diff --git a/.gitignore b/.gitignore index 0e391027..6d294739 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,6 @@ web/docs/public jsx-compiled dist public + +tags* +*yalc* diff --git a/__tests__/graphs.test.jsx b/__tests__/graphs.test.jsx index 88922ca1..58bb2433 100644 --- a/__tests__/graphs.test.jsx +++ b/__tests__/graphs.test.jsx @@ -11,10 +11,14 @@ import { DatamonkeyScatterplot, DatamonkeyGraphMenu } from "../src/jsx/components/graphs.jsx"; +import Enzyme from "enzyme"; +import Adapter from "enzyme-adapter-react-16"; import { mount } from "enzyme"; var _ = require("underscore"); +Enzyme.configure({ adapter: new Adapter() }); + describe("DatamonkeySeries", () => { var x = _.range(10); var y = [_.range(10)]; @@ -60,7 +64,6 @@ describe("DatamonkeyScatterplot", () => { }); }); - describe("GraphMenu", () => { var x_options = ["Site"]; var y_options = ["alpha", "beta"]; @@ -94,11 +97,5 @@ describe("GraphMenu", () => { let menu = no_ylabel_component.toJSON(); expect(menu).toMatchSnapshot(); - - - }); - - - }); diff --git a/__tests__/tables.test.jsx b/__tests__/tables.test.jsx index 740c6566..51db7c1f 100644 --- a/__tests__/tables.test.jsx +++ b/__tests__/tables.test.jsx @@ -7,6 +7,8 @@ import ReactDOM from "react-dom"; import TestUtils from "react-dom/test-utils"; import renderer from "react-test-renderer"; import { DatamonkeyTable } from "../src/jsx/components/tables.jsx"; +import Enzyme from "enzyme"; +import Adapter from "enzyme-adapter-react-16"; import { mount } from "enzyme"; var _ = require("underscore"); @@ -15,6 +17,8 @@ import $ from "jquery"; global.$ = global.jQuery = $; require("jquery-ui-bundle"); +Enzyme.configure({ adapter: new Adapter() }); + describe("DatamonkeyTable", () => { var mle_headers = [ { value: "Site", sortable: true, abbr: "Site Position" }, @@ -78,7 +82,12 @@ describe("DatamonkeyTable", () => { var elem = table.find("th").at(1); elem.simulate("click"); elem.simulate("click"); - expect(table.find("td").at(1).text()).toBe("119.000"); + expect( + table + .find("td") + .at(1) + .text() + ).toBe("119.000"); }); it("sort columns that are already sorted (tests bug fix)", () => { @@ -94,6 +103,11 @@ describe("DatamonkeyTable", () => { var elem = table.find("th").at(0); elem.simulate("click"); elem.simulate("click"); - expect(table.find("td").at(0).text()).toBe("10"); + expect( + table + .find("td") + .at(0) + .text() + ).toBe("10"); }); }); diff --git a/data/json_files/busted/CD2.fasta.BUSTED-SRV.json b/data/json_files/busted/CD2.fasta.BUSTED-SRV.json new file mode 100644 index 00000000..aba54ddd --- /dev/null +++ b/data/json_files/busted/CD2.fasta.BUSTED-SRV.json @@ -0,0 +1,1517 @@ +{ + "Evidence Ratios": { + "constrained": [ + [ + 1.757499296557763, + 0.9487913337256307, + 0.9573957840532279, + 1.834671460669817, + 1.508414550291836, + 2.099445585966095, + 7.211270682908296, + 3.893071076045686, + 2.562293867000863, + 0.7238451118744089, + 0.3179552076143249, + 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been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead.