@euphrasiologist/lwphylo 1.1.12 → 1.1.14
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +1 -1
- package/package.json +1 -1
- package/src/radial/getArcs.js +50 -37
- package/src/radial/polarToCartesian.js +35 -5
package/dist/index.js
CHANGED
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
const n={circular:()=>{let n=200,t=2,e=[0,0],r={},i=0,s=0,c=n*n,a=10;function o(){const e=Math.exp(t);return i=e/(e-1)*n,s=t/n,c=n*n,
|
|
1
|
+
const n={circular:()=>{let n=200,t=2,e=[0,0],r={},i=0,s=0,c=n*n,a=10;function o(){const e=Math.exp(t);return i=e/(e-1)*n,s=t/n,c=n*n,l}function l(n){!function(){if(!r||"function"!=typeof r.xscale||"function"!=typeof r.yscale)throw new Error("phisheye.circular: call .scales(xscale, yscale) before using the fisheye.")}();const t=r.xscale(n.x),o=r.yscale(n.y),l=t-e[0],h=o-e[1],d=l*l+h*h;if(0===d||d>=c)return{x:t,y:o,z:d>=c?1:a};const u=Math.sqrt(d),f=i*(1-Math.exp(-u*s))/u*.75+.25;return{x:e[0]+l*f,y:e[1]+h*f,z:Math.min(f,a)}}return l.radius=function(t){return arguments.length?(n=Math.max(0,+t),o()):n},l.distortion=function(n){return arguments.length?(t=Math.max(0,+n),o()):t},l.focus=function(n){if(!arguments.length)return e.slice();if(!Array.isArray(n)||2!==n.length)throw new Error("focus expects [x, y] in pixels.");return e=[+n[0],+n[1]],l},l.scales=function(n,t){return arguments.length?(r={xscale:n,yscale:t},l):r},l.setScales=l.scales,l.clampZ=function(n){return arguments.length?(a=Math.max(1,+n),l):a},l.focusFromEvent=function(n,t){const e=t.getBoundingClientRect(),r=n.clientX-e.left,i=n.clientY-e.top;return l.focus([r,i])},o()}};function t(n,e,r,i,s){const c=2*Math.PI,a=n=>(n%c+c)%c,o=a(i),l=a(s),h=(l-o+c)%c,d=(o-l+c)%c,u=d<h?1:0,f=Math.min(h,d),p=f>Math.PI?1:0;if(f<1e-9){const i=t(n,e,r,o);return`M ${i.x} ${i.y}`}const I=t(n,e,r,o),g=t(n,e,r,l);return`M ${I.x} ${I.y} A ${r} ${r} 0 ${p} ${u} ${g.x} ${g.y}`}function e(n,e,r,i,s){const c=2*Math.PI,a=n=>(n%c+c)%c;let o=a(i),l=a(s),h=l-o;h<0&&(h+=c);const d=h>Math.PI?1:0,u=t(n,e,r,o),f=t(n,e,r,l);return["M",u.x,u.y,"A",r,r,0,d,1,f.x,f.y].join(" ")}function r(n,t=[]){t.push(n);for(let e=0;e<(n.children?.length||0);e++)t=r(n.children[e],t);return t}function i(n,t=!0){var e=[];for(const t of r(n))null===t.parent?e.push({parentId:null,parentLabel:null,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:0,isTip:!1,x:t.x,y:t.y,angle:t.angle}):e.push({parentId:t.parent.id,parentLabel:t.parent.label,thisId:t.id,thisLabel:t.label,children:t.children.map(n=>n.id),branchLength:t.branchLength,isTip:0==t.children.length,x:t.x,y:t.y,angle:t.angle});return t&&(e=e.sort(function(n,t){return n.thisId-t.thisId})),e}function s(n){const t=2*Math.PI,e=i(n,!0),r=new Map(e.map(n=>[n.thisId,n])),s=new Map(e.map(n=>[n.thisId,n.children||[]]));let c=null;for(const n of e)if(null==n.parentId){c=n.thisId;break}const a=[];!function n(t){const e=s.get(t)||[];if(0!