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Allow NEXUS export with all colorings included as annotations
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Similar to current Newick export except in a format conforming with BEAST such that it can be read by FigTree.
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@jameshadfield
jameshadfield committed Dec 17, 2020
1 parent 9681c1f commit 9f3561f
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Showing 2 changed files with 78 additions and 11 deletions.
18 changes: 15 additions & 3 deletions src/components/download/downloadButtons.js
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ const iconWidth = 25;
* A React Component displaying buttons which trigger data-downloads. Intended for display within the
* larger Download modal component
*/
export const DownloadButtons = ({dispatch, t, tree, entropy, metadata, mutType, panelsToDisplay, panelLayout, filters, visibility, visibleStateCounts, relevantPublications}) => {
export const DownloadButtons = ({dispatch, t, tree, entropy, metadata, colorBy, mutType, panelsToDisplay, panelLayout, filters, visibility, visibleStateCounts, relevantPublications}) => {
const totalTipCount = metadata.mainTreeNumTips;
const selectedTipsCount = getNumSelectedTips(tree.nodes, tree.visibility);
const partialData = selectedTipsCount !== totalTipCount;
Expand All @@ -34,13 +34,25 @@ export const DownloadButtons = ({dispatch, t, tree, entropy, metadata, mutType,
name="Tree (Newick)"
description="Phylogenetic tree in Newick format with branch lengths in units of divergence."
icon={<RectangularTreeIcon width={iconWidth} selected />}
onClick={() => helpers.newick(dispatch, filePrefix, tree, false)}
onClick={() => helpers.exportTree({isNewick: true, dispatch, filePrefix, tree, temporal: false})}
/>
<Button
name="TimeTree (Newick)"
description="Phylogenetic tree in Newick format with branch lengths measured in years."
icon={<RectangularTreeIcon width={iconWidth} selected />}
onClick={() => helpers.newick(dispatch, filePrefix, tree, true)}
onClick={() => helpers.exportTree({isNewick: true, dispatch, filePrefix, tree, temporal: true})}
/>
<Button
name="Tree (Nexus)"
description="Phylogeny in Nexus format with branch lengths in units of divergence. Colorings are included as annotations."
icon={<RectangularTreeIcon width={iconWidth} selected />}
onClick={() => helpers.exportTree({dispatch, filePrefix, tree, colorings: metadata.colorings, colorBy, temporal: false})}
/>
<Button
name="TimeTree (Nexus)"
description="Phylogeny in Neexus format with branch lengths measured in years. Colorings are included as annotations."
icon={<RectangularTreeIcon width={iconWidth} selected />}
onClick={() => helpers.exportTree({dispatch, filePrefix, tree, colorings: metadata.colorings, colorBy, temporal: true})}
/>
<Button
name="Metadata (TSV)"
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71 changes: 63 additions & 8 deletions src/components/download/helperFunctions.js
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import { getTraitFromNode, getDivFromNode, getFullAuthorInfoFromNode, getVaccine
import { numericToCalendar } from "../../util/dateHelpers";
import { NODE_VISIBLE } from "../../util/globals";
import { createSummary } from "../info/info";
import { isColorByGenotype } from "../../util/getGenotype";

export const isPaperURLValid = (d) => {
return (
Expand All @@ -15,7 +16,7 @@ export const isPaperURLValid = (d) => {
};

/* this function based on https://github.com/daviddao/biojs-io-newick/blob/master/src/newick.js */
const treeToNewick = (tree, temporal) => {
const treeToNewick = (tree, temporal, internalNodeNames=false, nodeAnnotation=() => "") => {
const getXVal = temporal ? (n) => getTraitFromNode(n, "num_date") : getDivFromNode;

function recurse(node, parentX) {
Expand All @@ -27,10 +28,11 @@ const treeToNewick = (tree, temporal) => {
const subtree = recurse(child, getXVal(node));
return subtree;
});
return `(${childSubtrees.filter((t) => !!t).join(",")})${node.name}:${getXVal(node) - parentX}`;
return `(${childSubtrees.filter((t) => !!t).join(",")})` +
`${internalNodeNames?node.name:""}${nodeAnnotation(node)}:${getXVal(node) - parentX}`;
}
/* terminal node */
const leaf = `${node.name}:${getXVal(node) - parentX}`;
const leaf = `${node.name}${nodeAnnotation(node)}:${getXVal(node) - parentX}`;
return leaf;
}

