From 7761950c9074c1aedc574f91552b0e37bf202fa0 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Fri, 16 Feb 2024 11:27:42 -0800 Subject: [PATCH] Add Triptych for set to set comparison (#591) (making a PR from the branch because I want to play with the deploy preview) --------- Co-authored-by: Vincent Rubinetti --- .DS_Store | 0 .../fixtures/phenotype_explorer_compare.py | 10 +- .../fixtures/phenotype_explorer_search.py | 26 +- backend/tests/fixtures/search_response.py | 2 +- frontend/README.md | 10 +- .../fixtures/phenotype-explorer-compare.json | 10 +- .../fixtures/phenotype-explorer-search.json | 12 +- frontend/src/api/phenotype-explorer.ts | 123 +++------- frontend/src/components/AppRing.vue | 2 +- frontend/src/components/AppTabs.vue | 2 +- frontend/src/components/AppUpload.vue | 1 + frontend/src/global/icons.ts | 1 + frontend/src/pages/explore/PagePhenogrid.vue | 13 +- .../pages/explore/TabPhenotypeExplorer.vue | 230 ++++++++++++++---- .../src/pages/explore/TabTextAnnotator.vue | 1 + 15 files changed, 263 insertions(+), 180 deletions(-) delete mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index e69de29bb..000000000 diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 625c9c6fa..033f9c27f 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -69,8 +69,8 @@ def phenotype_explorer_compare(): "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0010771", - "match_target_label": "integument phenotype (MPO)", + "match_target": "MP:0002169", + "match_target_label": "no abnormal phenotype detected (MPO)", "score": 1.5540019332516637, "match_subsumer": None, "match_subsumer_label": None, @@ -78,7 +78,7 @@ def phenotype_explorer_compare(): "subject_id": "HP:0004325", "subject_label": None, "subject_source": None, - "object_id": "MP:0010771", + "object_id": "MP:0002169", "object_label": None, "object_source": None, "ancestor_id": "UPHENO:0001003", @@ -87,10 +87,10 @@ def phenotype_explorer_compare(): "object_information_content": None, "subject_information_content": None, "ancestor_information_content": 1.5540019332516637, - "jaccard_similarity": 0.24, + "jaccard_similarity": 0.23076923076923078, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.61070489107293, + "phenodigm_score": 0.5988454147360435, }, } }, diff --git a/backend/tests/fixtures/phenotype_explorer_search.py b/backend/tests/fixtures/phenotype_explorer_search.py index 591060f32..904cf8435 100644 --- a/backend/tests/fixtures/phenotype_explorer_search.py +++ b/backend/tests/fixtures/phenotype_explorer_search.py @@ -68,8 +68,8 @@ def phenotype_explorer_search(): "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)") }, object_termset={ - "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), + "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), }, subject_best_matches={ "ZP:0018569": BestMatch( @@ -427,8 +427,8 @@ def phenotype_explorer_search(): "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0018568": BestMatch( @@ -622,8 +622,8 @@ def phenotype_explorer_search(): score=7.234842285670967, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), + "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), }, object_termset={ "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), @@ -716,8 +716,8 @@ def phenotype_explorer_search(): "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -725,7 +725,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -734,10 +734,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.8650294287846346, ), ), }, @@ -881,8 +881,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -890,7 +890,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -899,10 +899,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.34615384615384615, + jaccard_similarity=0.3333333333333333, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.773384910034319, + phenodigm_score=1.7402346054863809, ), ), "HP:0012378": BestMatch( diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 18c37ed19..afbd49ce7 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -5,7 +5,7 @@ def search_response(): return { "responseHeader": { - "QTime": 3, + "QTime": 