationFilter/mutation-filter.tsx +62 -14
- package/src/preact/mutations/getInsertionsTableData.spec.ts +6 -4
- package/src/preact/mutations/getInsertionsTableData.ts +1 -1
- package/src/preact/mutations/getMutationsTableData.spec.ts +9 -19
- package/src/preact/mutations/getMutationsTableData.ts +1 -1
- package/src/preact/mutations/mutations-insertions-table.tsx +3 -1
- package/src/preact/mutations/mutations-table.tsx +3 -1
- package/src/preact/mutations/mutations.stories.tsx +8 -1
- package/src/preact/mutations/mutations.tsx +16 -5
- package/src/preact/prevalenceOverTime/prevalence-over-time-bar-chart.tsx +1 -0
- package/src/preact/prevalenceOverTime/prevalence-over-time-bubble-chart.tsx +1 -0
- package/src/preact/prevalenceOverTime/prevalence-over-time-line-chart.tsx +1 -0
- package/src/preact/prevalenceOverTime/prevalence-over-time.stories.tsx +4 -0
- package/src/preact/prevalenceOverTime/prevalence-over-time.tsx +17 -9
- package/src/preact/relativeGrowthAdvantage/relative-growth-advantage-chart.tsx +8 -5
- package/src/preact/relativeGrowthAdvantage/relative-growth-advantage.stories.tsx +12 -0
- package/src/preact/relativeGrowthAdvantage/relative-growth-advantage.tsx +13 -8
- package/src/preact/shared/sort/sortInsertions.spec.ts +11 -10
- package/src/preact/shared/sort/sortInsertions.ts +10 -17
- package/src/preact/shared/sort/sortSubstitutionsAndDeletions.spec.ts +19 -10
- package/src/preact/shared/sort/sortSubstitutionsAndDeletions.ts +45 -12
- package/src/preact/textInput/text-input.stories.tsx +22 -1
- package/src/preact/textInput/text-input.tsx +3 -1
- package/src/utils/typeAssertions.spec.ts +31 -0
- package/src/utils/typeAssertions.ts +16 -0
- package/src/web-components/PreactLitAdapter.tsx +0 -1
- package/src/web-components/app.stories.ts +129 -0
- package/src/web-components/app.ts +27 -6
- package/src/web-components/display/aggregate-component.stories.ts +21 -11
- package/src/web-components/display/aggregate-component.tsx +12 -5
- package/src/web-components/display/mutation-comparison-component.stories.ts +29 -11
- package/src/web-components/display/mutation-comparison-component.tsx +72 -4
- package/src/web-components/display/mutations-component.stories.ts +14 -13
- package/src/web-components/display/mutations-component.tsx +14 -1
- package/src/web-components/display/prevalence-over-time-component.stories.ts +20 -18
- package/src/web-components/display/prevalence-over-time-component.tsx +12 -0
- package/src/web-components/display/relative-growth-advantage-component.stories.ts +11 -10
- package/src/web-components/display/relative-growth-advantage-component.tsx +12 -0
- package/src/web-components/input/date-range-selector-component.stories.ts +35 -8
- package/src/web-components/input/date-range-selector-component.tsx +18 -5
- package/src/web-components/input/location-filter-component.stories.ts +15 -4
- package/src/web-components/input/location-filter-component.tsx +2 -6
- package/src/web-components/input/mutation-filter-component.stories.ts +20 -9
- package/src/web-components/input/mutation-filter-component.tsx +10 -2
- package/src/web-components/input/text-input-component.stories.ts +13 -4
- package/src/web-components/input/text-input-component.tsx +11 -2
- package/src/web-components/display/aggregate-component.mdx +0 -25
- package/src/web-components/input/location-filter.mdx +0 -25
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import { type FunctionComponent } from 'preact';
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export type Size = {
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width?: string;
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height?: string;
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export interface ResizeContainerProps {
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defaultSize: Size;
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}
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export const ResizeContainer: FunctionComponent<ResizeContainerProps> = ({ children, size, defaultSize }) => {
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const extendByDefault = (size: Size | undefined, defaultSize: Size) => {
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return defaultSize;
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}
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return { ...defaultSize, ...size };
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import { type PaginationConfig } from 'gridjs/dist/src/view/plugin/pagination';
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import { type ComponentChild } from 'preact';
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import { useEffect, useRef } from 'preact/hooks';
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import 'gridjs/dist/theme/mermaid.css';
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export const tableStyle = {
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@@ -51,10 +51,10 @@ export const TabsWithToolbarOnlyShowingOnSecondTab: StoryObj = {
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play: async ({ canvasElement }) => {
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const canvas = within(canvasElement);
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await waitFor(() => expect(canvas.
