diff --git a/src/LandingPage/components/figure1c.jsx b/src/LandingPage/components/figure1c.jsx new file mode 100644 index 00000000..cafebb30 --- /dev/null +++ b/src/LandingPage/components/figure1c.jsx @@ -0,0 +1,367 @@ +import React, { useRef } from 'react'; +import * as d3 from 'd3'; + +const dataset = require('./figure1c_data.json'); + +const figureTissueProps = require('./figureTissueProps.json'); + +const tissueLabels = [ + 'BLOOD', + 'PLASMA', + 'HEART', + 'VENACV', + 'SPLEEN', + 'SKM-GN', + 'SKM-VL', + 'WAT-SC', + 'BAT', + 'LIVER', + 'LUNG', + 'KIDNEY', + 'ADRNL', + 'CORTEX', + 'HYPOTH', + 'HIPPOC', + 'SMLINT', + 'COLON', + 'OVARY', + 'TESTES', +]; + +const omeLabels = [ + 'METAB', + 'IMMUNO', + 'UBIQ', + 'ACETYL', + 'PHOSPHO', + 'PROT', + 'TRNSCRPT', + 'ATAC', + 'METHYL', +]; + +const assayMap = { + METAB: 'Metabolomics', + IMMUNO: 'Immunoassays', + UBIQ: 'Ubiquitylome', + ACETYL: 'Acetylproteomics', + PHOSPHO: 'Phosphoproteomics', + PROT: 'Global proteomics', + TRNSCRPT: 'RNA-Seq', + ATAC: 'ATAC-seq', + METHYL: 'RRBS', +}; + +const omeColors = [ + { type: 'Genomics', color: '#FC8D62' }, + { type: 'Proteomics', color: '#8DA0CB' }, + { type: 'Metabolomics', color: '#66C2A5' }, + { type: 'Immunoassays', color: '#E78AC3' }, +]; + +/** + * Renders landscape paper figure 1c heatmap + * + * @returns {Object} JSX representation of figure 1c heatmap + */ +function Figure1C() { + const svgRef = useRef(); + + function renderHeatmap() { + // set the dimensions and margins of the graph + const margin = { top: 0, right: 20, bottom: 100, left: 130 }; + // calc width by number of pass1b-06 tissues (20) vs each square's pixel width + const width = 20 * 55; + // calc height by number of omes vs each sqaure's pixel height + const height = 9 * 55; + + // select DOM element to draw graph + const div = d3.select(svgRef.current); + div.selectAll('*').remove(); + + // append the svg object to the selected DOM element + // append a 'group' element to 'svg' + // moves the 'group' element to the top left margin + const svg = div + .append('svg') + .attr('width', width + margin.left + margin.right) + .attr('height', height + margin.top + margin.bottom) + .attr('class', 'heatmap-svg') + .append('g') + .attr('transform', 'translate(' + margin.left + ',' + margin.top + ')'); + + // build X scales and axis + const x = d3 + .scaleBand() + .range([0, width]) + .domain(tissueLabels) + .padding(0.1); + + // draw X axis + svg + .append('g') + .attr('transform', 'translate(0,' + height + ')') + .call(d3.axisBottom(x).tickSize(0).tickPadding(0)) + .selectAll('text') + .attr('transform', 'translate(-10, 8)rotate(-90)') + .style('text-anchor', 'end') + .style('color', '#ffffff') + .style('font-size', '20px') + .style('font-weight', '500') + .select('.domain') + .remove(); + + // Remove X axis line + svg.call(d3.axisBottom(x).tickSize(0)).select('.domain').remove(); + + // build Y scales and axis + const y = d3.scaleBand().range([height, 0]).domain(omeLabels).padding(0.1); + + // draw Y axis + svg + .append('g') + .attr('class', 'heatmap-y-axis') + .call(d3.axisLeft(y).tickSize(0).tickPadding(6)) + .style('color', '#ffffff') + .style('font-size', '20px') + .style('font-weight', '500') + .select('.domain') + .remove(); + + // build color scale + const colorScale = d3 + .scaleSequential() + .interpolator(d3.interpolateViridis) + .domain([0, 0.1]); + + // create a tooltip + const tooltip = d3 + .select('body') + .append('div') + .style('opacity', 0) + .attr('class', 'heatmap-tooltip'); + + // Tooltip functions + const onMouseOver = (event, d) => { + if (d.featureCnt !== null) { + d3.select(event.currentTarget).attr('rx', 12).attr('ry', 12); + } + }; + const onMouseMove = (event, d) => { + if (d.featureCnt !== null) { + tooltip + .html( + 'Tissue: ' + + figureTissueProps[d.tissue].label + + '