==e.length)for(const t of e)n(t);else a.push(t)}(c);const o=Math.max(1,a.length),l=new Map;a.forEach((n,e)=>{l.set(n,e/o*t)}),function n(e){const r=s.get(e)||[];for(const t of r)n(t);if(r.length>0){let n=0,i=0;for(const t of r){const e=l.get(t);n+=Math.cos(e),i+=Math.sin(e)}l.set(e,(Math.atan2(i,n)%t+t)%t)}}(c);const h=new Map;h.set(c,0),function n(t){const e=s.get(t)||[],i=h.get(t)||0;for(const t of e){const e=r.get(t),s=e?.branchLength??0;h.set(t,i+s),n(t)}}(c);for(const n of e){const t=l.get(n.thisId)??0,e=h.get(n.thisId)??0;n.angle=t,n.r=e,n.x=e*Math.cos(t),n.y=e*Math.sin(t)}return e}function c(n){const t={};return t.data=s(n),t.radii=function(n){const t=s(n),e=new Map(t.map(n=>[n.thisId,n])),r=t.find(n=>null==n.parentId)?.thisId,i=[];for(const n of t){if(n.thisId===r)continue;const t=e.get(n.parentId);if(!t)continue;const s=n.angle,c=t.r,a=n.r;i.push({parentId:t.thisId,childId:n.thisId,x0:c*Math.cos(s),y0:c*Math.sin(s),x1:a*Math.cos(s),y1:a*Math.sin(s),isTip:!!n.isTip})}return i}(n),t.arcs=function(n){const t=2*Math.PI;new Map(n.map(n=>[n.thisId,n]));const e=new Map;let r=null;for(const t of n)null==t.parentId&&(r=t.thisId),e.has(t.parentId)||e.set(t.parentId,[]),e.get(t.parentId).push(t);const i=[];for(const s of n){const n=s.thisId;if(n===r)continue;const c=e.get(n)||[];if(c.length<2)continue;const a=c.map(n=>(n.angle%t+t)%t).sort((n,t)=>n-t),o=a[0],l=a[a.length-1],h=l-o,d=t-h;let u,f,p;h<=d?(u=o,f=l,p=h):(u=l,f=o,p=d),p<1e-6||!isFinite(s.r)||s.r<=0||i.push({start:u,end:f,radius:s.r,thisId:n,parentId:s.parentId})}return i}(t.data),t}function a(n){const t=i(n),e=new Map(t.map((n,t)=>[n.thisId,t])),r=[];!function n(t){t.children&&0!==t.children.length?t.children.forEach(n):r.push(t.id)}(n);const s=new Map(r.map((n,t)=>[n,t+1]));return function n(r){const i=e.get(r.id);if(!r.children||0===r.children.length){const n=s.get(r.id);return t[i].y0=n,t[i].y1=n,n}const c=function(n){let t=0,e=0;for(let r of n)null!=r&&(r=+r)>=r&&(++t,e+=r);if(t)return e/t}(r.children.map(n));return t[i].y0=c,t[i].y1=c,c}(n),function n(r,i){const s=e.get(r.id),c=i??0,a=c+(t[s].branchLength??0);t[s].x0=c,t[s].x1=a,r.children&&r.children.length&&r.children.forEach(t=>n(t,a))}(n,0),t.map(n=>{const{y:t,x:e,angle:r,...i}=n;return i})}function o(n){const t=a(n),e=function(n){const t=a(n),e=new Map;for(const n of t){if(null==n.parentId)continue;const t=e.get(n.parentId);t?t.push(n):e.set(n.parentId,[n])}const r=[];for(const[n,t]of e.entries()){if(!t.length)continue;const e=t.map(n=>n.y0),i=Math.min(...e),s=Math.max(...e),c=t[0].x0;r.push({parentId:n,x0:c,x1:c,y0:i,y1:s,heights:s-i})}return r}(n),r=function(n){const t=a(n),e=new Map(t.map(n=>[n.thisId,n])),r=[];for(const n of t){if(null==n.parentId)continue;const t=e.get(n.parentId);if(!t)continue;const i=n.x0,s=n.y0,c=t.y0,a=Math.min(s,c),o=Math.max(s,c);r.push({parentId:n.parentId,childId:n.thisId,x:i,y0:a,y1:o})}return r}(n);new Map(t.map(n=>[n.thisId,n]));const i=t.filter(n=>null!