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"https://opencollective.com/webpack" } }, + "node_modules/world-calendars": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.3.tgz", + "integrity": "sha512-sAjLZkBnsbHkHWVhrsCU5Sa/EVuf9QqgvrN8zyJ2L/F9FR9Oc6CvVK0674+PGAtmmmYQMH98tCUSO4QLQv3/TQ==", + "peer": true, + "dependencies": { + "object-assign": "^4.1.0" + } + }, "node_modules/wrap-ansi": { "version": "7.0.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz", "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==", - "dev": true, "dependencies": { "ansi-styles": "^4.0.0", "string-width": "^4.1.0", @@ -15950,7 +18824,6 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", - "dev": true, "engines": { "node": ">=0.4" } diff --git a/package.json b/package.json index b646ddf58..656d5c23a 100644 --- a/package.json +++ b/package.json @@ -53,10 +53,14 @@ "react-toastify": "^9.1.2", "react-twitter-embed": "4.0.4", "react-use": "^17.4.0", + "react-vega": "^7.6.0", "ro-crate": "^3.2.1", "textarea-sequence": "3.5.1", "universal-cookie": "4.0.4", - "uuid": "^8.3.2" + "uuid": "^8.3.2", + "vega": "^5.25.0", + "vega-embed": "^6.22.1", + "vega-lite": "^5.13.0" }, "devDependencies": { "@cypress/code-coverage": "3.9.12", diff --git a/src/components/Analysis/Functional/GO/BarChart.tsx b/src/components/Analysis/Functional/GO/BarChart.tsx index c06835448..ebe9b5ce3 100644 --- a/src/components/Analysis/Functional/GO/BarChart.tsx +++ b/src/components/Analysis/Functional/GO/BarChart.tsx @@ -23,6 +23,17 @@ const GOBarChart: React.FC = ({ color, containerId, }) => { + // Sort the data in descending order based on the series values + const sortedData = series + .map((value, index) => ({ + category: categories[index], + value, + })) + .sort((a, b) => b.value - a.value); // Sort in descending order + + const sortedCategories = sortedData.map((data) => data.category); + const sortedSeries = sortedData.map((data) => data.value); + const chartComponentRef = useRef(null); const options: Record = { chart: { @@ -44,7 +55,7 @@ const GOBarChart: React.FC = ({ }, }, xAxis: { - categories, + categories: sortedCategories, }, plotOptions: { series: { @@ -68,7 +79,7 @@ const GOBarChart: React.FC = ({ series: [ { name: 'annotations', - data: series, + data: sortedSeries, color, }, ], @@ -82,4 +93,5 @@ const GOBarChart: React.FC = ({ /> ); }; + export default GOBarChart; diff --git a/src/components/Analysis/Functional/GO/index.tsx b/src/components/Analysis/Functional/GO/index.tsx index 16455bd7a..2b10efd45 100644 --- a/src/components/Analysis/Functional/GO/index.tsx +++ b/src/components/Analysis/Functional/GO/index.tsx @@ -7,6 +7,7 @@ import FetchError from 'components/UI/FetchError'; import { MGnifyDatum } from 'hooks/data/useData'; import { TAXONOMY_COLOURS } from 'utils/taxon'; import useQueryParamState from 'hooks/queryParamState/useQueryParamState'; +import GOBar from 'src/components/VegaCharts/GOBar'; import GOBarChart from './BarChart'; import GOPieChart from './PieChart'; @@ -104,6 +105,8 @@ const GO: React.FC = () => { containerId="cellular-component-bar-chart" /> + + )} {chart === 'pie' && dataBundles && ( diff --git a/src/components/Analysis/Functional/InterPro/index.tsx b/src/components/Analysis/Functional/InterPro/index.tsx index f5c00f03c..c1248e877 100644 --- a/src/components/Analysis/Functional/InterPro/index.tsx +++ b/src/components/Analysis/Functional/InterPro/index.tsx @@ -9,6 +9,7 @@ import Loading from 'components/UI/Loading'; import FetchError from 'components/UI/FetchError'; import ExtLink from 'components/UI/ExtLink'; import useQueryParamState from 'hooks/queryParamState/useQueryParamState'; +import InterProBar from 'src/components/VegaCharts/InterproBar'; import InterProMatchesChart from './InterProMatchesChart'; import InterProQCChart from './QCChart'; @@ -91,6 +92,7 @@ const InterPro: React.FC = () => {
+
InterPro match summary
diff --git a/src/components/Analysis/Functional/KO/index.tsx b/src/components/Analysis/Functional/KO/index.tsx index 3c0739113..2bd29f49c 100644 --- a/src/components/Analysis/Functional/KO/index.tsx +++ b/src/components/Analysis/Functional/KO/index.tsx @@ -1,12 +1,24 @@ -import React from 'react'; -import PfamTable from './Table'; -import PfamBarChart from './BarChart'; +import React, { useContext } from 'react'; +import VerticalBarChart from 'src/components/VegaCharts/VerticalBar'; +import AnalysisContext from 'src/pages/Analysis/AnalysisContext'; +import KOTable from './Table'; +import KOBarChart from './BarChart'; const PfamTab: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const accession = `analyses/${overviewData.id}/kegg-orthologs`; return (
- - + + + +
); }; diff --git a/src/components/Analysis/Functional/Pfam/index.tsx b/src/components/Analysis/Functional/Pfam/index.tsx index 6ea167c58..ba8ccb51e 100644 --- a/src/components/Analysis/Functional/Pfam/index.tsx +++ b/src/components/Analysis/Functional/Pfam/index.tsx @@ -1,14 +1,26 @@ -import React from 'react'; -import KOTable from './Table'; -import KOBarChart from './BarChart'; +import React, { useContext } from 'react'; +import VerticalBarChart from 'src/components/VegaCharts/VerticalBar'; +import AnalysisContext from 'src/pages/Analysis/AnalysisContext'; +import PfamTable from './Table'; +import BarChart from './BarChart'; -const KOTab: React.FC = () => { +const PfamTab: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const accession = `analyses/${overviewData.id}/pfam-entries`; return (
- - + + + +
); }; -export default KOTab; +export default PfamTab; diff --git a/src/components/Analysis/Pathways/AntiSMASH/index.tsx b/src/components/Analysis/Pathways/AntiSMASH/index.tsx index ed550a22d..042fbf606 100644 --- a/src/components/Analysis/Pathways/AntiSMASH/index.tsx +++ b/src/components/Analysis/Pathways/AntiSMASH/index.tsx @@ -1,11 +1,24 @@ -import React from 'react'; +import React, { useContext } from 'react'; +import VerticalBarChart from 'src/components/VegaCharts/VerticalBar'; +import AnalysisContext from 'src/pages/Analysis/AnalysisContext'; import AntiSMASHTable from './Table'; import AntiSMASHBarChart from './BarChart'; const KOTab: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const accession = `analyses/${overviewData.id}/antismash-gene-clusters`; return (
+
); diff --git a/src/components/Analysis/Pathways/KeggModule/index.tsx b/src/components/Analysis/Pathways/KeggModule/index.tsx index 8c3ce0f2f..3f49bbafb 100644 --- a/src/components/Analysis/Pathways/KeggModule/index.tsx +++ b/src/components/Analysis/Pathways/KeggModule/index.tsx @@ -1,11 +1,32 @@ -import React from 'react'; +import React, { useContext } from 'react'; +import AnalysisContext from 'src/pages/Analysis/AnalysisContext'; +import VerticalBarChart from 'src/components/VegaCharts/VerticalBar'; import KeggTable from './Table'; import KeggBarChart from './BarChart'; const KOTab: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const accession = `analyses/${overviewData.id}/kegg-modules`; return (
+ +
); diff --git a/src/components/Analysis/QualityControl/index.tsx b/src/components/Analysis/QualityControl/index.tsx index 0e14086a0..aa3d8029c 100644 --- a/src/components/Analysis/QualityControl/index.tsx +++ b/src/components/Analysis/QualityControl/index.tsx @@ -4,6 +4,8 @@ import useMGnifyData from 'hooks/data/useMGnifyData'; import Loading from 'components/UI/Loading'; import { ResponseFormat } from 'hooks/data/useData'; import AnalysisContext from 'pages/Analysis/AnalysisContext'; +import NucleotideHistogram from 'src/components/VegaCharts/NucleotidesHistogram'; +import QCStdDevChart from 'src/components/VegaCharts/QCStdDevChart'; import QualityControlChart from './QCChart'; import ContigsHistogram from './ContigsHistogram'; import NucleotidesHistogram from './NucleotidesHistogram'; @@ -12,6 +14,7 @@ import SeqLengthChart from './SeqLengthChart'; import GCContentChart from './GCContentChart'; import './style.css'; +import VegaQC from '../../VegaCharts/QCChart'; const QualityControl: React.FC = () => { const { overviewData: analysisData } = useContext(AnalysisContext); @@ -41,6 +44,8 @@ const QualityControl: React.FC = () => { number given by ENA.