Expand All @@ -46,6 +48,54 @@ const MIME = {
svg: "image/svg+xml;charset=utf-8"
};

const treeToNexus = (tree, colorings, colorBy, temporal) => {
/**
* Create a NEXUS-type node-annotation conforming with BEAST export format
* For example:
* [&country=Thailand,region=SoutheastAsia,lbi=0.3355275145752664,gt-NS1_349=M]
* Simple key+value pairs look like `key=value` (value can be string or numeric & doesn't need to be quoted.
* Ranges can be included like `key={v1,v2}` (v1,v2 are usually numeric)
* Square brackets cannot be in the key or value, neither can curly brackets (except as noted above)
* not can commas or equals signs, except as noted above.
* We also strip non-latin characters, which cause issues for FigTree
*
* We export all node_attrs which are colorings, as well as divergence if the tree is temporally scaled.
* If the current color-by is a genotype, we export this.
*/
const makeNodeAnnotation = () => {
const t = (x) => String(x).replace(/[[\]{}=,]/g, '').replace(/[\u0250-\ue007]/g, '');
const genotype = isColorByGenotype(colorBy) ? t(colorBy.replace(/,/g, '/')) : undefined;
return (node) => {
const annotations = [];
Object.keys(colorings).forEach((c) => {
if (c.includes("_lab") || c.includes("author")) return;
const v = getTraitFromNode(node, c);
if (v) {
annotations.push(`${t(c)}=${t(v)}`);
const conf = getTraitFromNode(node, c, {confidence: true});
if (Array.isArray(conf) && conf.length===2) {
annotations.push(`${t(c)}_CI={${conf.map((cv) => t(cv)).join(",")}}`);
}
}
});
if (genotype) {
annotations.push(`${genotype}=${t(node.currentGt.replace(/\s/g, ""))}`);
}
if (temporal) { // if temporal metric, export `div` as an attr if it exists
const div = getDivFromNode(node);
if (div!==undefined) annotations.push(`div=${div}`);
}
if (!annotations.length) return ``;
return `[&${annotations.join(',')}]`;
};
};
return [
'#nexus',
'begin trees;',
" tree one = "+treeToNewick(tree, temporal, true, makeNodeAnnotation()),
"end;"
].join("\n");
};

const write = (filename, type, content) => {
/* https://stackoverflow.com/questions/18848860/javascript-array-to-csv/18849208#comment59677504_18849208 */
Expand Down Expand Up @@ -207,11 +257,16 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
dispatch(infoNotification({message: `Metadata exported to ${filename}`}));
};

export const newick = (dispatch, filePrefix, tree, temporal) => {
const fName = temporal ? filePrefix + "_timetree.nwk" : filePrefix + "_tree.nwk";
const treeString = treeToNewick(tree, temporal);
write(fName, MIME.text, treeString);
dispatch(infoNotification({message: `${temporal ? "TimeTree" : "Tree"} written to ${fName}`}));
export const exportTree = ({dispatch, filePrefix, tree, isNewick, temporal, colorings, colorBy}) => {
try {
const fName = `${filePrefix}_${temporal?'timetree':'tree'}.${isNewick?'nwk':'nexus'}`;
const treeString = isNewick ? treeToNewick(tree, temporal) : treeToNexus(tree, colorings, colorBy, temporal);
write(fName, MIME.text, treeString);
dispatch(infoNotification({message: `${temporal ? "TimeTree" : "Tree"} written to ${fName}`}));
} catch (err) {
console.error(err);
dispatch(warningNotification({message: "Error saving tree!"}));
}
};

const processXMLString = (input) => {
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