=n.parentId).map(n=>({parentId:n.parentId,childId:n.thisId,thisId:n.thisId,thisLabel:n.thisLabel,isTip:n.isTip,x0:n.x0,x1:n.x1,y0:n.y0,y1:n.y0}));return{data:t,vertical_lines:e,child_vertical_lines:r,horizontal_lines:i}}function l(n){null===n.parent&&(function n(t){if(!t.children||0===t.children.length)return t.ntips=1,1;let e=0;for(const r of t.children)e+=n(r);return t.ntips=e,e}(n),n.start=0,n.end=2,n.angle=0,n.ntips=function(n){var t=0;for(const e of function(n){const t=[n],e=[];for(;t.length;){const n=t.shift();e.push(n);for(const e of n.children)t.push(e)}return e}(n))0==e.children.length&&t++;return t}(n),n.x=0,n.y=0);let t=n.start;for(let e=0;e<n.children.length;e++){const r=n.children[e],i=(n.end-n.start)*(r.ntips/n.ntips);r.start=t,r.end=t+i,r.angle=r.start+(r.end-r.start)/2,t=r.end;const s=r.angle*Math.PI,c=r.branchLength??0;r.x=n.x+c*Math.sin(s),r.y=n.y+c*Math.cos(s),l(r)}return n}function h(n){var t={},e=i(l(n));return t.data=e,t.edges=function(n,t=!1){const e=[...n].sort((n,t)=>n.thisId-t.thisId),r=new Map(e.map(n=>[n.thisId,n])),i=[];for(const n of e){if(null==n.parentId)continue;const e=r.get(n.parentId);e&&(t?(i.push({x1:n.x,y1:n.y,id1:n.thisId,x2:e.x,y2:n.y,id2:void 0}),i.push({x1:e.x,y1:n.y,id1:void 0,x2:e.x,y2:e.y,id2:n.parentId})):i.push({x1:n.x,y1:n.y,id1:n.thisId,x2:e.x,y2:e.y,id2:n.parentId}))}return i}(e),t}function d(n,t){const e=function(n,t="thisId"){return new Map(n.map(n=>[n[t],n]))}(t),r=e.get(n.parentId);return r?{px:r.fisheye.x,py:r.fisheye.y}:null}function u(n){const t=(n=String(n).replace(/\s+/g,"")).split(/(;|\(|\)|,)/),e={parent:null,children:[]};let r=e,i=0;for(const n of t)if(n&&";"!==n)if("("===n){const n={parent:r,children:[]};r.children.push(n),r=n}else if(","===n){r=r.parent;const n={parent:r,children:[]};r.children.push(n),r=n}else if(")"===n){if(r=r.parent,null===r)break}else{const t=n.split(":");1===t.length?n.startsWith(":")?(r.label="",r.branchLength=parseFloat(t[0])):(r.label=t[0],r.branchLength=null):2===t.length?(r.label=t[0],r.branchLength=parseFloat(t[1])):(console.warn(n,"Unhandled token with multiple ':' characters"),r.label=t[0]||"",r.branchLength=parseFloat(t[t.length-1])),r.id=i++}return null==e.id&&(e.id=i),e}function f(n,t){let e={};n.data.forEach(n=>{e[n.thisId]={...n}});let r={};const i=function(n){e[n]&&(r[n]=e[n],e[n].children&&e[n].children.forEach(n=>{i(n)}))};i(t);const s=[["data",Object.values(r)]],c=s[0][1].map(n=>n.thisId);var a=[];for(const t in n)"data"!==t&&a.push([t,n[t]]);var o=a.map(n=>[n[0],n[1].filter(n=>c.includes(n.thisId))]);return Object.fromEntries(s.concat(o))}export{e as describeArc,d as parentFisheye,n as phisheye,c as radialLayout,u as readTree,o as rectangleLayout,f as subTree,h as unrooted};
|
|
2
2
|
//# sourceMappingURL=index.js.map
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@euphrasiologist/lwphylo",
|
|
3
|
-
"version": "1.1.