+

Vega

+ {summaryData && Number(analysisData.attributes['pipeline-version']) > 2 && ( <>

@@ -62,12 +67,28 @@ const QualityControl: React.FC = () => {

+ +
+
+ +
+
+ +
+

The graph below show the relative abundance of nucletotides (A, C, G, T, or ambiguous base "N") at each position starting from the beginning of each {unit} up to the first 500 base pairs.

+ )} diff --git a/src/components/Analysis/Taxonomy/PhylumCharts/index.tsx b/src/components/Analysis/Taxonomy/PhylumCharts/index.tsx index 54f399521..60c495a02 100644 --- a/src/components/Analysis/Taxonomy/PhylumCharts/index.tsx +++ b/src/components/Analysis/Taxonomy/PhylumCharts/index.tsx @@ -6,6 +6,7 @@ import FetchError from 'components/UI/FetchError'; import useMGnifyData from 'hooks/data/useMGnifyData'; import { MGnifyDatum } from 'hooks/data/useData'; import { TAXONOMY_COLOURS } from 'utils/taxon'; +import TaxBar from 'src/components/VegaCharts/TaxBar'; import PhylumTable from '../PhylumTable'; import PhylumPie from './Pie'; import PhylumColumn from './Column'; @@ -156,6 +157,12 @@ const PhylumCharts: React.FC = ({ title="Domain composition" sequencesType={sequencesType} /> + )} {chartType === 'column' && ( @@ -167,6 +174,12 @@ const PhylumCharts: React.FC = ({ sequencesType={sequencesType} showTotal /> + )} {chartType === 'stacked-column' && ( diff --git a/src/components/Genomes/COGAnalysis/index.tsx b/src/components/Genomes/COGAnalysis/index.tsx index 7a1f68acd..8f6258a6d 100644 --- a/src/components/Genomes/COGAnalysis/index.tsx +++ b/src/components/Genomes/COGAnalysis/index.tsx @@ -11,6 +11,7 @@ import { MGnifyDatum, MGnifyResponseList } from 'hooks/data/useData'; import useURLAccession from 'hooks/useURLAccession'; import useDefaultGenomeConfig from 'hooks/genomes/useDefaultConfig'; import { TAXONOMY_COLOURS } from 'utils/taxon'; +import VerticalBarChart from 'src/components/VegaCharts/VerticalBar'; addExportMenu(Highcharts); @@ -23,7 +24,7 @@ const COGAnalises: React.FC<{ includePangenomes?: boolean }> = ({ const { data, loading, error } = useMGnifyData(`genomes/${accession}/cogs`, { page_size: 100, }); - + const accession1 = `genomes/${accession}/cogs`; if (loading) return ; if (error) return ; if (!data) return ; @@ -95,6 +96,16 @@ const COGAnalises: React.FC<{ includePangenomes?: boolean }> = ({ options={options} ref={chartComponentRef} /> + = ({ page_size: keggPageSize, } ); - + const accession1 = `genomes/${accession}/kegg-class`; if (loading) return ; if (error) return ; if (!data) return ; @@ -118,6 +119,15 @@ const KEGGClassAnalises: React.FC<{ includePangenomes?: boolean }> = ({ options={options} ref={chartComponentRef} /> + = ({ page_size: keggmodPageSize, } ); - + const accession1 = `genomes/${accession}/kegg-module`; if (loading) return ; if (error) return ; if (!data) return ; @@ -118,6 +119,16 @@ const KEGGClassModulesAnalises: React.FC<{ includePangenomes?: boolean }> = ({ options={options} ref={chartComponentRef} /> + + { + const { overviewData } = useContext(AnalysisContext); + const [isLoading, setIsLoading] = useState(true); + const [isLoaded, setIsLoaded] = useState(false); + + const spec: VisualizationSpec = { + $schema: 'https://vega.github.io/schema/vega-lite/v5.json', + data: { + url: `${config.api}analyses/${overviewData.id}/go-slim`, + format: { type: 'json', property: 'data' }, + }, + params: [ + { + name: 'hover', + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, // hover functionality + }, + { + name: 'Input', // slider functionality + value: 15, + bind: { input: 'range', min: 10, max: 43, step: 1 }, + }, + ], + transform: [ + { calculate: 'datum.attributes.lineage', as: 'lineage' }, + { calculate: 'datum.attributes.description', as: 'description' }, + { calculate: 'datum.attributes.count', as: 'annotations' }, + ], + // Using hconcat to create 3 charts in one row + hconcat: [ + { + title: 'Biological Process', + height: 800, + mark: { + type: 'bar', + tooltip: true, + }, + encoding: { + x: { + field: 'annotations', + type: 'quantitative', + }, + y: { + field: 'description', + type: 'nominal', + sort: '-x', + }, + fill: { + condition: { + test: { + param: 'hover', + empty: false, + }, + value: '#C4ECF4', + }, + value: '#ABD3DB', + }, + }, + // Filter the data to only show the annotations wrt the slider value + transform: [ + { + filter: "datum.lineage === 'biological_process'", + }, + { + sort: [{ field: 'annotations', order: 'descending' }], + window: [{ op: 'rank', field: 'annotations', as: 'rank' }], + }, + { filter: 'datum.rank <= Input' }, + ], + }, + { + title: 'Molecular Function', + height: 800, + mark: { type: 'bar', tooltip: true }, + encoding: { + x: { field: 'annotations', type: 'quantitative' }, + y: { field: 'description', type: 'nominal', sort: '-x' }, + fill: { + // Change the colour of the bar when hovered over + condition: { + test: { param: 'hover', empty: false }, + value: '#78aeae', + }, + value: '#5f9595', + }, + }, + transform: [ + { filter: "datum.lineage === 'molecular_function'" }, + { + sort: [{ field: 'annotations', order: 'descending' }], + window: [{ op: 'rank', field: 'annotations', as: 'rank' }], + }, + { filter: 'datum.rank <= Input' }, + ], + }, + { + title: 'Cellular Component', + height: 800, + mark: { type: 'bar', tooltip: true }, + encoding: { + x: { field: 'annotations', type: 'quantitative' }, + y: { field: 'description', type: 'nominal', sort: '-x' }, + fill: { + condition: { + test: { param: 'hover', empty: false }, + value: '#f2ddd1', + }, + value: '#d9c4b8', + }, + }, + transform: [ + { filter: "datum.lineage === 'cellular_component'" }, + { + sort: [{ field: 'annotations', order: 'descending' }], + window: [{ op: 'rank', field: 'annotations', as: 'rank' }], + }, + { filter: 'datum.rank <= Input' }, + ], + }, + ], + config: { + view: { stroke: 'transparent' }, + + axis: { + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 12, + titleFontSize: 12, + titleFontWeight: 'normal', + titlePadding: 5, + }, + axisX: { orient: 'top', tickMinStep: 2000 }, + axisY: { title: null }, + title: { + fontSize: 18, + font: 'Lucida Grande', + fontWeight: 'normal', + offset: 10, + }, + scale: { bandPaddingInner: 0.5 }, + }, + }; + + const handleChartLoaded = () => { + setIsLoading(false); + setIsLoaded(true); + }; + + return ( + <> + {isLoading && } +

Vega

+ + {isLoaded && ( + + )} + + ); +}; + +export default GOBar; diff --git a/src/components/VegaCharts/InterproBar.tsx b/src/components/VegaCharts/InterproBar.tsx new file mode 100644 index 000000000..16b6e51c2 --- /dev/null +++ b/src/components/VegaCharts/InterproBar.tsx @@ -0,0 +1,129 @@ +import React, { useContext, useState } from 'react'; +import Loading from 'components/UI/Loading'; +import AnalysisContext from 'pages/Analysis/AnalysisContext'; + +import { VegaLite, VisualizationSpec } from 'react-vega'; +import config from 'src/utils/config'; + +const InterProBar: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const isAssembly = overviewData.attributes['experiment-type'] === 'assembly'; + const prefix = isAssembly ? 'Contigs' : 'Reads'; + + const [isLoading, setIsLoading] = useState(true); + + const spec: VisualizationSpec = { + $schema: 'https://vega.github.io/schema/vega-lite/v5.json', + height: 125, + width: 'container', + title: 'Sequence feature summary', + data: { + url: `${config.api}analyses/${overviewData.id}`, + format: { type: 'json', property: 'data.attributes.analysis-summary' }, + }, + // Transforming the data directly to the format we need for the chart + // (i.e. pre-process data with the prefixes - 'Reads' or 'Contigs') + transform: [ + { + calculate: `datum.key === 'Reads with predicted CDS' ? '${prefix} with predicted CDS' : + datum.key === 'Reads with predicted RNA' ? '${prefix} with predicted RNA' : + datum.key === 'Reads with InterProScan match' ? '${prefix} with InterProScan match' : + datum.key === 'Predicted CDS' ? 'Predicted CDS' : + datum.key === 'Predicted CDS with InterProScan match' ? 'Predicted CDS with InterProScan match' : + null`, + as: 'description', + }, + { calculate: 'datum.value', as: 'count' }, + { + filter: 'datum.description !== null', + }, + ], + mark: { type: 'bar' }, + encoding: { + x: { + field: 'count', + type: 'quantitative', + scale: { + type: 'log', + base: 2, // Using log2 scale + }, + axis: { + title: 'Count (note the logarithmic scale)', + tickCount: 10, + format: '.2s', // Using SI prefix notation for the tick labels + }, + }, + y: { + field: 'description', + type: 'nominal', + axis: { title: null }, + // Sorting the labels in the order we want + sort: [ + `${prefix} with predicted CDS`, + `${prefix} with predicted RNA`, + `${prefix} with InterProScan match`, + 'Predicted CDS', + 'Predicted CDS with InterProScan match', + ], + }, + tooltip: [ + { field: 'description', type: 'nominal', title: 'Description' }, + { field: 'count', type: 'quantitative', title: 'Count', format: ',' }, + ], + fill: { + condition: { + test: { param: 'hover', empty: false }, + value: '#1EA6E0', + }, + value: '#058DC7', + }, + }, + // Adding the hover functionality + params: [ + { + name: 'hover', + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, + }, + ], + config: { + view: { + stroke: 'transparent', + }, + axis: { + ticks: false, + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 11, + titleFontSize: 12, + titleFontWeight: 'normal', + labelPadding: 15, + labelLimit: 0, + }, + tooltipFormat: { + numberFormat: '.2s', + }, + title: { fontSize: 18, font: 'Lucida Grande', fontWeight: 'normal' }, + scale: { bandPaddingInner: 0.5 }, + }, + }; + + const handleChartLoaded = () => { + setIsLoading(false); + }; + + return ( + <> + {isLoading && } +