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await waitFor(() => expect(canvas.getByRole('button', { name: 'SecondTab' })).toBeVisible());
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await expect(canvas.queryByText('Toolbar')).not.toBeInTheDocument();
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await fireEvent.click(canvas.
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await fireEvent.click(canvas.getByRole('button', { name: 'SecondTab' }));
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await waitFor(() => expect(canvas.getByText('Toolbar')).toBeVisible());
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import { Fragment, type FunctionComponent } from 'preact';
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import { useEffect, useRef, useState } from 'preact/hooks';
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import { type JSXInternal } from 'preact/src/jsx';
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type Tab = {
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const Tabs: FunctionComponent<ComponentTabsProps> = ({ tabs, toolbar }) => {
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const [activeTab, setActiveTab] = useState(tabs[0].title);
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const [heightOfTabs, setHeightOfTabs] = useState('3rem');
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const tabRef = useRef<HTMLDivElement>(null);
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useEffect(() => {
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const heightOfTabs = tabRef.current.getBoundingClientRect().height;
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setHeightOfTabs(`${heightOfTabs}px`);
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}
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}, []);
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const tabElements = (
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{tabs.map((tab) => {
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return (
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<Fragment key={tab.title}>
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<button
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className={`px-4 py-2 text-sm font-medium leading-5 transition-colors duration-150 ${
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activeTab === tab.title
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? 'border-b-2 border-gray-400'
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: 'text-gray-600 hover:bg-gray-100 hover:text-gray-700'
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}`}
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onClick={() => {
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setActiveTab(tab.title);
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}}
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>
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{tab.title}
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</Fragment>
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);
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})}
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<div ref={tabRef} className='flex flex-row justify-between'>
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{tabElements}
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{toolbar && <div className='py-2'>{toolbarElement}</div>}
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</div>
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<div
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className={`p-2 border-2 border-gray-100 rounded-b-md rounded-tr-md ${activeTab === tabs[0].title ? '' : 'rounded-tl-md'}`}
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style={{ height: `calc(100% - ${heightOfTabs})` }}
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>
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{tabs.map((tab) => (
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<div className='h-full overflow-auto' key={tab.title} hidden={activeTab !== tab.title}>
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import { withActions } from '@storybook/addon-actions/decorator';
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import { type Meta, type StoryObj } from '@storybook/preact';
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import {
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import {
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DateRangeSelector,
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type DateRangeSelectorProps,
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PRESET_VALUE_ALL_TIMES,