|
|
3
|
+
"version": "1.1.14",
|
|
4
4
|
"description": "A lightweight, low level javascript library to plot phylogenies from Newick files.",
|
|
5
5
|
"main": "dist/@euphrasiologist/lwphylo.js",
|
|
6
6
|
"unpkg": "dist/@euphrasiologist/lwphylo.min.js",
|
package/src/radial/getArcs.js
CHANGED
|
@@ -1,52 +1,65 @@
|
|
|
1
1
|
/**
|
|
2
|
-
* Build
|
|
3
|
-
*
|
|
4
|
-
*
|
|
5
|
-
*
|
|
6
|
-
* Input: a "radialData" array with fields:
|
|
7
|
-
* thisId, parentId, angle (radians), r (radius at this node)
|
|
8
|
-
*
|
|
9
|
-
* Output: [{ parentId, childId, radius, start, end }]
|
|
10
|
-
* where start/end are angles (radians), radius is parent's r
|
|
2
|
+
* Build arc descriptors for each internal parent:
|
|
3
|
+
* - One arc per internal node at radius = parent.r
|
|
4
|
+
* - Start/end angles choose the *shortest* wrap-aware span covering the children
|
|
5
|
+
* - Skips degenerate spans (delta ~ 0)
|
|
11
6
|
*/
|
|
12
|
-
|
|
13
|
-
function normalize(theta) {
|
|
14
|
-
const t = theta % (2 * Math.PI);
|
|
15
|
-
return t < 0 ? t + 2 * Math.PI : t;
|
|
16
|
-
}
|
|
17
|
-
|
|
18
|
-
function minorArc(a, b) {
|
|
19
|
-
// returns [start, end] representing the minor arc from a -> b
|
|
20
|
-
a = normalize(a); b = normalize(b);
|
|
21
|
-
let diff = b - a;
|
|
22
|
-
if (diff <= -Math.PI) diff += 2 * Math.PI;
|
|
23
|
-
else if (diff > Math.PI) diff -= 2 * Math.PI;
|
|
24
|
-
return [a, a + diff]; // draw from a to a+diff
|
|
25
|
-
}
|
|
26
|
-
|
|
27
7
|
export default function getArcs(pd) {
|
|
8
|
+
const TAU = Math.PI * 2;
|
|
9
|
+
const norm = (t) => ((t % TAU) + TAU) % TAU;
|
|
10
|
+
const EPS = 1e-6;
|
|
11
|
+
|
|
12
|
+
// Quick lookups
|
|
28
13
|
const byId = new Map(pd.map(d => [d.thisId, d]));
|
|
29
|
-
|
|
30
|
-
|
|
14
|
+
const childrenByParent = new Map();
|
|
15
|
+
let root = null;
|
|
31
16
|
|
|
32
|
-
const arcs = [];
|
|
33
17
|
for (const d of pd) {
|
|
34
|
-
if (d.
|
|
35
|
-
|
|
36
|
-
|
|
18
|
+
if (d.parentId == null) root = d.thisId;
|
|
19
|
+
if (!childrenByParent.has(d.parentId)) childrenByParent.set(d.parentId, []);
|
|
20
|
+
childrenByParent.get(d.parentId).push(d);
|
|
21
|
+
}
|
|
37
22
|
|
|
38
|
-
|
|
39
|
-
|
|
23
|
+
const arcs = [];
|
|
24
|
+
|
|
25
|
+
for (const parent of pd) {
|
|
26
|
+
const pid = parent.thisId;
|
|
27
|
+
if (pid === root) continue; // no arc above root
|
|
28
|
+
const kids = childrenByParent.get(pid) || [];
|
|
29
|
+
if (kids.length < 2) continue; // need at least two children
|
|
30
|
+
|
|
31
|
+
// Collect & sort child angles
|
|
32
|
+
const A = kids.map(k => norm(k.angle)).sort((a, b) => a - b);
|
|
33
|
+
const aMin = A[0], aMax = A[A.length - 1];
|
|
34
|
+
|
|
35
|
+
// Two candidate spans: direct (aMin -> aMax) and wrapped (aMax -> aMin across 2π)
|
|
36
|
+
const direct = aMax - aMin;
|
|
37
|
+
const wrapped = TAU - direct;
|
|
38
|
+
|
|
39
|
+
// Choose the shorter span. We'll draw **CCW** (sweepFlag = 0) in describeArc.