Vega

+ + + ); +}; + +export default InterProBar; diff --git a/src/components/VegaCharts/NucleotidesHistogram.tsx b/src/components/VegaCharts/NucleotidesHistogram.tsx new file mode 100644 index 000000000..78a518ca6 --- /dev/null +++ b/src/components/VegaCharts/NucleotidesHistogram.tsx @@ -0,0 +1,166 @@ +import React, { useContext, useState } from 'react'; +import Loading from 'components/UI/Loading'; +import AnalysisContext from 'pages/Analysis/AnalysisContext'; + +import { VegaLite, VisualizationSpec } from 'react-vega'; +import config from 'src/utils/config'; + +const NucleotideHistogram: React.FC = () => { + const { overviewData } = useContext(AnalysisContext); + const [isLoading, setIsLoading] = useState(true); + + const spec: VisualizationSpec = { + $schema: 'https://vega.github.io/schema/vega-lite/v5.json', + height: 300, + width: 'container', + title: { + text: 'Nucleotide position histogram', + fontSize: 16, + fontWeight: 'bold', + }, + data: { + url: `${config.api}analyses/${overviewData.id}/nucleotide-distribution`, + format: { type: 'tsv' }, + }, + transform: [ + { fold: ['A', 'T', 'C', 'G', 'N'] }, // fold the columns into a single column + { + calculate: "{'A':4, 'T':3, 'C':2, 'G':1, 'N':0}[datum.key]", // assign a value to each nucleotide for sorting + as: 'order', + }, + { calculate: 'datum.pos * 1', as: 'pos' }, // convert the position to a number + ], + encoding: { + x: { + field: 'pos', + type: 'quantitative', + scale: { domainMax: { expr: "data('source_0')[0].MaxVal" } }, + }, + tooltip: [ + { field: 'pos', title: 'Position' }, + { field: 'A', type: 'quantitative' }, + { field: 'T', type: 'quantitative' }, + { field: 'C', type: 'quantitative' }, + { field: 'G', type: 'quantitative' }, + { field: 'N', type: 'quantitative' }, + ], + }, + layer: [ + { + width: 'container', + mark: { type: 'area', line: { size: 2 } }, + params: [ + { + name: 'nuc', // nucleotide selection from the legend + select: { type: 'point', fields: ['key'] }, + bind: 'legend', + }, + ], + transform: [{ filter: { param: 'nuc', empty: true } }], // filter the data based on the selection + encoding: { + x: { + field: 'pos', + type: 'quantitative', + axis: { labelAngle: -20, tickCount: 56 }, + }, + y: { + field: 'value', + type: 'quantitative', + stack: 'zero', + scale: { domain: [0, 100] }, + axis: { tickCount: 4, grid: true }, + }, + color: { + scale: { + domain: ['A', 'T', 'C', 'G', 'N'], + range: [ + 'rgb(16, 150, 24)', + 'rgb(220, 57, 18)', + 'rgb(51, 102, 204)', + 'rgb(255, 153, 0)', + 'rgb(138, 65, 23)', + ], + }, + field: 'key', + type: 'ordinal', + title: 'Shift+Click for nucleotide multi-selection', + }, + order: { field: 'order', type: 'ordinal' }, // sort the nucleotides + opacity: { value: 0.7 }, + }, + }, + { + // Rule for the hover and zoom (clearly shows the nucleotide position) + mark: 'rule', + params: [ + { + name: 'hover', // Hover functionality + select: { + type: 'point', + on: 'mousemove', + + clear: 'mouseout', + nearest: true, + }, + }, + { + name: 'zoom', // Zoom functionality + bind: 'scales', + select: { + type: 'interval', + encodings: ['x'], + zoom: 'wheel!', + mark: { fill: '#111', fillOpacity: 0.5, stroke: '#595959' }, + }, + }, + ], + encoding: { + color: { + condition: { param: 'hover', empty: false, value: '#595959' }, + value: 'transparent', + }, + }, + }, + ], + config: { + view: { stroke: 'transparent' }, + axis: { + grid: false, + title: null, + domain: false, + tickColor: '#ccc', + labelColor: '#666', + labelFontSize: 12, + titleFontSize: 14, + titleFontWeight: 'normal', + }, + legend: { + labelFontSize: 14, + labelFontWeight: 'bold', + labelFont: 'Lucida Grande', + orient: 'bottom', + titleFontSize: 9, + titleFontWeight: 'lighter', + }, + title: { fontSize: 20, font: 'Lucida Grande', fontWeight: 'normal' }, + }, + }; + + const handleChartLoaded = () => { + setIsLoading(false); + }; + + return ( + <> + {isLoading && } +