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PRESET_VALUE_LAST_3_MONTHS,
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PRESET_VALUE_LAST_6_MONTHS,
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PRESET_VALUE_LAST_MONTH,
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} from './date-range-selector';
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const meta: Meta<DateRangeSelectorProps<'CustomDateRange'>> = {
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title: 'Input/DateRangeSelector',
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control: {
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},
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options: [
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'CustomDateRange',
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/>
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const getDatesForSelectorValue = (
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earliestDate: string,
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) => {
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);
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}
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}
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|
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|
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}
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|
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case
|
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+
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|
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|
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twoMonthsAgo.setMonth(today.getMonth() - 2);
|
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|
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|
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|
}
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|
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case
|
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|
+
case PRESET_VALUE_LAST_3_MONTHS: {
|
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|
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|
|
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|
threeMonthsAgo.setMonth(today.getMonth() - 3);
|
|
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|
return { dateFrom: threeMonthsAgo, dateTo: today };
|
|
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|
}
|
|
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|
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case
|
|
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|
+
case PRESET_VALUE_LAST_6_MONTHS: {
|
|
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|
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|
|
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|
sixMonthsAgo.setMonth(today.getMonth() - 6);
|
|
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|
return { dateFrom: sixMonthsAgo, dateTo: today };
|
|
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|
}
|
|
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|
-
case
|
|
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|
+
case PRESET_VALUE_ALL_TIMES: {
|
|
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237
|
return { dateFrom: new Date(earliestDate), dateTo: today };
|
|
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|
}
|
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|
default:
|
|
@@ -5,11 +5,11 @@ import { LapisUrlContext } from '../LapisUrlContext';
|
|
|
5
5
|
import { useQuery } from '../useQuery';
|
|
6
6
|
|
|
7
7
|
export type LocationFilterProps = {
|
|
8
|
-
|
|
8
|
+
initialValue?: string;
|
|
9
9
|
fields: string[];
|
|
10
10
|
};
|
|
11
11
|
|
|
12
|
-
export const LocationFilter = ({
|
|
12
|
+
export const LocationFilter = ({ initialValue, fields }: LocationFilterProps) => {
|
|
13
13
|
const lapis = useContext(LapisUrlContext);
|
|
14
14
|
|
|
15
15
|
const [value, setValue] = useState(initialValue ?? '');
|
|
@@ -51,12 +51,12 @@ describe('getPrevalenceOverTimeTableData', () => {
|
|
|
51
51
|
|
|
52
52
|
expect(result).toEqual([
|
|
53
53
|
{
|
|
54
|
-
mutation: '
|
|
54
|
+
mutation: new Substitution(undefined, 'A', 'T', 123),
|
|
55
55
|
'Test 1 prevalence': 0.123,
|
|
56
56
|
'Test 2 prevalence': 0.345,
|
|
57
57
|
},
|
|
58
58
|
{
|
|
59
|
-
mutation: '
|
|
59
|
+
mutation: new Substitution(undefined, 'G', 'A', 234),
|
|
60
60
|
'Test 1 prevalence': 0.567,
|
|
61
61
|
'Test 2 prevalence': 0.789,
|
|
62
62
|
},
|
|
@@ -106,17 +106,17 @@ describe('getPrevalenceOverTimeTableData', () => {
