Merge branch 'develop' into AG-1374-sage-rebrand

package.json

@@ -1,8 +1,8 @@
 {
   "name": "agora",
-  "version": "3.3.0",
+  "version": "3.4.0",
   "data-file": "syn13363290",
-  "data-version": "66",
+  "data-version": "68",
   "private": true,
   "scripts": {
     "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",

src/app/features/charts/charts.module.ts

@@ -7,6 +7,7 @@ import {
   BoxPlotComponent,
   CandlestickChartComponent,
   MedianChartComponent,
+  MedianBarChartComponent,
   RowChartComponent,
   ScoreChartComponent,
   ScoreBarChartComponent,
@@ -19,6 +20,7 @@ import {
     BoxPlotComponent,
     CandlestickChartComponent,
     MedianChartComponent,
+    MedianBarChartComponent,
     RowChartComponent,
     ScoreChartComponent,
     ScoreBarChartComponent,
@@ -30,6 +32,7 @@ import {
     BoxPlotComponent,
     CandlestickChartComponent,
     MedianChartComponent,
+    MedianBarChartComponent,
     RowChartComponent,
     ScoreChartComponent,
     ScoreBarChartComponent,

src/app/features/charts/components/index.ts

@@ -1,6 +1,7 @@
 export * from './box-plot-chart';
 export * from './candlestick-chart';
 export * from './median-chart';
+export * from './median-barchart';
 export * from './row-chart';
 export * from './score-chart';
 export * from './score-barchart';

src/app/features/charts/components/median-barchart/index.ts

@@ -0,0 +1 @@
+export * from './median-barchart.component';

src/app/features/charts/components/median-barchart/median-barchart.component.html

@@ -0,0 +1,12 @@
+<div id="median-barchart" #medianBarChartContainer class="chart-d3">
+  <div
+    id="tooltip"
+    class="arrow-above tooltip-arrow"
+    #tooltip
+    (mouseout)="hideTooltip()"
+  ></div>
+  <svg #chart></svg>
+  <div class="chart-no-data" *ngIf="data.length === 0">
+    <div class="chart-no-data-text">No data is currently available.</div>
+  </div>
+</div>

src/app/features/charts/components/median-barchart/median-barchart.component.scss

@@ -0,0 +1,26 @@
+#median-barchart {
+  .x-axis-label, .y-axis-label {
+    font-size: var(--font-size-lg);
+    font-weight: 700;
+    color: var(--color-chart-axis-label);
+    fill: var(--color-chart-axis-label);
+  }
+
+  .y-axis .tick {
+    text {
+      font-size: var(--font-size-sm);
+    }
+  }
+
+  .x-axis .tick {
+    text {
+      font-size: var(--font-size-md);
+      font-weight: 700;
+    }
+  }
+
+  .bar-labels {
+    font-size: var(--font-size-sm);
+    text-anchor: middle;
+  }
+}

src/app/features/charts/components/median-barchart/median-barchart.component.spec.ts