Vega

+ + + ); +}; + +export default NucleotideHistogram; diff --git a/src/components/VegaCharts/QC-chart-components/VConcatBottom.tsx b/src/components/VegaCharts/QC-chart-components/VConcatBottom.tsx new file mode 100644 index 000000000..d114f7f52 --- /dev/null +++ b/src/components/VegaCharts/QC-chart-components/VConcatBottom.tsx @@ -0,0 +1,157 @@ +import { NonNormalizedSpec } from 'vega-lite/build/src/spec'; + +// eslint-disable-next-line consistent-return +const VConcatBottom = (type: string): NonNormalizedSpec => { + if (type === 'seq-length') { + return { + width: 500, + height: 80, + data: { + name: 'summaryData', + }, + transform: [ + { + filter: { + field: 'key', + oneOf: ['length_min', 'average_length', 'length_max'], // filter the data to only include the fields we want + }, + }, + { + // make the key more descriptive(used for labelling the bars) + calculate: + "if(datum.key == 'length_min', 'Minimum', datum.key == 'average_length' ? 'Average' : 'Maximum')", + as: 'label', + }, + ], + // Bar chart for the sequence length (min, avg, max) + mark: { type: 'bar', opacity: 0.9 }, + params: [ + { + name: 'highlight', + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, // bar highlight over hover functionality + }, + ], + encoding: { + y: { + field: 'label', + type: 'nominal', + axis: { + title: null, + }, + sort: ['Minimum', 'Average', 'Maximum'], + }, + x: { + field: 'value', + type: 'quantitative', + axis: { tickCount: 5, format: '.2s', title: 'Sequence length (bp)' }, + }, + color: { + field: 'label', + sort: ['Minimum', 'Average', 'Maximum'], + scale: { range: ['#72bf3f', 'red', '#723fbf'] }, + legend: null, + }, + opacity: { + condition: { + test: { param: 'highlight', empty: false }, + value: 1, + }, + }, + tooltip: [ + { field: 'label', type: 'nominal', title: 'Description' }, + { + field: 'value', + type: 'quantitative', + title: 'Count', + format: ',.2f', + }, + ], + }, + }; + } + if (type === 'gc-distribution') { + return { + layer: [ + // Layered chart for the bar chart and error band (GC Content % distribution) + { + width: 500, + height: 30, + mark: { type: 'bar', opacity: 1 }, + params: [ + { + name: 'highlight', + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, // bar highlight over hover functionality + }, + ], + encoding: { + x: { + field: 'value', + type: 'quantitative', + stack: true, + axis: { tickCount: 10 }, + }, + color: { + field: 'content_type', + sort: 'descending', + scale: { range: ['#3f72bf', '#723fbf'] }, + }, + opacity: { + condition: { + test: { param: 'highlight', empty: true }, + value: 0.9, + }, + }, + order: { field: 'order', type: 'ordinal' }, + tooltip: [ + { field: 'content_type', title: 'Content Type' }, + { field: 'value', title: 'Percentage (%)', format: '.2f' }, + ], + }, + }, + { + mark: { type: 'errorband', opacity: 0.4, color: '#808080' }, + encoding: { + x: { + field: 'lower_bound_gc-distribution', + type: 'quantitative', + scale: { domain: [1, 100] }, + axis: { title: 'GC content (%)' }, + }, + x2: { field: 'upper_bound_gc-distribution' }, + + tooltip: [ + { + field: 'standard_deviation_gc_content', + title: 'Standard Deviation (±)', + format: '.2f', + }, + ], + }, + }, + { + mark: { + type: 'rule', + color: 'red', + size: 2, + }, + encoding: { + x: { + field: 'average_gc_content', + type: 'quantitative', + }, + + tooltip: [ + { + field: 'average_gc_content', + title: 'Mean', + format: '.2f', + }, + ], + }, + }, + ], + }; + } +}; + +export default VConcatBottom; diff --git a/src/components/VegaCharts/QC-chart-components/VConcatTop.tsx b/src/components/VegaCharts/QC-chart-components/VConcatTop.tsx new file mode 100644 index 000000000..14953811a --- /dev/null +++ b/src/components/VegaCharts/QC-chart-components/VConcatTop.tsx @@ -0,0 +1,265 @@ +import { NonNormalizedSpec } from 'vega-lite/build/src/spec'; + +const VConcatTop = ( + type: string, + accession: string, + api: string, + XScaleDomainMin?: number, + XScaleDomainMax?: number +): NonNormalizedSpec => { + let ChartTitle: string; + let Mean: string; + // Conditional rendering of the chart title and the standard deviation and mean values + if (type === 'seq-length') { + ChartTitle = 'Contigs length histogram'; + Mean = 'average_length'; + } else { + ChartTitle = 'Contigs GC distribution'; + Mean = 'average_gc_content'; + } + return { + // Layering the error band(standard dev) and the histogram + layer: [ + { + title: { + text: ChartTitle, + font: 'Lucida Grande', + fontSize: 16, + fontWeight: 'bold', + offset: 15, + }, + mark: { + type: 'text', + baseline: 'line-bottom', + align: 'center', + color: '#666', + dy: -15, + }, + encoding: { + x: { + field: Mean, + type: 'quantitative', + }, + y: { + value: 0, + }, + text: { + value: 'Standard Deviation', + }, + }, + }, + { + mark: { + type: 'text', + baseline: 'bottom', + align: 'center', + color: '#666', + }, + encoding: { + x: { + field: Mean, + type: 'quantitative', + }, + y: { + value: 0, + }, + text: { + field: `std_dev_text_${type}`, + }, + }, + }, + + { + mark: { + type: 'errorband', + opacity: 0.1, + color: '#808080', + }, + encoding: { + x: { + field: `lower_bound_${type}`, + type: 'quantitative', + }, + x2: { field: `upper_bound_${type}` }, + tooltip: [ + { + field: `std_dev_text_${type}`, + title: 'Standard Deviation', + }, + ], + }, + }, + + { + height: 340, + width: 500, + data: { + url: `${api}${accession}/${type}`, + format: { + type: 'tsv', + }, + }, + layer: [ + { + mark: { + type: 'area', + color: '#058dc7', + line: { + color: '#058dc7', + size: 2, + }, + }, + encoding: { + x: { + field: 'key', + type: 'quantitative', + scale: { + domainMin: XScaleDomainMin, + domainMax: XScaleDomainMax, + }, + axis: { grid: false, title: null, tickCount: 5, format: '.2s' }, + }, + y: { + field: 'value', + type: 'quantitative', + axis: { + tickCount: 5, + title: 'Number of Contigs', + }, + }, + }, + }, + { + mark: { + type: 'rule', + color: '#595959', + }, + encoding: { + x: { + field: 'key', + type: 'quantitative', + }, + opacity: { + condition: { + param: 'hover', + empty: false, + value: 1, + }, + value: 0, + }, + tooltip: [ + { + field: 'key', + type: 'quantitative', + title: + type === 'seq-length' + ? 'Sequence Length' + : 'GC Content (%)', + }, + { field: 'value', title: 'Contigs' }, + ], + }, + params: [ + { + name: 'hover', + select: { + type: 'point', + on: 'mousemove', + clear: 'mouseout', + nearest: true, + }, + }, + ], + }, + ], + }, + { + mark: { + type: 'rule', + color: 'red', + size: 2, + }, + encoding: { + x: { + field: Mean, + type: 'quantitative', + }, + tooltip: [ + { + field: Mean, + title: 'Mean', + format: '.2f', + }, + ], + }, + }, + ], + }; +}; + +export default VConcatTop; + +// { +// title: { +// text: ChartTitle, +// font: 'Lucida Grande', +// fontSize: 16, +// fontWeight: 'bold', +// }, +// mark: { +// type: 'errorband', +// opacity: 0.1, +// color: '#808080', +// }, +// encoding: { +// x: { +// field: `lower_bound_${type}`, +// type: 'quantitative', +// }, +// x2: { field: `upper_bound_${type}` }, +// tooltip: [ +// { +// field: standardDeviation, +// title: 'Standard Deviation (±)', +// format: '.2f', +// }, +// { +// field: Mean, +// title: 'Mean', +// format: '.2f', +// }, +// ], +// }, +// }, +// { +// height: 340, +// width: 500, +// data: { +// url: `${api}${accession}/${type}`, +// format: { type: 'tsv' }, +// }, +// mark: { type: 'area', color: '#058dc7', line: { color: '#058dc7' } }, +// encoding: { +// x: { +// field: 'key', +// type: 'quantitative', +// scale: { domainMin: XScaleDomainMin, domainMax: XScaleDomainMax }, +// axis: { grid: false, title: null, tickCount: 5, format: '.2s' }, +// }, +// y: { +// field: 'value', +// type: 'quantitative', +// axis: { tickCount: 5, title: 'Number of Contigs' }, +// }, + +// tooltip: [ +// { +// field: 'key', +// type: 'quantitative', +// title: +// type === 'seq-length' ? 'Sequence Length' : 'GC Content (%)', +// }, +// { field: 'value', title: 'Contigs' }, +// ], +// }, +// }, diff --git a/src/components/VegaCharts/QC-chart-components/transforms.tsx b/src/components/VegaCharts/QC-chart-components/transforms.tsx new file mode 100644 index 000000000..7f0624e7d --- /dev/null +++ b/src/components/VegaCharts/QC-chart-components/transforms.tsx @@ -0,0 +1,53 @@ +import { Transform } from 'vega-lite/build/src/transform'; + +const ChartTransforms: Transform[] = [ + { + // Filter the data to only include the fields we want + filter: { + field: 'key', + oneOf: [ + 'average_length', + 'standard_deviation_length', + 'average_gc_content', + 'standard_deviation_gc_content', + 'length_min', + 'length_max', + ], + }, + }, + // Pivot the data + { pivot: 'key', value: 'value' }, + // Calculate the lower and upper bounds for the standard deviation (sequence length and GC content) + { + calculate: 'datum.average_length - datum.standard_deviation_length', + as: 'lower_bound_seq-length', + }, + { + calculate: 'datum.average_length + datum.standard_deviation_length', + as: 'upper_bound_seq-length', + }, + { + calculate: 'datum.average_gc_content - datum.standard_deviation_gc_content', + as: 'lower_bound_gc-distribution', + }, + { + calculate: 'datum.average_gc_content + datum.standard_deviation_gc_content', + as: 'upper_bound_gc-distribution', + }, + { + calculate: "'± ' + datum.standard_deviation_gc_content", + as: 'std_dev_text_gc-distribution', + }, + { + calculate: "'± ' + datum.standard_deviation_length", + as: 'std_dev_text_seq-length', + }, + // Calculate the AT and GC content + { calculate: '100 - datum.average_gc_content', as: 'AT Content' }, + { calculate: 'datum.average_gc_content', as: 'GC Content' }, + { + fold: ['GC Content', 'AT Content'], // fold the columns into a single column (for stacked bar chart) + as: ['content_type', 'value'], + }, +]; +export default ChartTransforms; diff --git a/src/components/VegaCharts/QCChart.tsx b/src/components/VegaCharts/QCChart.tsx new file mode 100644 index 000000000..1ac644aec --- /dev/null +++ b/src/components/VegaCharts/QCChart.tsx @@ -0,0 +1,169 @@ +import React, { useContext, useState } from 'react'; +import { VegaLite, VisualizationSpec } from 'react-vega'; +import AnalysisContext from 'pages/Analysis/AnalysisContext'; +import Loading from 'components/UI/Loading'; + +type QualityControlProps = { + summaryData: { + [key: string]: string; + } | null; +}; + +const QCChart: React.FC = ({ summaryData }) => { + const { overviewData: analysisData } = useContext(AnalysisContext); + const isAssembly = analysisData.attributes['experiment-type'] === 'assembly'; + const unit = isAssembly ? 'contigs' : 'reads'; + const capUnit = isAssembly ? 'Contigs' : 'Reads'; + + const remaining = [0, 0, 0, 0, 0]; + const filtered = [0, 0, 0, 0, 0]; + const subsampled = [0, 0, 0, 0, 0]; + + const analysisSummary = {}; + ( + (analysisData.attributes?.