\n", + "requirements": "in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "version": "2.2" + }, + "background": 0, + "branch attributes": { + "0": { + "Baboon": { + "MG94xREV with separate rates for branch sets": 0.001772668685731004, + "Nucleotide GTR": 0.00167924111571506, + "constrained": 0.000504171442550285, + "original name": "Baboon", + "unconstrained": 0.000539422090424917 + }, + "Cat": { + "MG94xREV with separate rates for branch sets": 0.2738128248703174, + "Nucleotide GTR": 0.2661070738935581, + "constrained": 0.1155866193204029, + "original name": "Cat", + "unconstrained": 0.120097179634954 + }, + "Chimp": { + "MG94xREV with separate rates for branch sets": 0.001828152203049299, + "Nucleotide GTR": 0.001817521592053493, + "constrained": 0.0006183824448042049, + "original 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Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead.\n", + "requirements": "in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "version": "2.2" + }, + "background": 0, + "branch attributes": { + "0": { + "Baboon": { + "MG94xREV with separate rates for branch sets": 0.001771058491017039, + "Nucleotide GTR": 0.00167924111571506, + "constrained": 0.0005861467035833775, + "original name": "Baboon", + "unconstrained": 0.0006184697588670626 + }, + "Cat": { + "MG94xREV with separate rates for branch sets": 0.2735661063438983, + "Nucleotide GTR": 0.2661070738935581, + "constrained": 0.09492645928562321, + "original name": "Cat", + "unconstrained": 0.1085502855878957 + }, + "Chimp": { + "MG94xREV with separate rates for branch sets": 0.00182756556946826, + "Nucleotide GTR": 0.001817521592053493, + "constrained": 0.000608450638169511, + "original 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Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead.\n", + "requirements": "in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "version": "2.2" + }, + "background": 0, + "branch attributes": { + "0": { + "CHICKEN_HEBEI_326_2005": { + "MG94xREV with separate rates for branch sets": 0.03574465882364079, + "Nucleotide GTR": 0.03479903784324959, + "constrained": 0.01214387857038488, + "original name": "CHICKEN_HEBEI_326_2005", + "unconstrained": 0.01214715675167316 + }, + "CHICKEN_HONGKONG_915_97": { + "MG94xREV with separate rates for branch sets": 0, + "Nucleotide GTR": 0, + "constrained": 0, + "original name": "CHICKEN_HONGKONG_915_97", + "unconstrained": 0 + }, + "CHICKEN_THAILAND_KANCHANABURI_CK_160_2005": { + "MG94xREV with separate rates for branch sets": 0.00974953436839471, + "Nucleotide GTR": 0.00948189679446463, + "constrained": 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to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead.\n", + "requirements": "in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "version": "2.2" + }, + "background": 0, + "branch attributes": { + "0": { + "CHICKEN_HEBEI_326_2005": { + "MG94xREV with separate rates for branch sets": 0.03574465882364079, + "Nucleotide GTR": 0.03479903784324959, + "original name": "CHICKEN_HEBEI_326_2005", + "unconstrained": 0.01186323098522374 + }, + "CHICKEN_HONGKONG_915_97": { + "MG94xREV with separate rates for branch sets": 0, + "Nucleotide GTR": 0, + "original name": "CHICKEN_HONGKONG_915_97", + "unconstrained": 0 + }, + "CHICKEN_THAILAND_KANCHANABURI_CK_160_2005": { + "MG94xREV with separate rates for branch sets": 0.00974953436839471, + "Nucleotide GTR": 0.00948189679446463, + "original name": "CHICKEN_THAILAND_KANCHANABURI_CK_160_2005", + 