@@ -0,0 +1,219 @@
+// -------------------------------------------------------------------------- //
+// External
+// -------------------------------------------------------------------------- //
+import { TestBed, ComponentFixture, waitForAsync } from '@angular/core/testing';
+import { RouterTestingModule } from '@angular/router/testing';
+
+// -------------------------------------------------------------------------- //
+// Internal
+// -------------------------------------------------------------------------- //
+import { MedianBarChartComponent } from './';
+import { HelperService } from '../../../../core/services';
+import { geneMock1 } from '../../../../testing';
+import { MedianExpression } from '../../../../models/genes';
+
+// -------------------------------------------------------------------------- //
+// Tests
+// -------------------------------------------------------------------------- //
+const XAXIS_LABEL = 'BRAIN REGION';
+const YAXIS_LABEL = 'LOG2CPM';
+const FULL_MOCK_DATA = geneMock1.median_expression;
+const TISSUES = ['TCX', 'PHG', 'STG'];
+const SMALL_MOCK_DATA = [
+  {
+    min: -2.54173091337051,
+    first_quartile: -1.03358030635935,
+    median: 0.483801733963266,
+    mean: -0.517398199667356,
+    third_quartile: -0.0800759845652829,
+    max: 2.32290808871289,
+    tissue: TISSUES[0],
+  },
+  {
+    min: -2.44077907413711,
+    first_quartile: -0.592671867557559,
+    median: 0.013739530502129,
+    mean: -0.0324143336865,
+    third_quartile: 0.49577213202412,
+    max: 2.23019575245731,
+    tissue: TISSUES[1],
+  },
+  {
+    min: -5.03189866356294,
+    first_quartile: -1.02644563959975,
+    median: 0.176348063122062,
+    mean: -0.323038107200895,
+    third_quartile: 0.391874711168331,
+    max: 1.9113258251877,
+    tissue: TISSUES[2],
+  },
+];
+
+describe('Component: BarChart - Median', () => {
+  let fixture: ComponentFixture<MedianBarChartComponent>;
+  let component: MedianBarChartComponent;
+  let element: HTMLElement;
+
+  beforeEach(waitForAsync(() => {
+    TestBed.configureTestingModule({
+      declarations: [MedianBarChartComponent],
+      imports: [RouterTestingModule],
+      providers: [HelperService],
+    }).compileComponents();
+  }));
+
+  beforeEach(() => {
+    fixture = TestBed.createComponent(MedianBarChartComponent);
+    component = fixture.componentInstance;
+  });
+
+  const setUp = (
+    data: MedianExpression[] = FULL_MOCK_DATA,
+    xAxisLabel: string = XAXIS_LABEL,
+    yAxisLabel: string = YAXIS_LABEL
+  ) => {
+    component.data = data;
+    component.xAxisLabel = xAxisLabel;
+    component.yAxisLabel = yAxisLabel;
+
+    fixture.detectChanges();
+    element = fixture.nativeElement;
+    const chart = element.querySelector('svg g');
+    return { chart };
+  };
+
+  it('should create', () => {
+    setUp();
+    expect(component).toBeTruthy();
+  });
+
+  it('should not render the chart if there is no data', () => {
+    const { chart } = setUp([]);
+
+    expect(component.data?.length).toEqual(0);
+    expect(element.querySelector('.chart-no-data')).toBeTruthy();
+
+    expect(chart).toBeFalsy();
+  });
+
+  it('should not render the chart if all values are negative', () => {
+    const { chart } = setUp(
+      SMALL_MOCK_DATA.map((obj) => {
+        return { ...obj, median: -1 * obj.median };
+      })
+    );
+
+    expect(element.querySelector('.chart-no-data')).toBeTruthy();
+
+    expect(chart).toBeFalsy();
+  });
+
+  it('should render the chart if there is positive data', () => {
+    const createChartSpy = spyOn(component, 'createChart').and.callThrough();
+    const { chart } = setUp();
+
+    expect(component.data?.length).toEqual(FULL_MOCK_DATA.length);
+    expect(createChartSpy).toHaveBeenCalled();
+    expect(chart).toBeTruthy();
+
+    expect(element.querySelector('.chart-no-data')).toBeFalsy();
+  });
+
+  it('should render the chart axes', () => {
+    const { chart } = setUp();
+
+    expect(chart?.querySelector('.x-axis')).toBeTruthy();
+    expect(chart?.querySelector('.y-axis')).toBeTruthy();
+  });
+
+  it('should render the correct number of bars', () => {
+    const { chart } = setUp();
+
+    expect(chart?.querySelectorAll('rect').length).toEqual(
+      FULL_MOCK_DATA.length
+    );
+  });
+
+  it('should not render bars for negative values', () => {
+    const { chart } = setUp([
+      { ...SMALL_MOCK_DATA[0], median: -0.01 },
+      ...SMALL_MOCK_DATA.slice(1),
+    ]);
+
+    expect(chart?.querySelectorAll('rect').length).toEqual(
+      SMALL_MOCK_DATA.length - 1
+    );
+  });
+
+  it('should render the bar labels', () => {
+    const { chart } = setUp();
+
+    expect(chart?.querySelectorAll('text.bar-labels').length).toEqual(
+      FULL_MOCK_DATA.length
+    );
+  });
+
+  it('should render the labels for both axes', () => {
+    const { chart } = setUp();
+
+    expect(chart?.querySelector('.x-axis-label')?.textContent).toEqual(
+      XAXIS_LABEL
+    );
+    expect(chart?.querySelector('.y-axis-label')?.textContent).toEqual(
+      YAXIS_LABEL
+    );
+  });
+
+  it('should render the meaningful expression threshold when values are larger than threshold', () => {
+    const { chart } = setUp();
+
+    expect(
+      chart?.querySelector('.meaningful-expression-threshold-line')
+    ).toBeTruthy();
+  });
+
+  it('should not render the meaningful expression threshold when all values are smaller than threshold', () => {
+    const { chart } = setUp(SMALL_MOCK_DATA);
+
+    expect(
+      chart?.querySelector('.meaningful-expression-threshold-line')
+    ).toBeFalsy();
+  });
+
+  it('should alphabetize the x-axis values', () => {
+    setUp(SMALL_MOCK_DATA);
+
+    const sortedTissues = TISSUES.sort();
+    const xAxisTicks = element
+      .querySelector('svg g .x-axis')
+      ?.querySelectorAll('.tick');
+    xAxisTicks?.forEach((val, index) => {
+      expect(val.textContent).toEqual(sortedTissues[index]);
+    });
+  });
+
+  it('should show and hide tooltip', () => {
+    setUp();
+
+    const tooltip = element.querySelector<HTMLElement>('#tooltip');
+    expect(tooltip?.textContent).toBeFalsy();
+
+    const xAxisTick = element.querySelector('svg g .x-axis .tick');
+    const mouseEnterEvent = new MouseEvent('mouseenter', {
+      bubbles: true,
+      cancelable: true,
+    });
+    xAxisTick?.dispatchEvent(mouseEnterEvent);
+
+    expect(tooltip?.style.display).toEqual('block');
+    expect(tooltip?.textContent).toBeTruthy();
+
+    const mouseLeaveEvent = new MouseEvent('mouseleave', {
+      bubbles: true,
+      cancelable: true,
+    });
+    xAxisTick?.dispatchEvent(mouseLeaveEvent);
+
+    expect(tooltip?.style.display).toEqual('none');
+  });
+});