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[Platform]: Insilico predictors chart (#594)
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packages/sections/src/variant/InSilicoPredictors/InSilicoPredictorsPlot.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| import { useRef, useEffect } from "react"; | ||
| import * as PlotLib from "@observablehq/plot"; | ||
| import { rgb } from "d3"; | ||
| import { useMeasure } from "@uidotdev/usehooks"; | ||
| import { Box, Fade } from "@mui/material"; | ||
| import { grey } from "@mui/material/colors"; | ||
| import { DataDownloader } from "ui"; | ||
|
|
||
| const PRIORITISATION_COLORS = [ | ||
| rgb("#bc3a19"), | ||
| rgb("#d65a1f"), | ||
| rgb("#e08145"), | ||
| rgb("#e3a772"), | ||
| rgb("#e6ca9c"), | ||
| rgb("#eceada"), | ||
| rgb("#c5d2c1"), | ||
| rgb("#9ebaa8"), | ||
| rgb("#78a290"), | ||
| rgb("#528b78"), | ||
| rgb("#2f735f"), | ||
| ]; | ||
|
|
||
| function InSilicoPredictorsPlot({ data, query, variables, columns }) { | ||
| const [ref, { width }] = useMeasure(); | ||
| return ( | ||
| <div> | ||
| <Box> | ||
| <ChartControls data={data} query={query} variables={variables} columns={columns} /> | ||
| </Box> | ||
| <Box sx={{ width: "90%", margin: "0 auto", mb: 6 }} ref={ref}> | ||
| <Fade in> | ||
| <div> | ||
| <Plot data={data} width={width} /> | ||
| </div> | ||
| </Fade> | ||
| </Box> | ||
| </div> | ||
| ); | ||
| } | ||
|
|
||
| function ChartControls({ data, query, variables, columns }) { | ||
| return ( | ||
| <Box | ||
| sx={{ | ||
| borderColor: grey[300], | ||
| borderRadius: 1, | ||
| display: "flex", | ||
| justifyContent: "flex-end", | ||
| gap: 1, | ||
| }} | ||
| > | ||
| <DataDownloader | ||
| btnLabel="Export" | ||
| rows={data} | ||
| query={query} | ||
| variables={variables} | ||
| columns={columns} | ||
| /> | ||
| </Box> | ||
| ); | ||
| } | ||
|
|
||
| const colorScale = PRIORITISATION_COLORS.reverse(); | ||
| const getXLabel = (tick: number) => { | ||
| if (tick === -1) return "Likely benign"; | ||
| if (tick === 0) return "Uncertain"; | ||
| if (tick === 1) return "Likely deleterious"; | ||
| return ""; | ||
| }; | ||
|
|
||
| function Plot({ data, width }) { | ||
| const headerRef = useRef(); | ||
|
|
||
| useEffect(() => { | ||
| if (data === undefined || width === null) return; | ||
| const chart = PlotLib.plot({ | ||
| width: width, | ||
| height: 250, | ||
| label: null, | ||
| marginLeft: 120, | ||
| marginRight: 100, | ||
| x: { | ||
| axis: "bottom", | ||
| ticks: 2, | ||
| labelAnchor: "center", | ||
| tickFormat: d => getXLabel(d), | ||
| tickSize: 0, | ||
| domain: [-1, 1], | ||
| }, | ||
|
|
||
| color: { | ||
| legend: false, | ||
| type: "linear", | ||
| range: colorScale, | ||
| domain: [-1, 1], | ||
| interpolate: "hsl", | ||
| }, | ||
| style: { | ||
| fontSize: "15px", | ||
| }, | ||
| marks: [ | ||
| PlotLib.ruleY(data, { | ||
| x1: -0.99, | ||
| x2: 0.99, | ||
| y: "method", | ||
| stroke: grey[400], | ||
| strokeWidth: 1, | ||
| strokeDasharray: 6, | ||
| }), | ||
| PlotLib.dot(data, { | ||
| x: "normalisedScore", | ||
| y: "method", | ||
| r: 12, | ||
| fill: "normalisedScore", | ||
| stroke: grey[100], | ||
| strokeWidth: 4, | ||
| tip: { | ||
| fontSize: 14, | ||
| textPadding: 20, | ||
| format: { | ||
| x: false, | ||
| y: false, | ||
| fill: false, | ||
| normalisedScore: false, | ||
| }, | ||
| }, | ||
| channels: { | ||
| method: { | ||
| value: "method", | ||
| label: "", | ||
| }, | ||
| assessment: { | ||
| value: "assessment", | ||
| label: "Assessment:", | ||
| }, | ||
| score: { | ||
| value: "score", | ||
| label: "Score:", | ||
| }, | ||
| assessmentFlag: { | ||
| value: "assessmentFlag", | ||