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"CAT": "H", + "CCA": "P", + "CCC": "P", + "CCG": "P", + "CCT": "P", + "CGA": "R", + "CGC": "R", + "CGG": "R", + "CGT": "R", + "CTA": "T", + "CTC": "T", + "CTG": "T", + "CTT": "T", + "GAA": "E", + "GAC": "D", + "GAG": "E", + "GAT": "D", + "GCA": "A", + "GCC": "A", + "GCG": "A", + "GCT": "A", + "GGA": "G", + "GGC": "G", + "GGG": "G", + "GGT": "G", + "GTA": "V", + "GTC": "V", + "GTG": "V", + "GTT": "V", + "TAA": "*", + "TAC": "Y", + "TAG": "*", + "TAT": "Y", + "TCA": "S", + "TCC": "S", + "TCG": "S", + "TCT": "S", + "TGA": "W", + "TGC": "C", + "TGG": "W", + "TGT": "C", + "TTA": "L", + "TTC": "F", + "TTG": "L", + "TTT": "F", + "---": "-" + }, + "4": { + "AAA": "K", + "AAC": "N", + "AAG": "K", + "AAT": "N", + "ACA": "T", + "ACC": "T", + "ACG": "T", + "ACT": "T", + "AGA": "R", + "AGC": "S", + "AGG": "R", + "AGT": "S", + "ATA": "I", + "ATC": "I", + "ATG": "M", + "ATT": "I", + "CAA": "Q", + "CAC": "H", + "CAG": "Q", + "CAT": "H", + "CCA": "P", + "CCC": "P", + "CCG": "P", + "CCT": "P", + "CGA": "R", + "CGC": "R", + "CGG": "R", + "CGT": "R", + "CTA": "L", + "CTC": "L", + "CTG": "L", + "CTT": "L", + "GAA": "E", + "GAC": "D", + "GAG": "E", + "GAT": "D", + "GCA": "A", + "GCC": "A", + "GCG": "A", + "GCT": "A", + "GGA": "G", + "GGC": "G", + "GGG": "G", + "GGT": "G", + "GTA": "V", + "GTC": "V", + "GTG": "V", + "GTT": "V", + "TAA": "*", + "TAC": "Y", + "TAG": "*", + "TAT": "Y", + "TCA": "S", + "TCC": "S", + "TCG": "S", + "TCT": "S", + "TGA": "W", + "TGC": "C", + "TGG": "W", + "TGT": "C", + "TTA": "L", + "TTC": "F", + "TTG": "L", + "TTT": "F", + "---": "-" + }, + "5": { + "AAA": "K", + "AAC": "N", + "AAG": "K", + "AAT": "N", + "ACA": "T", + "ACC": "T", + "ACG": "T", + "ACT": "T", + "AGA": "S", + "AGC": "S", + "AGG": "S", + "AGT": "S", + "ATA": "M", + "ATC": "I", + "ATG": "M", + "ATT": "I", + "CAA": "Q", + "CAC": "H", + "CAG": "Q", + "CAT": "H", + "CCA": "P", + "CCC": "P", + "CCG": "P", + "CCT": "P", + "CGA": "R", + "CGC": "R", + "CGG": "R", + "CGT": "R", + "CTA": "L", + "CTC": "L", + "CTG": "L", + "CTT": "L", + "GAA": "E", + "GAC": "D", + "GAG": "E", + "GAT": "D", + "GCA": "A", + "GCC": "A", + "GCG": "A", + "GCT": "A", + "GGA": "G", + "GGC": "G", + "GGG": "G", + "GGT": "G", + "GTA": "V", + "GTC": "V", + "GTG": "V", + "GTT": "V", + "TAA": "*", + "TAC": "Y", + "TAG": "*", + "TAT": "Y", + "TCA": "S", + "TCC": "S", + "TCG": "S", + "TCT": "S", + "TGA": "W", + "TGC": "C", + "TGG": "W", + "TGT": "C", + "TTA": "L", + "TTC": "F", + "TTG": "L", + "TTT": "F", + "---": "-" + }, + "6": { + "AAA": "K", + "AAC": "N", + "AAG": "K", + "AAT": "N", + "ACA": "T", + "ACC": "T", + "ACG": "T", + "ACT": "T", + "AGA": "R", + "AGC": "S", + "AGG": "R", + "AGT": "S", + "ATA": "I", + "ATC": "I", + "ATG": "M", + "ATT": "I", + "CAA": "Q", + "CAC": "H", + "CAG": "Q", + "CAT": "H", + "CCA": "P", + "CCC": "P", + "CCG": "P", + "CCT": "P", + "CGA": "R", + "CGC": "R", + "CGG": "R", + "CGT": "R", + "CTA": "L", + "CTC": "L", + "CTG": "L", + "CTT": "L", + "GAA": "E", + "GAC": "D", + "GAG": "E", + "GAT": "D", + "GCA": "A", + "GCC": "A", + "GCG": "A", + "GCT": "A", + "GGA": "G", + "GGC": "G", + "GGG": "G", + "GGT": "G", + "GTA": "V", + "GTC": "V", + "GTG": "V", + "GTT": "V", + "TAA": "Q", + "TAC": "Y", + "TAG": "Q", + "TAT": "Y", + "TCA": "S", + "TCC": "S", + "TCG": "S", + "TCT": "S", + "TGA": "*", + "TGC": "C", + "TGG": "W", + "TGT": "C", + "TTA": "L", + "TTC": "F", + "TTG": "L", + "TTT": "F", + "---": "-" + } +} diff --git a/package.json b/package.json index 1ece098f..5fe665cc 100644 --- a/package.json +++ b/package.json @@ -20,12 +20,13 @@ "url": "git://github.com/veg/hyphy-vision.git" }, "main": "dist/hyphyvision.js", - "version": "2.5.0", + "version": "2.6.0", "dependencies": { "@fortawesome/fontawesome-free": "^5.3.1", - "alignment.js": "1.0.10", + "alignment.js": "0.0.1", "bootstrap": "4.x", "chi-squared": "^1.1.0", + "create-react-class": "^15.6.3", "csvexport": "1.1.0", "d3": "3.x", "d3-save-svg": "0.0.2", @@ -45,10 +46,11 @@ "popper.js": "^1.14.1", "pretty-data": "^0.40.0", "prop-types": "^15.5.10", - "react": "15.x.x", + "react": "16", "react-copy-to-clipboard": "^5.0.0", - "react-dom": "^15.4.1", + "react-dom": "16", "react-json-view": "^1.14.0", + "react-phylotree": "^0.0.1", "react-router-dom": "^4.2.2", "react-router-hash-link": "^1.1.1", "react-scrollchor": "^4.2.1", @@ -70,7 +72,8 @@ "copy-webpack-plugin": "^4.1.1", "css-loader": "^0.25.0", "electron": "^1.7.9", - "enzyme": "^2.9.1", + "enzyme": "3", + "enzyme-adapter-react-16": "^1.14.0", "eslint": "^4.0.0", "eslint-loader": "^1.8.0", "eslint-plugin-react": "^7.1.0", @@ -87,11 +90,11 @@ "less-loader": "^4.0.4", "node-sass": "^4.8.3", "npm-version": "^1.1.0", - "prettier": "1.12.1", + "prettier": "1.18.1", "pretty-quick": "^1.6.0", "react-addons-test-utils": "^15.6.0", "react-lazy-render": "0.3.0", - "react-test-renderer": "^15.5.4", + "react-test-renderer": "16", "sass-loader": "^6.0.7", "scss-loader": "^0.0.1", "style-loader": "^0.13.1", diff --git a/src/helpers/translate.js b/src/helpers/translate.js new file mode 100644 index 00000000..c34a5e0c --- /dev/null +++ b/src/helpers/translate.js @@ -0,0 +1,24 @@ +const translation_table = require("../../data/translation-table.json"); + +const ambiguous_nucleotides = [ + "R", + "Y", + "S", + "W", + "K", + "M", + "B", + "D", + "H", + "V", + "N" +]; + +function translate(codon, genetic_code) { + if (ambiguous_nucleotides.some(nucleotide => codon.includes(nucleotide))) { + return "X"; + } + return translation_table[genetic_code][codon]; +} + +export default translate; diff --git a/src/jsx/app.jsx b/src/jsx/app.jsx index a2394eb7..5335ae78 100644 --- a/src/jsx/app.jsx +++ b/src/jsx/app.jsx @@ -1,349 +1,361 @@ -import React from "react"; -import ReactDOM from "react-dom"; -import { BrowserRouter, Route, Redirect } from "react-router-dom"; - -import { Home } from "./home.jsx"; -import { BSREL } from "./absrel.jsx"; -import { BUSTED } from "./busted.jsx"; -import { RELAX } from "./relax.jsx"; -import { FEL } from "./fel.jsx"; -import { MEME } from "./meme.jsx"; -import { SLAC } from "./slac.jsx"; -import { FUBAR } from "./fubar.jsx"; -import { GARD } from "./gard.jsx"; -import { BGM } from "./bgm.jsx"; -import { FADE } from "./fade.jsx"; -import { Slatkin } from "./slatkin.jsx"; -import { NavBar } from "./components/navbar.jsx"; - -const path = require("path"); - -const href = window.location.href; -const is_electron = href.slice(0, 4) == "file"; -const base_url = is_electron ? path.dirname(path.dirname(href)) : ""; - -const fasta = require("../../data/fasta.json"); -/** - * HyPhyVision is the main component of the stand-alone HyPhy-Vision application (both web