|
|
|
106
106
|
|
|
107
107
|
expect(result).toEqual([
|
|
108
108
|
{
|
|
109
|
-
mutation: '
|
|
109
|
+
mutation: new Substitution(undefined, 'A', 'T', 200),
|
|
110
110
|
'Test 1 prevalence': inRange,
|
|
111
111
|
'Test 2 prevalence': belowRange,
|
|
112
112
|
},
|
|
113
113
|
{
|
|
114
|
-
mutation: '
|
|
114
|
+
mutation: new Substitution(undefined, 'A', 'T', 300),
|
|
115
115
|
'Test 1 prevalence': inRange,
|
|
116
116
|
'Test 2 prevalence': inRange,
|
|
117
117
|
},
|
|
118
118
|
{
|
|
119
|
-
mutation: '
|
|
119
|
+
mutation: new Substitution(undefined, 'A', 'T', 400),
|
|
120
120
|
'Test 1 prevalence': inRange,
|
|
121
121
|
'Test 2 prevalence': aboveRange,
|
|
122
122
|
},
|
|
@@ -1,35 +1,53 @@
|
|
|
1
1
|
import { type MutationData } from './queryMutationData';
|
|
2
2
|
import { type Dataset } from '../../operator/Dataset';
|
|
3
|
+
import { type Deletion, type Substitution } from '../../utils/mutations';
|
|
3
4
|
import { type ProportionInterval } from '../components/proportion-selector';
|
|
4
5
|
|
|
5
6
|
type Proportions = {
|
|
6
7
|
[displayName: string]: number;
|
|
7
8
|
};
|
|
8
9
|
|
|
10
|
+
type MutationComparisonRow = {
|
|
11
|
+
mutation: Substitution | Deletion;
|
|
12
|
+
proportions: Proportions;
|
|
13
|
+
};
|
|
14
|
+
|
|
9
15
|
export function getMutationComparisonTableData(data: Dataset<MutationData>, proportionInterval: ProportionInterval) {
|
|
10
|
-
const mutationsToProportions = new Map<string,
|
|
16
|
+
const mutationsToProportions = new Map<string, MutationComparisonRow>();
|
|
11
17
|
|
|
12
18
|
for (const mutationData of data.content) {
|
|
13
19
|
for (const mutationEntry of mutationData.data) {
|
|
14
|
-
const
|
|
15
|
-
const
|
|
16
|
-
|
|
17
|
-
|
|
20
|
+
const mutationKey = mutationEntry.mutation.toString();
|
|
21
|
+
const existingRow = mutationsToProportions.get(mutationKey);
|
|
22
|
+
|
|
23
|
+
if (!existingRow) {
|
|
24
|
+
mutationsToProportions.set(
|
|
25
|
+
mutationKey,
|
|
26
|
+
initializeMutationRow(mutationEntry.mutation, mutationData.displayName, mutationEntry.proportion),
|
|
27
|
+
);
|
|
28
|
+
} else {
|
|
29
|
+
existingRow.proportions = updateProportions(
|
|
30
|
+
existingRow.proportions,
|
|
31
|
+
mutationData.displayName,
|
|
32
|
+
mutationEntry.proportion,
|
|
33
|
+
);
|
|
34
|
+
mutationsToProportions.set(mutationKey, existingRow);
|
|
35
|
+
}
|
|
18
36
|
}
|
|
19
37
|
}
|
|
20
38
|
|
|
21
|
-
return [...mutationsToProportions.
|
|
22
|
-
.map((
|
|
39
|
+
return [...mutationsToProportions.values()]
|
|
40
|
+
.map((row) => {
|
|
23
41
|
return {
|
|
24
|
-
mutation,
|
|
42
|
+
mutation: row.mutation,
|
|
25
43
|
...data.content
|
|
26
44
|
.map((mutationData) => {
|
|
27
45
|
return {
|
|
28
|
-
[`${mutationData.displayName} prevalence`]: proportions[mutationData.displayName] || 0,
|
|
46
|
+
[`${mutationData.displayName} prevalence`]: row.proportions[mutationData.displayName] || 0,
|
|
29
47
|
};
|
|
30
48
|
})
|
|
31
49
|
.reduce((acc, val) => ({ ...acc, ...val }), {}),
|
|
32
|
-
} as { mutation:
|
|
50
|
+
} as { mutation: Substitution | Deletion } & Proportions;
|
|
33
51
|
})
|
|
34
52
|
.filter((row) =>
|
|
35
53
|
Object.values(row).some(
|
|
@@ -38,3 +56,20 @@ export function getMutationComparisonTableData(data: Dataset<MutationData>, prop
|
|
|
38
56
|
),
|
|
39
57
|
);
|
|
40
58
|
}
|
|
59
|
+
|
|
60
|
+
function initializeMutationRow(
|
|
61
|
+
mutation: Substitution | Deletion,
|
|
62
|
+
displayName: string,
|
|
63
|
+
proportion: number,
|
|
64
|
+
): MutationComparisonRow {
|
|
65
|
+
return {
|
|
66
|
+
mutation,
|
|
67
|
+
proportions: {
|
|
68
|
+
[displayName]: proportion,
|
|
69
|
+
},
|
|
70
|
+
};
|
|
71
|
+
}
|
|
72
|
+
|
|
73
|
+
function updateProportions(proportions: Proportions, displayName: string, proportion: number): Proportions {
|
|
74
|
+
return { ...proportions, [displayName]: proportion };
|
|
75
|
+
}
|
|
@@ -3,6 +3,7 @@ import { type FunctionComponent } from 'preact';
|
|
|
3
3
|
import { getMutationComparisonTableData } from './getMutationComparisonTableData';
|
|
4
4
|
import { type MutationData } from './queryMutationData';
|
|
5
5
|
import { type Dataset } from '../../operator/Dataset';
|
|
6
|
+
import { type Deletion, type Substitution } from '../../utils/mutations';
|
|
6
7
|
import { type ProportionInterval } from '../components/proportion-selector';
|
|
7
8
|
import { Table } from '../components/table';
|
|
8
9
|
import { sortSubstitutionsAndDeletions } from '../shared/sort/sortSubstitutionsAndDeletions';
|
|
@@ -14,30 +15,27 @@ export interface MutationsTableProps {
|
|
|
14
15
|
}
|
|
15
16
|
|
|
16
17
|
export const MutationComparisonTable: FunctionComponent<MutationsTableProps> = ({ data, proportionInterval }) => {