Assay: ' + + assayMap[d.ome], + ) + .style('top', event.pageY - 60 + 'px') + .style('left', event.pageX + 'px'); + tooltip.transition().duration(100).style('opacity', 1); + d3.select(this).style('opacity', 1); + } + }; + const onMouseLeave = (event, d) => { + if (d.featureCnt !== null) { + tooltip.transition().duration(100).style('opacity', 0); + d3.select(event.currentTarget).attr('rx', 4).attr('ry', 4); + } + }; + + // Draw squares + const rect = svg + .selectAll() + .data(dataset, (d) => d.tissue + ':' + d.ome) + .enter(); + + rect + .append('rect') + .attr('x', (d) => x(d.tissue)) + .attr('y', (d) => y(d.ome)) + .attr('rx', 4) + .attr('ry', 4) + .attr('width', x.bandwidth()) + .attr('height', y.bandwidth()) + .style('fill', (d) => + d.featureCnt !== null ? colorScale(d.diffProportion) : '#ffffff', + ) + .style('stroke-width', 0) + .style('stroke', 'none') + .on('mouseover', onMouseOver) + .on('mousemove', onMouseMove) + .on('mouseleave', onMouseLeave); + + // Draw text inside squares + rect + .append('text') + .attr('x', (d) => x(d.tissue) + 24) // Center text horizontally + .attr('y', (d) => y(d.ome) + 30) // Center text vertically + .attr('text-anchor', 'middle') // Center text horizontally + .attr('alignment-baseline', 'middle') // Center text vertically + .style('fill', (d) => (d.diffProportion > 0.04 ? '#000000' : '#ffffff')) + .style('font-size', '16px') + .style('cursor', 'default') + .text((d) => d.featureCnt); + + // Heatmap legend with continuous gradient + const legendMargin = { top: 15, bottom: 15, left: 20, right: 20 }; + const legendWidth = 120; + const legendHeight = 580; // Same as heatmap height + const legendColorScaleHeight = 340; + + // Append the svg legend to the body of the page + const legend = div + .append('svg') + .attr('width', legendWidth + legendMargin.left + legendMargin.right) + .attr('height', legendHeight + legendMargin.top + legendMargin.bottom); + + // legend color scale + const legendColorScale = d3 + .scaleSequential(d3.interpolateViridis) + .domain([0.1, 0]); + + // build legend Y scales and axis: + const legendYAxisScale = d3 + .scaleLinear() + .range([legendMargin.top + 260, legendHeight + 2]) + .domain(legendColorScale.domain()); + + const legendYAxisRight = (g) => + g + .attr('class', 'legend-y-axis') + .attr( + 'tranform', + `translate(${legendMargin.left + legendWidth}, ${legendMargin.top})`, + ) + .call( + d3 + .axisRight(legendYAxisScale) + .ticks(5) + .tickSize(0) + .tickPadding(40) + .tickFormat((i) => { + if (i === 0.1) { + return '0.1+'; + } + return i; + }), + ); + + const defs = legend.append('defs'); + // create gradient color scale in legend + // and reverse its vertical orientation + const linearGradient = defs + .append('linearGradient') + .attr('id', 'heatmapGradient') + .attr('x1', '0%') // bottom + .attr('y1', '100%') + .attr('x2', '0%') // to top + .attr('y2', '0%'); + + // append multiple color stops by using D3's data/enter step + linearGradient + .selectAll('stop') + .data( + legendColorScale.ticks().map((t, i, n) => ({ + offset: `${(100 * i) / n.length}%`, + color: legendColorScale(t), + })), + ) + .enter() + .append('stop') + .attr('offset', (d) => d.offset) + .attr('stop-color', (d) => d.color); + + // draw the rectangle and fill with gradient color scale + legend + .append('g') + .attr('transform', `translate(0, ${legendMargin.top})`) + .append('rect') + .attr('transform', `translate(0, 260)`) + .attr('width', 30) + .attr('rx', 4) + .attr('ry', 4) + .attr( + 'height', + legendColorScaleHeight - legendMargin.top - legendMargin.bottom, + ) + .style('fill', 'url(#heatmapGradient)'); + + // legend.selectAll('#heatmapGradient').attr('gradientTransform', 'rotate(0)'); + + // remove Y axis line + legend.append('g').call(legendYAxisRight).select('.domain').remove(); + + // draw legend title/label + legend + .append('text') + .attr('class', 'legend-title-diff-proportion') + .attr('x', 0) + .attr('y', legendMargin.top + 200) + .append('tspan') + .text('Differential') + .append('tspan') + .attr('x', 0) + .attr('y', legendMargin.top + 220) + .text('proportion') + .append('tspan') + .text('of analytes') + .attr('x', 0) + .attr('y', legendMargin.top + 240); + + // draw ome type legend title/label + legend + .append('text') + .attr('class', 'legend-title-ome-type') + .attr('x', 0) + .attr('y', legendMargin.top + 10) + .append('tspan') + .text('Ome Type'); + + // draw ome type legend + const legendOmeType = legend + .append('g') + .attr('class', 'legend-ome-type') + .attr('transform', `translate(0, ${legendMargin.top})`) + .selectAll('g') + .data(omeColors) + .enter() + .append('g') + .attr( + 'transform', + (d, i) => `translate(0, ${legendMargin.top + 10 + i * 36})`, + ); + + legendOmeType + .append('rect') + .attr('width', 30) + .attr('height', 30) + .attr('x', 0) + .attr('y', 0) + .attr('rx', 4) + .attr('ry', 4) + .style('fill', (d) => d.color); + + legendOmeType + .append('text') + .attr('x', 40) + .attr('y', 20) + .text((d) => d.type) + .style('font-size', '16px') + .style('font-weight', '400') + .style('fill', '#ffffff'); + } + + return ( +
+ {renderHeatmap()} +
+ ); +} + +export default Figure1C; diff --git a/src/LandingPage/components/figure1c_data.json b/src/LandingPage/components/figure1c_data.json new file mode 100644 index 00000000..6d1b77c4 --- /dev/null +++ b/src/LandingPage/components/figure1c_data.json @@ -0,0 +1,1622 @@ +[ + { + "ome": "METHYL", + "tissue": "BLOOD", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#DDA0DD" + }, + { + "ome": "ATAC", + "tissue": "BLOOD", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#DDA0DD" + }, + { + "ome": "TRNSCRPT", + "tissue": "BLOOD", + "omeType": "Genomics", + "featureCnt": 1582, + "diffProportion": 0.1, + "omeColor": "#FC8D62", + "tissueColor": "#DDA0DD" + }, + { + "ome": "PROT", + "tissue": "BLOOD", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#DDA0DD" + }, + { + "ome": "PHOSPHO", + "tissue": "BLOOD", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#DDA0DD" + }, + { + "ome": "ACETYL", + "tissue": "BLOOD", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#DDA0DD" + }, + { + "ome": "UBIQ", + "tissue": "BLOOD", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#DDA0DD" + }, + { + "ome": "IMMUNO", + "tissue": "BLOOD", + "omeType": "Immunoassays", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#66C2A5", + "tissueColor": "#DDA0DD" + }, + { + "ome": "METAB", + "tissue": "BLOOD", + "omeType": "Metabolomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#E78AC3", + "tissueColor": "#DDA0DD" + }, + { + "ome": "METHYL", + "tissue": "PLASMA", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#8c5220" + }, + { + "ome": "ATAC", + "tissue": "PLASMA", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#8c5220" + }, + { + "ome": "TRNSCRPT", + "tissue": "PLASMA", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#8c5220" + }, + { + "ome": "PROT", + "tissue": "PLASMA", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#8c5220" + }, + { + "ome": "PHOSPHO", + "tissue": "PLASMA", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#8c5220" + }, + { + "ome": "ACETYL", + "tissue": "PLASMA", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#8c5220" + }, + { + "ome": "UBIQ", + "tissue": "PLASMA", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#8c5220" + }, + { + "ome": "IMMUNO", + "tissue": "PLASMA", + "omeType": "Immunoassays", + "featureCnt": 