and electron). - * This component is primarily responsible for: - * 1. Rendering the appliction (render_app is called from index.js). - * 2. Routing between pages. - */ -class HyPhyVision extends React.Component { - constructor(props) { - super(props); - this.state = { - data: false - }; - } - - componentDidMount() { - // Corrects navbar offset when clicking anchor hash - var shiftWindow = function() { - scrollBy(0, -40); - }; - if (location.hash) shiftWindow(); - window.addEventListener("hashchange", shiftWindow); - } - - onFileChange = e => { - var self = this; - var files = e.target.files; // FileList object - - if (files.length == 1) { - var f = files[0]; - var reader = new FileReader(); - reader.onload = (function(theFile) { - return function(e) { - var data = JSON.parse(this.result); - self.setDataToState(data); - }; - })(f); - reader.readAsText(f); - } - e.preventDefault(); - }; - - changeMethod = () => { - // Change state.data to false when the method is changed so that the default results file is loaded. - var self = this; - self.setState({ data: false }); - }; - - setDataToState = data => { - var self = this; - self.setState({ - data: data - }); - }; - - render() { - return ( - -
- - {is_electron ? : null} -
- } /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> - ( - - )} - /> -
-
-
- ); - } -} - -function render_app() { - ReactDOM.render( - , - document.body.appendChild(document.createElement("div")) - ); -} - -module.exports = render_app; +import React from "react"; +import ReactDOM from "react-dom"; +import { BrowserRouter, Route, Redirect } from "react-router-dom"; + +import { Home } from "./home.jsx"; +import { BSREL } from "./absrel.jsx"; +import { BUSTED } from "./busted.jsx"; +import { RELAX } from "./relax.jsx"; +import { FEL } from "./fel.jsx"; +import { MEME } from "./meme.jsx"; +import { SLAC } from "./slac.jsx"; +import { FUBAR } from "./fubar.jsx"; +import { GARD } from "./gard.jsx"; +import { BGM } from "./bgm.jsx"; +import { FADE } from "./fade.jsx"; +import { Slatkin } from "./slatkin.jsx"; +import { NavBar } from "./components/navbar.jsx"; + +const path = require("path"); + +const href = window.location.href; +const is_electron = href.slice(0, 4) == "file"; +const base_url = is_electron ? path.dirname(path.dirname(href)) : ""; + +const fasta = require("../../data/fasta.json"); +/** + * HyPhyVision is the main component of the stand-alone HyPhy-Vision application (both web and electron). + * This component is primarily responsible for: + * 1. Rendering the appliction (render_app is called from index.js). + * 2. Routing between pages. + */ +class HyPhyVision extends React.Component { + constructor(props) { + super(props); + this.state = { + data: false + }; + } + + componentDidMount() { + // Corrects navbar offset when clicking anchor hash + var shiftWindow = function() { + scrollBy(0, -40); + }; + if (location.hash) shiftWindow(); + window.addEventListener("hashchange", shiftWindow); + } + + onFileChange = e => { + var self = this; + var files = e.target.files; // FileList object + + if (files.length == 1) { + var f = files[0]; + var reader = new FileReader(); + reader.onload = (function(theFile) { + return function(e) { + var data = JSON.parse(this.result); + self.setDataToState(data); + }; + })(f); + reader.readAsText(f); + } + e.preventDefault(); + }; + + changeMethod = () => { + // Change state.data to false when the method is changed so that the default results file is loaded. + var self = this; + self.setState({ data: false }); + }; + + setDataToState = data => { + var self = this; + self.setState({ + data: data + }); + }; + + render() { + return ( + +