['analysis-summary'] as { + key: string; + value: string; + }[]) || [] + ).forEach(({ key, value }) => { + analysisSummary[key] = value; + }); + + if (summaryData) subsampled[4] = Number(summaryData.sequence_count); + remaining[0] = Number(analysisSummary['Submitted nucleotide sequences']); + remaining[1] = Number( + analysisSummary['Nucleotide sequences after format-specific filtering'] + ); + remaining[2] = Number( + analysisSummary['Nucleotide sequences after length filtering'] + ); + remaining[3] = Number( + analysisSummary['Nucleotide sequences after undetermined bases filtering'] + ); + filtered[2] = remaining[1] - remaining[2]; + filtered[1] = remaining[0] - remaining[1]; + if (summaryData) filtered[4] = remaining[3] - remaining[4] - subsampled[4]; + const [isLoading, setIsLoading] = useState(true); + + // Defining the steps for the QC chart (y-axis labels) + const steps = [ + `Initial ${unit}`, + 'Trimming', + 'Length filtering', + 'Ambiguous base filtering', + `${capUnit} subsampled for QC analysis`, + ]; + + // Creating an array of objects for the chart data - {name, Remaining, Filtered, Subsampled, sno} + const DataArray = []; + for (let index = 0; index < 5; index++) { + // for each step + const stepObject = { + name: steps[index], + Remaining: remaining[index], + Filtered: filtered[index], + Subsampled: subsampled[index], + sno: index, + }; + DataArray.push(stepObject); + } + + const spec: VisualizationSpec = { + data: { + values: DataArray, + }, + title: 'Number of sequence contigs per QC step', + width: 'container', + params: [ + { + name: 'hover', // hover functionality + select: { type: 'point', fields: ['name'], on: 'mouseover' }, + }, + ], + mark: 'bar', + encoding: { + tooltip: [ + { field: 'name', type: 'nominal', title: 'QC step' }, + { field: 'field', type: 'nominal', title: 'Type' }, + { field: 'value', type: 'quantitative', title: 'Count', format: ',' }, + ], + y: { + field: 'name', + type: 'nominal', + title: null, + sort: { + field: 'sno', + }, + }, + x: { + stack: true, + field: 'value', + type: 'quantitative', + title: 'Count', + axis: { + format: 's', + }, + }, + color: { + field: 'field', + type: 'nominal', + scale: { + range: ['#ccccd3', '#058dc7', '#8dc7c7'], + }, + }, + opacity: { + condition: { + test: { param: 'hover', empty: false }, + value: 0.7, + }, + value: 1, + }, + }, + // Using fold transform to be able to stack the bars for the different types of sequences + transform: [ + { fold: ['Remaining', 'Filtered', 'Subsampled'], as: ['field', 'value'] }, + ], + + config: { + view: { + stroke: 'transparent', + }, + axis: { + ticks: false, + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 11, + titleFontSize: 12, + titleFontWeight: 'normal', + labelPadding: 15, + labelLimit: 0, + }, + legend: { + orient: 'bottom', + title: null, + labelFontSize: 13, + labelFontWeight: 'bold', + symbolType: 'circle', + }, + title: { fontSize: 18, font: 'Lucida Grande', fontWeight: 'normal' }, + scale: { bandPaddingInner: 0.5 }, + }, + }; + + const handleChartLoaded = () => { + setIsLoading(false); + }; + return ( + <> + {isLoading && } + + + ); +}; +export default QCChart; diff --git a/src/components/VegaCharts/QCStdDevChart.tsx b/src/components/VegaCharts/QCStdDevChart.tsx new file mode 100644 index 000000000..715a714f9 --- /dev/null +++ b/src/components/VegaCharts/QCStdDevChart.tsx @@ -0,0 +1,87 @@ +import React, { useState } from 'react'; +import Loading from 'components/UI/Loading'; + +import { VegaLite, VisualizationSpec } from 'react-vega'; +import config from 'src/utils/config'; +import { NonNormalizedSpec } from 'vega-lite/build/src/spec'; +import VConcatBottom from './QC-chart-components/VConcatBottom'; +import ChartTransforms from './QC-chart-components/transforms'; +import VConcatTop from './QC-chart-components/VConcatTop'; + +interface QCStdDevProps { + accession: string; + type: string; +} + +const QCStdDevChart: React.FC = ({ accession, type }) => { + const [isLoading, setIsLoading] = useState(true); + + // let VConcatBottom: NonNormalizedSpec | null = null; + let XScaleDomainMin: number; + let XScaleDomainMax: number; + // Conditional rendering of the Bottom Chart -> Seq length, GC distribution charts + if (type === 'seq-length') { + XScaleDomainMin = 0; + } else if (type === 'gc-distribution') { + XScaleDomainMin = 0; + XScaleDomainMax = 100; + } + + const spec: VisualizationSpec = { + $schema: 'https://vega.github.io/schema/vega-lite/v5.json', + width: 'container', + + data: { + name: 'summaryData', + url: `${config.api}${accession}/summary`, + format: { type: 'tsv' }, + }, + // Moved tranforms and vconcat charts to QC-chart-components for better readability + transform: ChartTransforms, + vconcat: [ + VConcatTop(type, accession, config.api, XScaleDomainMin, XScaleDomainMax), + VConcatBottom(type), + ], + config: { + view: { stroke: 'transparent' }, + axis: { + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 11, + + titleFontSize: 12, + titleFontWeight: 'normal', + titlePadding: 10, + }, + + legend: { + orient: 'bottom', + title: null, + labelFontSize: 13, + labelFontWeight: 'bold', + symbolType: 'circle', + }, + scale: { bandPaddingInner: 0.1 }, + }, + }; + + const handleChartLoaded = () => { + setIsLoading(false); + }; + + return ( + <> + {isLoading && } +

