From dea3dd2008bb120445b0791bb294947fcf802ea7 Mon Sep 17 00:00:00 2001 From: Graham McNeill Date: Mon, 9 Dec 2024 10:29:34 +0000 Subject: [PATCH] spacing and therapeutic areas labels --- .../src/variant/GWASCredibleSets/Body.tsx | 4 +- .../variant/GWASCredibleSets/PheWasPlot.tsx | 62 +++++++++---------- 2 files changed, 30 insertions(+), 36 deletions(-) diff --git a/packages/sections/src/variant/GWASCredibleSets/Body.tsx b/packages/sections/src/variant/GWASCredibleSets/Body.tsx index 97ac4c251..6b32e1e1c 100644 --- a/packages/sections/src/variant/GWASCredibleSets/Body.tsx +++ b/packages/sections/src/variant/GWASCredibleSets/Body.tsx @@ -281,8 +281,8 @@ function Body({ id, entity }: BodyProps) { loading={request.loading} data={request.data?.variant.gwasCredibleSets.rows} id={id} - referenceAllele={referenceAllele} - alternateAllele={alternateAllele} + referenceAllele={request.data?.variant.referenceAllele} + alternateAllele={request.data?.variant.alternateAllele} /> ); }} diff --git a/packages/sections/src/variant/GWASCredibleSets/PheWasPlot.tsx b/packages/sections/src/variant/GWASCredibleSets/PheWasPlot.tsx index 718430777..478737bc9 100644 --- a/packages/sections/src/variant/GWASCredibleSets/PheWasPlot.tsx +++ b/packages/sections/src/variant/GWASCredibleSets/PheWasPlot.tsx @@ -28,7 +28,7 @@ import { Fragment } from "react/jsx-runtime"; export default function PheWasPlot({ loading, data, id, referenceAllele, alternateAllele }) { - const plotHeight = 440; + const plotHeight = 450; const theme = useTheme(); const background = theme.palette.background.paper; const fontFamily = theme.typography.fontFamily; @@ -106,11 +106,6 @@ export default function PheWasPlot({ loading, data, id, referenceAllele, alterna xIntervals.get(id).end = xCumu; } - function xAnchor(row) { - const x = rowLookup.get(row).x; - return x < xCumu / 2 ? 'left' : 'right'; - } - const xScale = scaleLinear().domain([0, xCumu]); const yScale = scaleLinear().domain([yMin, yMax]).nice(); // ensure min scale value <= yMin yScale.domain([yScale.domain()[0], yMax]); // ensure max scale value is yMax - in case nice changed it @@ -141,20 +136,20 @@ export default function PheWasPlot({ loading, data, id, referenceAllele, alterna <> {/* legend */} - {/* Beta: △ positive, ▽ negative, ○ {naLabel} */} - - ▲ Beta > 0   - ▼ Beta < 0   - ● Beta {naLabel}   - Filled symbol: + + ▲ Beta > 0   + ▼ Beta < 0   + ● Beta {naLabel}   + Filled symbol:{" "} + {" "}is lead variant {/* plot */} @@ -165,7 +160,7 @@ export default function PheWasPlot({ loading, data, id, referenceAllele, alterna clearOnClick clearOnLeave height={plotHeight} - padding={{ top: 30, right: 40, bottom: 100, left: 90 }} + padding={{ top: 30, right: 50, bottom: 120, left: 90 }} fontFamily={fontFamily} data={sortedData} yReverse @@ -231,7 +226,6 @@ export default function PheWasPlot({ loading, data, id, referenceAllele, alterna rowLookup.get(d).x} y={d => yMin} - // y={pValue} pxWidth={360} pxHeight={350} content={tooltipContent} @@ -353,28 +347,28 @@ function tooltipContent(data) { } const therapeuticPriorities = { - MONDO_0045024: { name: "cell proliferation disorder", rank: 1 }, + MONDO_0045024: { name: "cell proliferation", rank: 1 }, EFO_0005741: { name: "infectious disease", rank: 2 }, - OTAR_0000014: { name: "pregnancy or perinatal disease", rank: 3 }, + OTAR_0000014: { name: "pregnancy or perinatal", rank: 3 }, EFO_0005932: { name: "animal disease", rank: 4 }, - MONDO_0024458: { name: "disease of visual system", rank: 5 }, - EFO_0000319: { name: "cardiovascular disease", rank: 6 }, - EFO_0009605: { name: "pancreas disease", rank: 7 }, - EFO_0010282: { name: "gastrointestinal disease", rank: 8 }, - OTAR_0000017: { name: "reproductive system or breast disease", rank: 9 }, - EFO_0010285: { name: "integumentary system disease", rank: 10 }, - EFO_0001379: { name: "endocrine system disease", rank: 11 }, - OTAR_0000010: { name: "respiratory or thoracic disease", rank: 12 }, - EFO_0009690: { name: "urinary system disease", rank: 13 }, - OTAR_0000006: { name: "musculoskeletal or connective tissue disease", rank: 14 }, + MONDO_0024458: { name: "visual system", rank: 5 }, + EFO_0000319: { name: "cardiovascular", rank: 6 }, + EFO_0009605: { name: "pancreas", rank: 7 }, + EFO_0010282: { name: "gastrointestinal", rank: 8 }, + OTAR_0000017: { name: "reproductive system or breast", rank: 9 }, + EFO_0010285: { name: "integumentary system", rank: 10 }, + EFO_0001379: { name: "endocrine system", rank: 11 }, + OTAR_0000010: { name: "respiratory or thoracic", rank: 12 }, + EFO_0009690: { name: "urinary system", rank: 13 }, + OTAR_0000006: { name: "musculoskeletal or connective ...", rank: 14 }, MONDO_0021205: { name: "disease of ear", rank: 15 }, - EFO_0000540: { name: "immune system disease", rank: 16 }, - EFO_0005803: { name: "hematologic disease", rank: 17 }, - EFO_0000618: { name: "nervous system disease", rank: 18 }, - MONDO_0002025: { name: "psychiatric disorder", rank: 19 }, - OTAR_0000020: { name: "nutritional or metabolic disease", rank: 20 }, - OTAR_0000018: { name: "genetic, familial or congenital disease", rank: 21 }, - OTAR_0000009: { name: "injury, poisoning or other complication", rank: 22 }, + EFO_0000540: { name: "immune system", rank: 16 }, + EFO_0005803: { name: "hematologic", rank: 17 }, + EFO_0000618: { name: "nervous system", rank: 18 }, + MONDO_0002025: { name: "psychiatric", rank: 19 }, + OTAR_0000020: { name: "nutritional or metabolic", rank: 20 }, + OTAR_0000018: { name: "genetic, familial or congenital", rank: 21 }, + OTAR_0000009: { name: "injury, poisoning or complication", rank: 22 }, EFO_0000651: { name: "phenotype", rank: 23 }, EFO_0001444: { name: "measurement", rank: 24 }, GO_0008150: { name: "biological process", rank: 25 },