14, + "diffProportion": 0.1, + "omeColor": "#66C2A5", + "tissueColor": "#8c5220" + }, + { + "ome": "METAB", + "tissue": "PLASMA", + "omeType": "Metabolomics", + "featureCnt": 529, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#8c5220" + }, + { + "ome": "METHYL", + "tissue": "HEART", + "omeType": "Genomics", + "featureCnt": 107, + "diffProportion": 0.0001094885656076, + "omeColor": "#FC8D62", + "tissueColor": "#d92c04" + }, + { + "ome": "ATAC", + "tissue": "HEART", + "omeType": "Genomics", + "featureCnt": 75, + "diffProportion": 0.0001029758652032, + "omeColor": "#FC8D62", + "tissueColor": "#d92c04" + }, + { + "ome": "TRNSCRPT", + "tissue": "HEART", + "omeType": "Genomics", + "featureCnt": 722, + "diffProportion": 0.0499826929733472, + "omeColor": "#FC8D62", + "tissueColor": "#d92c04" + }, + { + "ome": "PROT", + "tissue": "HEART", + "omeType": "Proteomics", + "featureCnt": 693, + "diffProportion": 0.0754573170731707, + "omeColor": "#8DA0CB", + "tissueColor": "#d92c04" + }, + { + "ome": "PHOSPHO", + "tissue": "HEART", + "omeType": "Proteomics", + "featureCnt": 436, + "diffProportion": 0.0108436132113012, + "omeColor": "#8DA0CB", + "tissueColor": "#d92c04" + }, + { + "ome": "ACETYL", + "tissue": "HEART", + "omeType": "Proteomics", + "featureCnt": 450, + "diffProportion": 0.0863226549012085, + "omeColor": "#8DA0CB", + "tissueColor": "#d92c04" + }, + { + "ome": "UBIQ", + "tissue": "HEART", + "omeType": "Proteomics", + "featureCnt": 24, + "diffProportion": 0.0033907883582933, + "omeColor": "#8DA0CB", + "tissueColor": "#d92c04" + }, + { + "ome": "IMMUNO", + "tissue": "HEART", + "omeType": "Immunoassays", + "featureCnt": 4, + "diffProportion": 0.1, + "omeColor": "#66C2A5", + "tissueColor": "#d92c04" + }, + { + "ome": "METAB", + "tissue": "HEART", + "omeType": "Metabolomics", + "featureCnt": 568, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#d92c04" + }, + { + "ome": "METHYL", + "tissue": "VENACV", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#5a2e15" + }, + { + "ome": "ATAC", + "tissue": "VENACV", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#5a2e15" + }, + { + "ome": "TRNSCRPT", + "tissue": "VENACV", + "omeType": "Genomics", + "featureCnt": 90, + "diffProportion": 0.0055086301872934, + "omeColor": "#FC8D62", + "tissueColor": "#5a2e15" + }, + { + "ome": "PROT", + "tissue": "VENACV", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#5a2e15" + }, + { + "ome": "PHOSPHO", + "tissue": "VENACV", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#5a2e15" + }, + { + "ome": "ACETYL", + "tissue": "VENACV", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#5a2e15" + }, + { + "ome": "UBIQ", + "tissue": "VENACV", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#5a2e15" + }, + { + "ome": "IMMUNO", + "tissue": "VENACV", + "omeType": "Immunoassays", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#66C2A5", + "tissueColor": "#5a2e15" + }, + { + "ome": "METAB", + "tissue": "VENACV", + "omeType": "Metabolomics", + "featureCnt": 23, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#5a2e15" + }, + { + "ome": "METHYL", + "tissue": "SPLEEN", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#f2e751" + }, + { + "ome": "ATAC", + "tissue": "SPLEEN", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#f2e751" + }, + { + "ome": "TRNSCRPT", + "tissue": "SPLEEN", + "omeType": "Genomics", + "featureCnt": 1099, + "diffProportion": 