0, "params": { "mm": "100%", "q": "fanconi", diff --git a/frontend/README.md b/frontend/README.md index e8292fb69..3063caaf8 100644 --- a/frontend/README.md +++ b/frontend/README.md @@ -95,14 +95,15 @@ Include the widget on your page like so: The widget accepts several URL parameters: - `source` - Comma-separated list of "source" phenotype IDs (set A). -- `target` - Comma-separated list of "target" phenotype IDs (set B). +- `target` - "target" group of phenotypes to compare to (group B). + See `src/api/phenotype-explorer.ts` groups for enumerated options. - `stylesheet` - A URI-encoded URL to a stylesheet that will be applied to the widget, for the purposes of matching its styles to your webpage. ### Events The widget also emits `message` events to the parent window when certain things change, and listens for `message` events from the parent window to receive information. -#### Listens for `MessageEvent<{ source: string[], target: string[] }>` +#### Listens for `MessageEvent<{ source: string[], target: string }>` Provide input phenotype lists to the widget when they might be [too long for a URL](https://www.google.com/search?q=max+url+length). @@ -110,7 +111,10 @@ Provide input phenotype lists to the widget when they might be [too long for a U // get your iframe dom element somehow const iframe = document.querySelector("iframe"); // send it a message -iframe.contentWindow.postMessage({ source: ["abc"], target: ["def"] }, "*"); +iframe.contentWindow.postMessage( + { source: ["HP:123,HP:456"], target: "Human Diseases" }, + "*", +); ``` #### Emits `MessageEvent<{ width: number; height: number; }>` diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index d0524b8dc..9f71ec202 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -75,8 +75,8 @@ "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0010771", - "match_target_label": "integument phenotype (MPO)", + "match_target": "MP:0002169", + "match_target_label": "no abnormal phenotype detected (MPO)", "score": 1.5540019332516637, "match_subsumer": null, "match_subsumer_label": null, @@ -84,7 +84,7 @@ "subject_id": "HP:0004325", "subject_label": null, "subject_source": null, - "object_id": "MP:0010771", + "object_id": "MP:0002169", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001003", @@ -93,10 +93,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.5540019332516637, - "jaccard_similarity": 0.24, + "jaccard_similarity": 0.23076923076923078, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.61070489107293 + "phenodigm_score": 0.5988454147360435 } } }, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index 417ee5fa7..9c6dcf5e7 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -1,11 +1,11 @@ { "items": [ - "{\"subject\":{\"id\":\"ZFIN:ZDB-GENE-990415-269\",\"category\":\"biolink:Gene\",\"name\":\"tpma\",\"full_name\":\"alpha-tropomyosin\",\"deprecated\":null,\"description\":null,\"xref\":[\"NCBIGene:30324\",\"ENSEMBL:ENSDARG00000033683\",\"UniProtKB:P13104\",\"PANTHER:PTHR19269\",\"ZFIN:ZDB-GENE-990415-269\"],\"provided_by\":\"alliance_gene_nodes\",\"in_taxon\":\"NCBITaxon:7955\",\"in_taxon_label\":\"Danio rerio\",\"symbol\":\"tpma\",\"synonym\":[\"TPM1-2 alpha\",\"wu:fb37a09\",\"tm\",\"fb37a09\",\"tropomyosin alpha chain\"],\"uri\":\"https://identifiers.org/zfin/ZDB-GENE-990415-269\",\"namespace\":\"ZFIN\",\"has_phenotype\":[\"ZP:0018569\"],\"has_phenotype_label\":[\"myeloid cell development absent, 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continuant\",\"continuant\",\"quality\",\"whole organism mobility, abnormal\",\"abnormal anatomical entity\",\"anatomical structure quality, abnormal\",\"Phenotypic abnormality\",\"whole organism quality, abnormal\",\"abnormal anatomical entity mobility\",\"Zebrafish Phenotype\",\"entity\",\"abnormal phenotype by ontology source\",\"decreased anatomical entity mobility\",\"zebrafish anatomical entity quality, abnormal\",\"whole organism physical object quality, abnormal\",\"whole organism decreased mobility, abnormal\",\"phenotype\",\"phenotype by ontology