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Undo selection appends genes from differential expression to user gene list (#1183)

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* Undo selection appends diffExp genes to user gene list

Fixes https://github.com/chanzuckerberg/cellxgene/issues/1171

Need: When a user performs a differential expression from within
a sub-selection (world) of the data and then resets the selection to all
cells (universe), the differential expression results are no longer
valid.

Approach:
* When the selection is reset, move the top (maxUserDefinedGenes
- len(userDefinedGenes) from the differential expression results to the
list of user defined genes
* Raise maxUserDefinedGenes to 25 to give users more room and
accommodate the extra genes transferred in from differential expression

Other commits:
* Choose different button icons
* Add diff exp genes to user defined genes on subset too
* Respond to feedback from @liaprins-czi and @bkmartinjr
This commit is contained in:
Matt Weiden
2020-03-02 12:07:12 -08:00
committed by GitHub
parent 87efcc0e99
commit 05323ae643
15 changed files with 231 additions and 246 deletions
Download Patch File Download Diff File Expand all files Collapse all files
client/__tests__/e2e/e2e.test.js
+47 -59
View File
@@ -20,9 +20,7 @@ beforeEach(async () => {
});
afterAll(() => {
if (!DEBUG) {
browser.close();
}
browser.close();
});
describe("did launch", () => {
@@ -111,16 +109,10 @@ describe("cell selection", () => {
describe("gene entry", () => {
test("search for single gene", async () => {
// blueprint's typeahead is treating typing weird, clicking & waiting first solves this
await utils.typeInto("gene-search", data.genes.search);
await page.keyboard.press("Enter");
await page.waitForSelector(
`[data-testid='histogram-${data.genes.search}']`
);
await cxgActions.addGeneToSearch(data.genes.search);
});
test("bulk add genes", async () => {
await cxgActions.reset();
const testGenes = data.genes.bulkadd;
await utils.clickOn("section-bulk-add");
await utils.typeInto("input-bulk-add", testGenes.join(","));
@@ -135,21 +127,9 @@ describe("gene entry", () => {
});
});
describe("diffexp", () => {
describe("differential expression", () => {
test("selects cells, saves them and performs diffexp", async () => {
for (const select of data.diffexp.cellset1) {
if (select.kind === "categorical") {
await cxgActions.selectCategory(select.metadata, select.values, true);
}
}
await cxgActions.cellSet(1);
for (const select of data.diffexp.cellset2) {
if (select.kind === "categorical") {
await cxgActions.selectCategory(select.metadata, select.values, true);
}
}
await cxgActions.cellSet(2);
await utils.clickOn("diffexp-button");
await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
const allHistograms = await cxgActions.getAllHistograms(
"histogram-diffexp",
data.diffexp["gene-results"]
@@ -161,7 +141,7 @@ describe("diffexp", () => {
});
});
describe("subset/reset", () => {
describe("subset", () => {
test("subset - cell count matches", async () => {
for (const select of data.subset.cellset1) {
if (select.kind === "categorical") {
@@ -180,39 +160,6 @@ describe("subset/reset", () => {
}
});
test("reset after subset", async () => {
for (const select of data.subset.cellset1) {
if (select.kind === "categorical") {
await cxgActions.selectCategory(select.metadata, select.values, true);
}
}
await utils.clickOn("subset-button");
for (const label in data.subset.categorical) {
const categories = await cxgActions.getAllCategoriesAndCounts(label);
expect(Object.keys(categories)).toMatchObject(
Object.keys(data.subset.categorical[label])
);
expect(Object.values(categories)).toMatchObject(
Object.values(data.subset.categorical[label])
);
}
await cxgActions.reset();
for (const label in data.categorical) {
await utils.waitByID(`category-${label}`);
const categoryName = await utils.getOneElementInnerText(
`[data-testid="category-${label}"]`
);
expect(categoryName).toMatch(label);
const categories = await cxgActions.getAllCategoriesAndCounts(label);
expect(Object.keys(categories)).toMatchObject(
Object.keys(data.categorical[label])
);
expect(Object.values(categories)).toMatchObject(
Object.values(data.categorical[label])
);
}
});
test("lasso after subset", async () => {
for (const select of data.subset.cellset1) {
if (select.kind === "categorical") {
@@ -233,11 +180,52 @@ describe("subset/reset", () => {
const cellCount = await cxgActions.cellSet(1);
expect(cellCount).toBe(data.subset.lasso.count);
});
test("undo selection appends the top diff exp genes to user defined genes", async () => {
const userDefinedGenes = ["ACD", "AAR2", "AATF", "ARSG"];
const diffExpGenes = data.diffexp["gene-results"];
for (const userDefinedGene of userDefinedGenes) {
await cxgActions.addGeneToSearch(userDefinedGene);
}
const userDefinedHistograms = await cxgActions.getAllHistograms("histogram-user-gene", userDefinedGenes);
expect(userDefinedHistograms).toStrictEqual(userDefinedGenes);
await cxgActions.subset({x1: 0.15, y1: 0.10, x2: 0.98, y2: 0.98});
await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
const diffExpHistograms = await cxgActions.getAllHistograms("histogram-diffexp", diffExpGenes);
expect(diffExpHistograms).toStrictEqual(diffExpGenes);
await utils.clickOn("reset-subset-button");
const expected = [].concat(userDefinedGenes, diffExpGenes);
const userDefinedHistogramsAfterSubset = await cxgActions.getAllHistograms(
"histogram-user-gene",
expected
);
expect(userDefinedHistogramsAfterSubset).toStrictEqual(expected);
});
test("subset selection appends the top diff exp genes to user defined genes", async () => {
const userDefinedGenes = ["ACD", "AAR2", "AATF", "ARSG"];
const diffExpGenes = data.diffexp["gene-results"];
for (const userDefinedGene of userDefinedGenes) {
await cxgActions.addGeneToSearch(userDefinedGene);
}
const userDefinedHistograms = await cxgActions.getAllHistograms("histogram-user-gene", userDefinedGenes);
expect(userDefinedHistograms).toStrictEqual(userDefinedGenes);
await cxgActions.subset({x1: 0.15, y1: 0.10, x2: 0.98, y2: 0.98});
await cxgActions.runDiffExp(data.diffexp.cellset1, data.diffexp.cellset2);
const diffExpHistograms = await cxgActions.getAllHistograms("histogram-diffexp", diffExpGenes);
expect(diffExpHistograms).toStrictEqual(diffExpGenes);
await cxgActions.subset({x1: 0.16, y1: 0.11, x2: 0.97, y2: 0.97});
const expected = [].concat(userDefinedGenes, diffExpGenes);
const userDefinedHistogramsAfterSubset = await cxgActions.getAllHistograms(
"histogram-user-gene",
expected
);
expect(userDefinedHistogramsAfterSubset).toStrictEqual(expected);
});
});
describe("scatter plot", () => {
test("scatter plot appears", async () => {
await cxgActions.reset();
const testGenes = data.scatter.genes;
await utils.clickOn("section-bulk-add");
await utils.typeInto("input-bulk-add", Object.values(testGenes).join(","));