0.0673448127949016, + "omeColor": "#FC8D62", + "tissueColor": "#f2e751" + }, + { + "ome": "PROT", + "tissue": "SPLEEN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f2e751" + }, + { + "ome": "PHOSPHO", + "tissue": "SPLEEN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f2e751" + }, + { + "ome": "ACETYL", + "tissue": "SPLEEN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f2e751" + }, + { + "ome": "UBIQ", + "tissue": "SPLEEN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f2e751" + }, + { + "ome": "IMMUNO", + "tissue": "SPLEEN", + "omeType": "Immunoassays", + "featureCnt": 12, + "diffProportion": 0.1, + "omeColor": "#66C2A5", + "tissueColor": "#f2e751" + }, + { + "ome": "METAB", + "tissue": "SPLEEN", + "omeType": "Metabolomics", + "featureCnt": 83, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#f2e751" + }, + { + "ome": "METHYL", + "tissue": "SKM-GN", + "omeType": "Genomics", + "featureCnt": 119, + "diffProportion": 0.0001077944441475, + "omeColor": "#FC8D62", + "tissueColor": "#f28b2f" + }, + { + "ome": "ATAC", + "tissue": "SKM-GN", + "omeType": "Genomics", + "featureCnt": 442, + "diffProportion": 0.0004507890337918, + "omeColor": "#FC8D62", + "tissueColor": "#f28b2f" + }, + { + "ome": "TRNSCRPT", + "tissue": "SKM-GN", + "omeType": "Genomics", + "featureCnt": 566, + "diffProportion": 0.0410919122985335, + "omeColor": "#FC8D62", + "tissueColor": "#f28b2f" + }, + { + "ome": "PROT", + "tissue": "SKM-GN", + "omeType": "Proteomics", + "featureCnt": 691, + "diffProportion": 0.1, + "omeColor": "#8DA0CB", + "tissueColor": "#f28b2f" + }, + { + "ome": "PHOSPHO", + "tissue": "SKM-GN", + "omeType": "Proteomics", + "featureCnt": 694, + "diffProportion": 0.0234056186975144, + "omeColor": "#8DA0CB", + "tissueColor": "#f28b2f" + }, + { + "ome": "ACETYL", + "tissue": "SKM-GN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f28b2f" + }, + { + "ome": "UBIQ", + "tissue": "SKM-GN", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#f28b2f" + }, + { + "ome": "IMMUNO", + "tissue": "SKM-GN", + "omeType": "Immunoassays", + "featureCnt": 7, + "diffProportion": 0.1, + "omeColor": "#66C2A5", + "tissueColor": "#f28b2f" + }, + { + "ome": "METAB", + "tissue": "SKM-GN", + "omeType": "Metabolomics", + "featureCnt": 298, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#f28b2f" + }, + { + "ome": "METHYL", + "tissue": "SKM-VL", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": 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"diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#6d86a5" + }, + { + "ome": "METHYL", + "tissue": "OVARY", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#a5415b" + }, + { + "ome": "ATAC", + "tissue": "OVARY", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#a5415b" + }, + { + "ome": "TRNSCRPT", + "tissue": "OVARY", + "omeType": "Genomics", + "featureCnt": 896, + "diffProportion": 0.0525975931904902, + "omeColor": "#FC8D62", + "tissueColor": "#a5415b" + }, + { + "ome": "PROT", + "tissue": "OVARY", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#a5415b" + }, + { + "ome": "PHOSPHO", + "tissue": "OVARY", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#a5415b" + }, + { + "ome": "ACETYL", + "tissue": "OVARY", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#a5415b" + }, + { + "ome": "UBIQ", + "tissue": "OVARY", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#a5415b" + }, + { + "ome": "IMMUNO", + "tissue": "OVARY", + "omeType": "Immunoassays", + "featureCnt": 0, + "diffProportion": 0, + "omeColor": "#66C2A5", + "tissueColor": "#a5415b" + }, + { + "ome": "METAB", + "tissue": "OVARY", + "omeType": "Metabolomics", + "featureCnt": 21, + "diffProportion": 