| label: "Assessment Flag:", | ||
| }, | ||
| normalisedScore: { | ||
| value: "normalisedScore", | ||
| label: "Normalised Score:", | ||
| }, | ||
| }, | ||
| }), | ||
| ], | ||
| }); | ||
| headerRef.current.append(chart); | ||
| return () => chart.remove(); | ||
| }, [data, width]); | ||
|
|
||
| return <Box ref={headerRef}></Box>; | ||
| } | ||
|
|
||
| export default InSilicoPredictorsPlot; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,55 @@ | ||
| import { faChartPie, faTableColumns } from "@fortawesome/free-solid-svg-icons"; | ||
| import { FormControl, MenuItem, Select, SelectChangeEvent, Box } from "@mui/material"; | ||
| import { ReactElement, useState } from "react"; | ||
| import { faChartLine, faTableColumns } from "@fortawesome/free-solid-svg-icons"; | ||
| import { ToggleButtonGroup, ToggleButton, styled } from "@mui/material"; | ||
| import { ReactElement, useState, MouseEvent } from "react"; | ||
| import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; | ||
| import { VIEW } from "../../constants"; | ||
|
|
||
| const menuItemStyles = { display: "flex", gap: 1 }; | ||
| const menuActiveStyles = { display: "flex", gap: 1, alignItems: "center" }; | ||
|
|
||
| type SectionViewToggleProps = { | ||
| defaultValue: string; | ||
| viewChange: (s: string) => void; | ||
| }; | ||
|
|
||
| const StyledToggleButtonGroup = styled(ToggleButtonGroup)` | ||
| padding: 0; | ||
| `; | ||
|
|
||
| const StyledToggleButton = styled(ToggleButton)(({ theme }) => ({ | ||
| paddingTop: theme.spacing(0.5), | ||
| paddingBottom: theme.spacing(0.5), | ||
| display: "flex", | ||
| alignItems: "center", | ||
| gap: theme.spacing(0.5), | ||
| })); | ||
|
|
||
| function SectionViewToggle({ | ||
| defaultValue = VIEW.table, | ||
| viewChange, | ||
| }: SectionViewToggleProps): ReactElement { | ||
| const [alignment, setAlignment] = useState(defaultValue); | ||
| const [sectionView, setView] = useState(defaultValue); | ||
|
|
||
| const handleAlignment = (event: SelectChangeEvent) => { | ||
| const handleViewChange = (event: MouseEvent) => { | ||
| event.preventDefault(); | ||
| if (event.target.value) { | ||
| setAlignment(event.target.value); | ||
| viewChange(event.target.value); | ||
| setView(event.target.value); | ||
| if (viewChange) viewChange(event.target.value); | ||
| } | ||
| }; | ||
|
|
||
| return ( | ||
| <FormControl size="small"> | ||
| <Select | ||
| sx={{ typography: "body2" }} | ||
| value={alignment} | ||
| onChange={handleAlignment} | ||
| renderValue={view => { | ||
| const iconView = VIEW.table ? faTableColumns : faChartPie; | ||
| return ( | ||
| <Box sx={menuActiveStyles}> | ||
| <FontAwesomeIcon icon={iconView} /> {view} view | ||
| </Box> | ||
| ); | ||
| }} | ||
| > | ||
| <MenuItem value={VIEW.table} sx={menuItemStyles}> | ||
| <FontAwesomeIcon icon={faTableColumns} /> | ||
| {VIEW.table} | ||
| </MenuItem> | ||
| <MenuItem value={VIEW.chart} sx={menuItemStyles}> | ||
| <FontAwesomeIcon icon={faChartPie} /> {VIEW.chart} | ||
| </MenuItem> | ||
| </Select> | ||
| </FormControl> | ||
| <StyledToggleButtonGroup | ||
| sx={{ typography: "body2" }} | ||
| value={sectionView} | ||
| onChange={handleViewChange} | ||
| > | ||
| <StyledToggleButton aria-label="Switch to table view" value={VIEW.table}> | ||
| <FontAwesomeIcon icon={faTableColumns} /> | ||
| {VIEW.table} view | ||
| </StyledToggleButton> | ||
| <StyledToggleButton aria-label="Switch to chartn view" value={VIEW.chart}> | ||
| <FontAwesomeIcon icon={faChartLine} /> | ||
| {VIEW.chart} | ||
| </StyledToggleButton> | ||
| </StyledToggleButtonGroup> | ||
| ); | ||
| } | ||
| export default SectionViewToggle; |
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