Vega

+ + + ); +}; + +export default QCStdDevChart; diff --git a/src/components/VegaCharts/TaxBar.tsx b/src/components/VegaCharts/TaxBar.tsx new file mode 100644 index 000000000..cfd9a3268 --- /dev/null +++ b/src/components/VegaCharts/TaxBar.tsx @@ -0,0 +1,109 @@ +import React, { useState } from 'react'; +import Loading from 'components/UI/Loading'; + +import { VegaLite, VisualizationSpec } from 'react-vega'; +import { TaxDatum } from 'src/components/Analysis/Taxonomy/PhylumCharts'; + +interface TaxBarProps { + ChartTitle: string; + title: string; + sequencesType?: string; + clusteredData: Array; +} +const TaxBar: React.FC = ({ + ChartTitle, + clusteredData, + sequencesType = 'reads', + title, +}) => { + const [isLoading, setIsLoading] = useState(true); + + const spec: VisualizationSpec = { + title: ChartTitle, + data: { values: clusteredData }, + height: 300, + width: 'container', + mark: 'bar', + transform: [ + { calculate: "split(datum.name, ' ')", as: 'lablelName' }, + { calculate: 'datum.percentage / 100', as: 'percentage' }, + ], + encoding: { + x: { + field: 'lablelName', + sort: '-y', + axis: { + title: null, + labelOverlap: false, + labelAngle: 360, + labelPadding: 7, + }, + }, + y: { + field: 'y', + type: 'quantitative', + axis: { + title: 'Number of sequences', + tickCount: 4, + }, + }, + color: { field: 'color', type: 'nominal', scale: null }, + opacity: { + condition: { + test: { param: 'hover', empty: false }, + value: 0.8, + }, + value: 1, + }, + tooltip: [ + { field: 'name', type: 'nominal', title: `${title}` }, + { field: 'y', type: 'quantitative', title: `${sequencesType}` }, + { + field: 'percentage', + type: 'quantitative', + format: '.2%', + }, + ], + }, + params: [ + { + name: 'hover', + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, + }, + ], + config: { + view: { stroke: 'transparent' }, + axis: { + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 12, + titleFontSize: 12, + titleFontWeight: 'normal', + titlePadding: 10, + }, + + title: { fontSize: 20, font: 'Lucida Grande', fontWeight: 'normal' }, + scale: { bandPaddingInner: 0.5 }, + }, + }; + + const handleLoaded = () => { + setIsLoading(false); + }; + + return ( + <> + {isLoading && } +