0.0921052631578947, + "omeColor": "#E78AC3", + "tissueColor": "#a5415b" + }, + { + "ome": "METHYL", + "tissue": "TESTES", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#214da6" + }, + { + "ome": "ATAC", + "tissue": "TESTES", + "omeType": "Genomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#FC8D62", + "tissueColor": "#214da6" + }, + { + "ome": "TRNSCRPT", + "tissue": "TESTES", + "omeType": "Genomics", + "featureCnt": 107, + "diffProportion": 0.0061639495362636, + "omeColor": "#FC8D62", + "tissueColor": "#214da6" + }, + { + "ome": "PROT", + "tissue": "TESTES", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#214da6" + }, + { + "ome": "PHOSPHO", + "tissue": "TESTES", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#214da6" + }, + { + "ome": "ACETYL", + "tissue": "TESTES", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#214da6" + }, + { + "ome": "UBIQ", + "tissue": "TESTES", + "omeType": "Proteomics", + "featureCnt": null, + "diffProportion": 0, + "omeColor": "#8DA0CB", + "tissueColor": "#214da6" + }, + { + "ome": "IMMUNO", + "tissue": "TESTES", + "omeType": "Immunoassays", + "featureCnt": 4, + "diffProportion": 0.0869565217391304, + "omeColor": "#66C2A5", + "tissueColor": "#214da6" + }, + { + "ome": "METAB", + "tissue": "TESTES", + "omeType": "Metabolomics", + "featureCnt": 44, + "diffProportion": 0.1, + "omeColor": "#E78AC3", + "tissueColor": "#214da6" + } +] \ No newline at end of file diff --git a/src/LandingPage/components/figureTissueProps.json b/src/LandingPage/components/figureTissueProps.json new file mode 100644 index 00000000..737f3bf0 --- /dev/null +++ b/src/LandingPage/components/figureTissueProps.json @@ -0,0 +1,226 @@ +{ + "BLOOD": { + "label": "Blood RNA", + "hoverLabelColor": "#D92C04", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq" + ] + }, + "PLASMA": { + "label": "Plasma", + "hoverLabelColor": "#F1997C", + "hoverLabelTextColor": "#000000", + "assays": [ + "metab", + "cytokine" + ] + }, + "HEART": { + "label": "Heart", + "hoverLabelColor": "#F28B2F", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "prot-ac", + "prot-ub", + "metab", + "cytokine" + ] + }, + "VENACV": { + "label": "Vena Cava", + "hoverLabelColor": "#A5415B", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq" + ] + }, + "SPLEEN": { + "label": "Spleen", + "hoverLabelColor": "#F3C288", + "hoverLabelTextColor": "#000000", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "SKM-GN": { + "label": "Gastrocnemius", + "hoverLabelColor": "#088C03", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "metab", + "cytokine" + ] + }, + "SKM-VL": { + "label": "Vastus Lateralis", + "hoverLabelColor": "#025939", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "WAT-SC": { + "label": "White Adipose", + "hoverLabelColor": "#214DA6", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "metab", + "cytokine" + ] + }, + "BAT": { + "label": "Brown Adipose", + "hoverLabelColor": "#8C5220", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "metab", + "cytokine" + ] + }, + "LIVER": { + "label": "Liver", + "hoverLabelColor": "#DA6C75", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "prot-ac", + "prot-ub", + "metab", + "cytokine" + ] + }, + "LUNG": { + "label": "Lung", + "hoverLabelColor": "#04BF8A", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "metab", + "cytokine" + ] + }, + "KIDNEY": { + "label": "Kidney", + "hoverLabelColor": "#7553A7", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rrbs", + "atac-seq", + "rna-seq", + "prot-pr", + "prot-ph", + "metab", + "cytokine" + ] + }, + "ADRNL": { + "label": "Adrenal", + "hoverLabelColor": "#DDA0DD", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "CORTEX": { + "label": "Cortex", + "hoverLabelColor": "#F2E751", + "hoverLabelTextColor": "#000000", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "HYPOTH": { + "label": "Hypothalamus", + "hoverLabelColor": "#F2B443", + "hoverLabelTextColor": "#000000", + "assays": [ + "rna-seq", + "metab" + ] + }, + "HIPPOC": { + "label": "Hippocampus", + "hoverLabelColor": "#BF7534", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "atac-seq", + "rna-seq", + "metab", + "cytokine" + ] + }, + "SMLINT": { + "label": "Small Intestine", + "hoverLabelColor": "#A18277", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "COLON": { + "label": "Colon", + "hoverLabelColor": "#5A2E15", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "OVARY": { + "label": "Ovary", + "hoverLabelColor": "#F2CED0", + "hoverLabelTextColor": "#000000", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + }, + "TESTES": { + "label": "Testes", + "hoverLabelColor": "#6D86A5", + "hoverLabelTextColor": "#FFFFFF", + "assays": [ + "rna-seq", + "metab", + "cytokine" + ] + } +} diff --git a/src/LandingPage/landingPage.jsx b/src/LandingPage/landingPage.jsx index 70bc391e..6706d822 100644 --- a/src/LandingPage/landingPage.jsx +++ b/src/LandingPage/landingPage.jsx @@ -12,10 +12,10 @@ import IconSet from '../lib/iconSet'; import LayerRunner from '../assets/LandingPageGraphics/Data_Layer_Runner.png'; import RatFigurePaass1b from '../assets/LandingPageGraphics/rat-figure-pass1b.svg'; -import DifferentialAnalytesHeatmap from '../assets/LandingPageGraphics/figure1c-differential-analytes-grid.svg'; import TutorialVideoPreviewImage from '../assets/LandingPageGraphics/tutorial_video_preview_image.jpg'; import LandscapePreprintAbstract from '../assets/LandingPageGraphics/landscape_preprint_abstract.jpg'; import BackgroundVideo from './components/backgroundVideo'; +import Figure1C from './components/figure1c'; // import figure 4E visualization dataset const figure4eData = require('../data/landscape_figure_4e.json'); @@ -240,7 +240,7 @@ export function LandingPage({ isAuthenticated, profile }) { getNodes={getNodes} />
-

+

A network of genes functionally related to longevity, muscle system processes, and response to mechanical stimulus

@@ -252,13 +252,7 @@ export function LandingPage({ isAuthenticated, profile }) {
- - Rat Figure - Endurance Training - +

Visualize the number of training-differential features whose diff --git a/src/sass/_landingPage.scss b/src/sass/_landingPage.scss index 4a324160..8fad0f98 100644 --- a/src/sass/_landingPage.scss +++ b/src/sass/_landingPage.scss @@ -89,7 +89,7 @@ .section-content-container { height: 75vh; - padding-top: 15px; + padding-top: 72px; padding-bottom: 15px; .vis-tooltip { @@ -121,6 +121,11 @@ img { margin-left: 15em; margin-right: 15em; + + &.img-fluid { + max-width: 70%; + height: auto; + } } } @@ -249,6 +254,78 @@ body.homepage { display: block; } } + + #heatmap-container { + min-width: 1450px !important; + min-height: 610px; + } + + .heatmap-y-axis { + .tick { + text { + font-size: 1.35rem; + font-weight: 800; + } + } + .tick:last-child, + .tick:nth-child(7), + .tick:nth-child(8) { + text { + fill: #FC8D62; + } + } + .tick:nth-child(3), + .tick:nth-child(4), + .tick:nth-child(5), + .tick:nth-child(6) { + text { + fill: #8DA0CB; + } + } + .tick:nth-child(2) { + text { + fill: #66C2A5; + } + } + .tick:first-child { + text { + fill: #E78AC3; + } + } + } + + .heatmap-tooltip { + background: #000; + border-radius: 4px; + color: #ffffff; + font-size: 0.7rem; + font-weight: 600; + padding: 9px 13px; + position: absolute; + text-align: left; + } + + .legend-title-diff-proportion, + .legend-title-ome-type { + tspan { + fill: #fff; + font-size: 1.0rem; + } + } + + .legend-y-axis { + font-size: 0.7rem; + + .tick { + text { + fill: #fff; + font-size: 0.85rem; + } + text::before { + content: '%'; + } + } + } } section.first {