|
|
17
|
-
const
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
compare: (a: string, b: string) => {
|
|
23
|
-
return sortSubstitutionsAndDeletions(a, b);
|
|
24
|
-
},
|
|
25
|
-
},
|
|
18
|
+
const headers = [
|
|
19
|
+
{
|
|
20
|
+
name: 'Mutation',
|
|
21
|
+
sort: {
|
|
22
|
+
compare: sortSubstitutionsAndDeletions,
|
|
26
23
|
},
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
24
|
+
formatter: (cell: Substitution | Deletion) => cell.toString(),
|
|
25
|
+
},
|
|
26
|
+
{
|
|
27
|
+
name: 'Prevalence',
|
|
28
|
+
columns: data.content.map((mutationData) => {
|
|
29
|
+
return {
|
|
30
|
+
name: mutationData.displayName,
|
|
31
|
+
sort: true,
|
|
32
|
+
formatter: (cell: number) => formatProportion(cell),
|
|
33
|
+
};
|
|
34
|
+
}),
|
|
35
|
+
},
|
|
36
|
+
];
|
|
39
37
|
|
|
40
38
|
const tableData = getMutationComparisonTableData(data, proportionInterval).map((row) => Object.values(row));
|
|
41
39
|
|
|
42
|
-
return <Table data={tableData} columns={
|
|
40
|
+
return <Table data={tableData} columns={headers} pagination={true} />;
|
|
43
41
|
};
|
|
@@ -64,6 +64,7 @@ export const MutationComparisonVenn: FunctionComponent<MutationComparisonVennPro
|
|
|
64
64
|
type: 'venn',
|
|
65
65
|
data: sets,
|
|
66
66
|
options: {
|
|
67
|
+
maintainAspectRatio: false,
|
|
67
68
|
scales: {
|
|
68
69
|
x: {
|
|
69
70
|
ticks: {
|
|
@@ -114,9 +115,11 @@ export const MutationComparisonVenn: FunctionComponent<MutationComparisonVennPro
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}
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return (
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-
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-
<
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<div className='h-full flex flex-col'>
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<div className='flex-1'>
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<GsChart configuration={config} />
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</div>
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<div class='flex flex-wrap break-words m-2' ref={divRef} />
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</div>
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);
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};
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@@ -27,6 +27,7 @@ const meta: Meta<MutationComparisonProps> = {
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options: ['table', 'venn'],
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control: { type: 'check' },
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},
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size: [{ control: 'object' }],
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},
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parameters: {
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fetchMock: {
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@@ -75,7 +76,12 @@ const Template: StoryObj<MutationComparisonProps> = {
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render: (args) => (
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<LapisUrlContext.Provider value={LAPIS_URL}>
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<ReferenceGenomeContext.Provider value={referenceGenome}>
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<MutationComparison
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<MutationComparison
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variants={args.variants}
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sequenceType={args.sequenceType}
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views={args.views}
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size={args.size}
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/>
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</ReferenceGenomeContext.Provider>
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</LapisUrlContext.Provider>
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),
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@@ -101,6 +107,7 @@ export const TwoVariants: StoryObj<MutationComparisonProps> = {
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],
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sequenceType: 'nucleotide',
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views: ['table', 'venn'],
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size: { width: '100%', height: '700px' },
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},
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};
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