source\"],\"has_phenotype_count\":1},\"score\":2.0320941603922114,\"similarity\":{\"subject_termset\":{\"ZP:0003210\":{\"id\":\"ZP:0003210\",\"label\":\"whole organism decreased mobility, abnormal (ZPO)\"}},\"object_termset\":{\"HP:0012378\":{\"id\":\"HP:0012378\",\"label\":\"Fatigue (HPO)\"},\"HP:0002104\":{\"id\":\"HP:0002104\",\"label\":\"Apnea (HPO)\"}},\"subject_best_matches\":{\"ZP:0003210\":{\"match_source\":\"ZP:0003210\",\"match_source_label\":\"whole organism decreased mobility, abnormal (ZPO)\",\"match_target\":\"HP:0002104\",\"match_target_label\":\"Apnea (HPO)\",\"score\":2.1482519460253453,\"match_subsumer\":null,\"match_subsumer_label\":null,\"similarity\":{\"subject_id\":\"ZP:0003210\",\"subject_label\":null,\"subject_source\":null,\"object_id\":\"HP:0002104\",\"object_label\":null,\"object_source\":null,\"ancestor_id\":\"UPHENO:0075696\",\"ancestor_label\":\"abnormal anatomical entity\",\"ancestor_source\":null,\"object_information_content\":null,\"subject_information_content\":null,\"ancestor_information_content\":2.1482519460253453,\"jaccard_similarity\":0.3225806451612903,\"cosine_similarity\":null,\"dice_similarity\":null,\"phenodigm_score\":0.8324569050214271}}},\"object_best_matches\":{\"HP:0002104\":{\"match_source\":\"HP:0002104\",\"match_source_label\":\"Apnea (HPO)\",\"match_target\":\"ZP:0003210\",\"match_target_label\":\"whole organism decreased mobility, abnormal (ZPO)\",\"score\":2.1482519460253453,\"match_subsumer\":null,\"match_subsumer_label\":null,\"similarity\":{\"subject_id\":\"HP:0002104\",\"subject_label\":null,\"subject_source\":null,\"object_id\":\"ZP:0003210\",\"object_label\":null,\"object_source\":null,\"ancestor_id\":\"UPHENO:0075696\",\"ancestor_label\":\"abnormal anatomical entity\",\"ancestor_source\":null,\"object_information_content\":null,\"subject_information_content\":null,\"ancestor_information_content\":2.1482519460253453,\"jaccard_similarity\":0.3225806451612903,\"cosine_similarity\":null,\"dice_similarity\":null,\"phenodigm_score\":0.8324569050214271}},\"HP:0012378\":{\"match_source\":\"HP:0012378\",\"match_source_label\":\"Fatigue (HPO)\",\"match_target\":\"ZP:0003210\",\"match_target_label\":\"whole organism decreased mobility, abnormal (ZPO)\",\"score\":1.6836208034928104,\"match_subsumer\":null,\"match_subsumer_label\":null,\"similarity\":{\"subject_id\":\"HP:0012378\",\"subject_label\":null,\"subject_source\":null,\"object_id\":\"ZP:0003210\",\"object_label\":null,\"object_source\":null,\"ancestor_id\":\"UPHENO:0001005\",\"ancestor_label\":\"abnormal phenotype by ontology source\",\"ancestor_source\":null,\"object_information_content\":null,\"subject_information_content\":null,\"ancestor_information_content\":1.6836208034928104,\"jaccard_similarity\":0.34782608695652173,\"cosine_similarity\":null,\"dice_similarity\":null,\"phenodigm_score\":0.765249786669359}}},\"average_score\":2.0320941603922114,\"best_score\":2.1482519460253453,\"metric\":\"ancestor_information_content\"}}", diff --git a/frontend/src/api/phenotype-explorer.ts b/frontend/src/api/phenotype-explorer.ts index 0cd7f7dd0..0172cedf7 100644 --- a/frontend/src/api/phenotype-explorer.ts +++ b/frontend/src/api/phenotype-explorer.ts @@ -8,7 +8,7 @@ import type { Options, OptionsFunc } from "@/components/AppSelectTags.vue"; import type { Phenogrid } from "@/components/ThePhenogrid.vue"; import { stringify } from "@/util/object"; import { apiUrl, request } from "./"; -import { getAutocomplete, getSearch } from "./search"; +import { getAutocomplete } from "./search"; /** search individual phenotypes or gene/disease phenotypes */ export const getPhenotypes = async (search = ""): ReturnType => { @@ -21,9 +21,6 @@ export const getPhenotypes = async (search = ""): ReturnType => { return { autoAccept: true, options: ids.map((id) => ({ id })), - message: ids.every((id) => id.startsWith("HP:")) - ? "" - : 'One or more pasted IDs were not valid HPO phenotype IDs (starting with "HP:")', }; /** otherwise perform string search for phenotypes/genes/diseases */ @@ -89,103 +86,41 @@ export const compareSetToSet = async ( const url = `${apiUrl}/semsim/compare`; const response = await