Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

modify temporal color scale & legend to focus on tip dates #544

Merged
merged 2 commits into from
May 1, 2018
Merged

modify temporal color scale & legend to focus on tip dates #544

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4899ef4
modify temporal color scale & legend to focus on tip dates
jameshadfield Apr 23, 2018
b7e1760
space colorScale according to tip sampling
jameshadfield Apr 23, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
94 changes: 64 additions & 30 deletions src/util/colorScale.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,18 +10,9 @@ import { setGenotype, orderOfGenotypeAppearance } from "./setGenotype";

const unknownColor = "#DDDDDD";

const continuousScale = (x0, x1) => {
const scale = scaleLinear()
.domain(genericDomain.map((d) => x0 + d * (x1 - x0)))
.range(colors[9]);
return (val) => (val === undefined || val === false) ? unknownColor : scale(val);
};

const getMinMaxFromTree = (nodes, nodesToo, attr) => {
const vals = nodes.map((n) => n.attr[attr]);
if (nodesToo) {
nodesToo.forEach((n) => vals.push(n.attr[attr]));
}
const arr = nodesToo ? nodes.concat(nodesToo) : nodes.slice();
const vals = arr.map((n) => n.attr[attr]);
vals.filter((n) => n !== undefined)
.filter((item, i, ar) => ar.indexOf(item) === i);
return [min(vals), max(vals)];
Expand Down Expand Up @@ -75,10 +66,19 @@ const createDiscreteScale = (domain) => {
return (val) => (val === undefined || val === false) ? unknownColor : scale(val);
};

const valBetween = (x0, x1) => {
return x0 + 0.5*(x1-x0);
const createLegendBounds = (legendValues) => {
const valBetween = (x0, x1) => x0 + 0.5*(x1-x0);
const len = legendValues.length;
const legendBounds = {};
legendBounds[legendValues[0]] = [0, valBetween(legendValues[0], legendValues[1])];
for (let i = 1; i < len - 1; i++) {
legendBounds[legendValues[i]] = [valBetween(legendValues[i-1], legendValues[i]), valBetween(legendValues[i], legendValues[i+1])];
}
legendBounds[legendValues[len-1]] = [valBetween(legendValues[len-2], legendValues[len-1]), 10000];
return legendBounds;
};


export const calcColorScale = (colorBy, controls, tree, treeToo, metadata) => {
// console.log(`calcColorScale for ${colorBy}. TreeToo? ${!!treeToo}`)
let genotype;
Expand Down Expand Up @@ -128,24 +128,58 @@ export const calcColorScale = (colorBy, controls, tree, treeToo, metadata) => {
} else if (colorOptions && colorOptions[colorBy].type === "continuous") {
// console.log("making a continuous color scale for ", colorBy)
continuous = true;
const minMax = colorBy === "lbi" ?
[0, 0.7] :
getMinMaxFromTree(tree.nodes, treeTooNodes, colorBy, colorOptions[colorBy]);
colorScale = continuousScale(...minMax);
const spread = minMax[1] - minMax[0];
const dp = spread > 5 ? 2 : 3;
legendValues = colorBy === "lbi" ?
[0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7] :
genericDomain.map((d) => parseFloat((minMax[0] + d*spread).toFixed(dp)));
if (legendValues[0] === -0) legendValues[0] = 0; /* hack to avoid bugs */
/* sort out ranges */
const len = legendValues.length;
legendBounds = {};
legendBounds[legendValues[0]] = [0, valBetween(legendValues[0], legendValues[1])];
for (let i = 1; i < len - 1; i++) {
legendBounds[legendValues[i]] = [valBetween(legendValues[i-1], legendValues[i]), valBetween(legendValues[i], legendValues[i+1])];
let minMax;
switch (colorBy) {
case "lbi":
minMax = [0, 0.7];
break;
case "num_date":
break; /* minMax not needed for num_date */
default:
minMax = getMinMaxFromTree(tree.nodes, treeTooNodes, colorBy, colorOptions[colorBy]);
}

/* make the continuous scale */
let domain, range;
switch (colorBy) {
case "num_date":
/* we want the colorScale to "focus" on the tip dates, and be spaced according to sampling */
let rootDate = tree.nodes[0].attr.num_date;
let vals = tree.nodes.filter((n) => !n.hasChildren).map((n) => n.attr.num_date);
if (treeTooNodes) {
if (treeTooNodes[0].attr.num_date < rootDate) rootDate = treeTooNodes[0].attr.num_date;
vals.concat(treeTooNodes.filter((n) => !n.hasChildren).map((n) => n.attr.num_date));
}
vals = vals.sort();
domain = [rootDate];
const n = 10;
const spaceBetween = parseInt(vals.length / (n - 1), 10);
for (let i = 0; i < (n-1); i++) domain.push(vals[spaceBetween*i]);
domain.push(vals[vals.length-1]);
range = colors[n]; /* contains n+1 values */
break;
default:
range = colors[9];
domain = genericDomain.map((d) => minMax[0] + d * (minMax[1] - minMax[0]));
}
legendBounds[legendValues[len-1]] = [valBetween(legendValues[len-2], legendValues[len-1]), 10000];
const scale = scaleLinear().domain(domain).range(range);
colorScale = (val) => (val === undefined || val === false) ? unknownColor : scale(val);

/* construct the legend values & their respective bounds */
switch (colorBy) {
case "lbi":
legendValues = [0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7];
break;
case "num_date":
legendValues = domain.slice(1);
break;
default:
const spread = minMax[1] - minMax[0];
const dp = spread > 5 ? 2 : 3;
legendValues = genericDomain.map((d) => parseFloat((minMax[0] + d*spread).toFixed(dp)));
}
if (legendValues[0] === -0) legendValues[0] = 0; /* hack to avoid bugs */
legendBounds = createLegendBounds(legendValues);
}
} else {
error = true;
Expand Down