+ + {is_electron ? : null} +
+ } /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> + ( + + )} + /> +
+
+
+ ); + } +} + +function render_app() { + ReactDOM.render( + , + document.body.appendChild(document.createElement("div")) + ); +} + +module.exports = render_app; diff --git a/src/jsx/busted.jsx b/src/jsx/busted.jsx index b1f8dbdd..7f0fcc14 100644 --- a/src/jsx/busted.jsx +++ b/src/jsx/busted.jsx @@ -4,8 +4,10 @@ var React = require("react"), ReactDOM = require("react-dom"), d3 = require("d3"), d3_save_svg = require("d3-save-svg"), - _ = require("underscore"); + _ = require("underscore"), + createReactClass = require("create-react-class"); +import Phylotree, { placenodes, phylotreev1 } from "react-phylotree"; import { Tree } from "./components/tree.jsx"; import { PropChart } from "./components/prop_chart.jsx"; import { DatamonkeyTable } from "./components/tables.jsx"; @@ -13,8 +15,10 @@ import { saveSvgAsPng } from "save-svg-as-png"; import { Header } from "./components/header.jsx"; import { MainResult } from "./components/mainresult.jsx"; import { ResultsPage } from "./components/results_page.jsx"; +import { BaseSVGAlignment, SitePlotAxis, fastaParser } from "alignment.js"; +import translate from "../helpers/translate"; -var BUSTEDSiteChartAndTable = React.createClass({ +var BUSTEDSiteChartAndTable = createReactClass({ getInitialState: function() { return { lower_site_range: 0, @@ -135,8 +139,7 @@ var BUSTEDSiteChartAndTable = React.createClass({ .append("g") .attr("transform", "translate(" + margin.left + "," + margin.top + ")"); - g - .selectAll(".axis-line") + g.selectAll(".axis-line") .data(yAxisTicks) .enter() .append("line") @@ -146,37 +149,31 @@ var BUSTEDSiteChartAndTable = React.createClass({ .attr("y2", d => y(d)) .style("stroke", "#eee") .style("stroke-width", 1); - g - .append("path") + g.append("path") .attr("class", "line") .attr("d", oner_line(self.props.data)) .style("fill", "none") .style("stroke-width", 2) .style("stroke", "#000"); - g - .append("path") + g.append("path") .attr("class", "line") .attr("d", cer_line(self.props.data)) .style("fill", "none") .style("stroke-width", 2) .style("stroke", "#00a99d"); - g - .append("g") + g.append("g") .attr("class", "x axis") .attr("transform", "translate(0," + height + ")") .call(xAxis); - g - .append("text") + g.append("text") .attr("x", width / 2) .attr("y", height + margin.bottom) .style("text-anchor", "middle") .text("Site index"); - g - .append("g") + g.append("g") .attr("class", "y axis") .call(yAxis); - g - .append("text") + g.append("text") .attr("transform", "rotate(-90)") .attr("x", -height / 2) .attr("y", -margin.left) @@ -244,8 +241,7 @@ var BUSTEDSiteChartAndTable = React.createClass({ .x(x) .on("brushend", brushend); - g - .append("g") + g.append("g") .attr("class", "brush") .call(brush) .selectAll("rect") @@ -416,7 +412,7 @@ var BUSTEDSiteChartAndTable = React.createClass({ "form-group" + (this.state.CERwarning ? " has-error" : "") } > -