request(url, {}, options); - /** get high level data */ - const summary = Object.values(response.subject_best_matches || {}).map( - (match) => ({ + /** map matches into nicer format */ + const mapMatches = ( + matches: + | TermSetPairwiseSimilarity["subject_best_matches"] + | TermSetPairwiseSimilarity["object_best_matches"], + ) => + Object.values(matches || {}).map((match) => ({ source: match.match_source, source_label: match.match_source_label, target: match.match_target, target_label: match.match_target_label, score: match.score, - }), - ); - summary.sort((a, b) => b.score - a.score); - - /** turn objects into array of cols */ - let cols: Phenogrid["cols"] = Object.values( - response.object_termset || {}, - ).map((col) => ({ - ...col, - total: 0, - })); - /** turn subjects into array of rows */ - let rows: Phenogrid["rows"] = Object.values( - response.subject_termset || {}, - ).map((row) => ({ - ...row, - total: 0, - })); + ...pick(match.similarity, [ + "ancestor_id", + "ancestor_label", + "jaccard_similarity", + "phenodigm_score", + ]), + })); - /** make map of col/row id to cells */ - const cells: Phenogrid["cells"] = {}; - - /** collect unmatched phenotypes */ - let unmatched: Phenogrid["unmatched"] = []; - - /** get subject matches */ - const subjectMatches = Object.values(response.subject_best_matches || {}); - const objectMatches = Object.values(response.object_best_matches || {}); - - for (const col of cols) { - for (const row of rows) { - /** find match corresponding to col/row id */ - const match = - subjectMatches.find( - ({ match_source, match_target }) => - match_source === row.id && match_target === col.id, - ) || - objectMatches.find( - ({ match_source, match_target }) => - match_source === col.id && match_target === row.id, - ); - - /** sum up row and col scores */ - col.total += match?.score || 0; - row.total += match?.score || 0; - - /** assign cell */ - cells[col.id + row.id] = { - score: match?.score || 0, - strength: 0, - ...pick(match?.similarity, [ - "ancestor_id", - "ancestor_label", - "jaccard_similarity", - "phenodigm_score", - ]), - }; - } - } - - /** filter out unmatched phenotypes */ - cols = cols.filter((col) => { - if (!col.total) unmatched.push({ ...col }); - return col.total; - }); - rows = rows.filter((row) => { - if (!row.total) unmatched.push({ ...row }); - return row.total; - }); - - /** deduplicate unmatched phenotypes */ - unmatched = uniqBy(unmatched, "id"); - - /** normalize cell scores to 0-1 */ - const scores = Object.values(cells) - .map((value) => value.score) - .filter(Boolean); - const min = Math.min(...scores); - const max = Math.max(...scores); - Object.values(cells).forEach( - (value) => - (value.strength = - max - min === 0 ? 0.5 : (value.score - min) / (max - min || 0)), + /** get high level data */ + const subjectMatches = mapMatches(response.subject_best_matches); + const objectMatches = mapMatches(response.object_best_matches); + subjectMatches.sort((a, b) => b.score - a.score); + objectMatches.sort((a, b) => b.score - a.score); + + /** find unmatched */ + const subjectUnmatched = Object.values(response.subject_termset || {}).filter( + (term) => !(term.id in (response.subject_best_matches || {})), + ); + const objectUnmatched = Object.values(response.object_termset || {}).filter( + (term) => !(term.id in (response.object_best_matches || {})), ); - /** assemble all data needed for phenogrid */ - const phenogrid = { cols, rows, cells, unmatched } satisfies Phenogrid; - - return { summary, phenogrid }; + return { subjectMatches, objectMatches, subjectUnmatched, objectUnmatched }; }; export type SetToSet = Awaited>; @@ -200,6 +135,8 @@ export const groups = [ "C. Elegans Genes", ] as const; +export type Group = (typeof groups)[number]; + /** compare a set of phenotypes to a group of phenotypes */ export const compareSetToGroup = async ( phenotypes: string[], diff --git a/frontend/src/components/AppRing.vue b/frontend/src/components/AppRing.vue index 2f8f379da..34bd3b404 100644 --- a/frontend/src/components/AppRing.vue +++ b/frontend/src/components/AppRing.vue @@ -4,7 +4,7 @@