Vega

+ + + ); +}; + +export default TaxBar; diff --git a/src/components/VegaCharts/VerticalBar.tsx b/src/components/VegaCharts/VerticalBar.tsx new file mode 100644 index 000000000..5087e2c29 --- /dev/null +++ b/src/components/VegaCharts/VerticalBar.tsx @@ -0,0 +1,172 @@ +import React, { useState } from 'react'; +import Loading from 'components/UI/Loading'; + +import { VegaLite, VisualizationSpec } from 'react-vega'; +import config from 'src/utils/config'; + +import './styles.css'; // styles for the slider + +// Props for the VerticalBarChart component +interface VerticalBarChartProps { + ChartTitle: string; + titleX?: string; + titleY?: string; + accession: string; + tooltipKey1?: string; + tooltipVal1?: string; + tooltipKey2?: string; + tooltipVal2?: string; + tooltipKey3?: string; + y?: string; + x?: string; + lAngle?: number; + paddingLabel?: number; + maxSlider?: number; + sliderValue?: number; + overlapLabels?: boolean; +} + +const VerticalBarChart: React.FC = ({ + ChartTitle, + titleX = null, + titleY = 'Number of Matches', + accession, + tooltipKey1 = null, + tooltipKey2 = null, + tooltipKey3 = 'Count', + tooltipVal1 = null, + tooltipVal2 = null, + y = 'count', + x = 'accession', + lAngle = -20, + paddingLabel = 5, + maxSlider = 30, + sliderValue = 10, + overlapLabels = false, +}) => { + const [isLoading, setIsLoading] = useState(true); // loading state for the Loading component + const [isLoaded, setIsLoaded] = useState(false); // loaded state for the slider to appear after the chart is loaded + + // Vega-Lite spec contains the data, transforms(data wrangling), and encoding(visual graphics) + const spec: VisualizationSpec = { + $schema: 'https://vega.github.io/schema/vega-lite/v5.json', + height: 300, + width: 'container', + title: ChartTitle, + + data: { + url: `${config.api}${accession}`, // data access via URL + format: { type: 'json', property: 'data' }, // format of the data + }, + transform: [ + // Filter the data to only include the fields we want, rename the fields + { calculate: 'datum.attributes.name', as: 'name' }, + { calculate: 'datum.attributes.accession', as: 'id' }, + { calculate: `datum.attributes['${x}']`, as: `${x}` }, + { calculate: `datum.attributes['${y}']`, as: `${y}` }, + { calculate: 'datum.attributes.description', as: 'description' }, + { window: [{ op: 'rank', as: 'rank' }] }, // rank the data (sorts) + { filter: 'datum.rank <= Input' }, // filter the data based on the slider input + ], + mark: 'bar', // type of mark + // encoding for the visual graphics + encoding: { + // encode the x and y axis -> type of data, field, axis title, etc. + x: { + field: `${x}`, + type: 'ordinal', + sort: { field: `${y}`, order: 'descending' }, + axis: { + labelBaseline: 'line-top', + labelPadding: paddingLabel, + labelAngle: lAngle, + labelAlign: 'center', + labelOverlap: overlapLabels, + labelSeparation: 2, + }, + title: titleX, + }, + y: { + field: `${y}`, + type: 'quantitative', + axis: { title: titleY, tickCount: 4 }, + }, + tooltip: [ + { field: tooltipVal1, title: tooltipKey1 }, // tooltip + { field: tooltipVal2, title: tooltipKey2 }, + { field: `${y}`, title: tooltipKey3 }, + ], + fill: { + // color for the bar, changes color on hover + condition: { + test: { param: 'hover', empty: false }, + value: '#95CEFF', + }, + value: '#7cb5ec', + }, + }, + params: [ + { + name: 'hover', // parameter for the hover selection + select: { type: 'point', on: 'mouseover', clear: 'mouseout' }, + }, + { + name: 'Input', // parameter for the slider + value: sliderValue, + bind: { input: 'range', min: 5, max: maxSlider, step: 1 }, + }, + ], + + // configuration for the visual graphics (axis, legend, title, etc.) + config: { + view: { stroke: 'transparent' }, + axis: { + domain: false, + tickColor: '#ccc', + labelColor: '#666', + titleColor: '#666', + labelFontSize: 12, + + titleFontSize: 14, + titleFontWeight: 'normal', + titlePadding: 10, + }, + legend: { + labelFontSize: 12, + titleFontSize: 14, + titleFontWeight: 'normal', + }, + title: { fontSize: 20, font: 'Lucida Grande', fontWeight: 'normal' }, + scale: { bandPaddingInner: 0.5 }, + }, + }; + + const handleLoaded = () => { + setIsLoading(false); + setIsLoaded(true); + }; + + return ( + <> + {isLoading && } +

Vega

+ + {/* The slider is hidden until the chart is loaded */} + {isLoaded && ( + + )} + + ); +}; + +export default VerticalBarChart; diff --git a/src/components/VegaCharts/styles.css b/src/components/VegaCharts/styles.css new file mode 100644 index 000000000..42cba67c9 --- /dev/null +++ b/src/components/VegaCharts/styles.css @@ -0,0 +1,30 @@ +/* This file includes css for the slider being used in the Bar Charts */ +.vega-bind input[type="range"] { + -webkit-appearance: none; + -moz-appearance: none; + appearance: none; + background-color: #ccc; + border-radius: 5px; + height: 5px; + } + + .vega-bind input[type="range"]::-webkit-slider-thumb { + -webkit-appearance: none; + appearance: none; + width: 20px; + height: 20px; + border-radius: 50%; + background-color: #7cb5ec; + box-shadow: 0 2px 4px rgba(0, 0, 0, 0); + cursor: pointer; + } + + .vega-bind span { + color: #666; + padding-top: 10px; + padding: 5px; + } + + .vega-bindings { + display: none; + } \ No newline at end of file