|
|
40
|
+
let start, end, span;
|
|
41
|
+
if (direct <= wrapped) {
|
|
42
|
+
start = aMin;
|
|
43
|
+
end = aMax;
|
|
44
|
+
span = direct;
|
|
45
|
+
} else {
|
|
46
|
+
// wrapped is shorter: go CCW from aMax up through 2π to aMin
|
|
47
|
+
start = aMax;
|
|
48
|
+
end = aMin;
|
|
49
|
+
span = wrapped;
|
|
50
|
+
}
|
|
51
|
+
|
|
52
|
+
if (span < EPS || !isFinite(parent.r) || parent.r <= 0) continue;
|
|
40
53
|
|
|
41
|
-
if (!isFinite(parent.r) || parent.r === 0 || start === end) continue;
|
|
42
54
|
arcs.push({
|
|
43
|
-
parentId: parent.thisId,
|
|
44
|
-
childId: d.thisId,
|
|
45
|
-
radius: parent.r,
|
|
46
55
|
start,
|
|
47
|
-
end
|
|
56
|
+
end,
|
|
57
|
+
radius: parent.r,
|
|
58
|
+
thisId: pid,
|
|
59
|
+
parentId: parent.parentId
|
|
48
60
|
});
|
|
49
61
|
}
|
|
62
|
+
|
|
50
63
|
return arcs;
|
|
51
64
|
}
|
|
52
65
|
|
|
@@ -1,7 +1,37 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
1
|
+
import polarToCartesian from "./polarToCartesian.js";
|
|
2
|
+
|
|
3
|
+
/**
|
|
4
|
+
* Draw the shortest arc between startAngle and endAngle on a circle.
|
|
5
|
+
* - Angles are radians.
|
|
6
|
+
* - Works with Y-inverted screen coords (our polarToCartesian already inverts Y).
|
|
7
|
+
* - Automatically picks CW or CCW sweep to follow the *shorter* path.
|
|
8
|
+
*/
|
|
9
|
+
export default function describeArc(cx, cy, radius, startAngle, endAngle) {
|
|
10
|
+
const TAU = Math.PI * 2;
|
|
11
|
+
const norm = (t) => ((t % TAU) + TAU) % TAU;
|
|
12
|
+
|
|
13
|
+
const a0 = norm(startAngle);
|
|
14
|
+
const a1 = norm(endAngle);
|
|
15
|
+
|
|
16
|
+
// CCW delta (a0 -> a1), and CW delta (a0 -> a1 going the other way)
|
|
17
|
+
const ccw = (a1 - a0 + TAU) % TAU;
|
|
18
|
+
const cw = (a0 - a1 + TAU) % TAU;
|
|
19
|
+
|
|
20
|
+
// Choose the shorter sweep
|
|
21
|
+
const sweepFlag = cw < ccw ? 1 : 0; // 1 = CW, 0 = CCW (SVG spec)
|
|
22
|
+
const delta = Math.min(ccw, cw);
|
|
23
|
+
const largeArcFlag = delta > Math.PI ? 1 : 0;
|
|
24
|
+
|
|
25
|
+
// If degenerate, just move to the point
|
|
26
|
+
if (delta < 1e-9) {
|
|
27
|
+
const p = polarToCartesian(cx, cy, radius, a0);
|
|
28
|
+
return `M ${p.x} ${p.y}`;
|
|
29
|
+
}
|
|
30
|
+
|
|
31
|
+
// Use the original angles; sweepFlag picks direction
|
|
32
|
+
const p0 = polarToCartesian(cx, cy, radius, a0);
|
|
33
|
+
const p1 = polarToCartesian(cx, cy, radius, a1);
|
|
34
|
+
|
|
35
|
+
return `M ${p0.x} ${p0.y} A ${radius} ${radius} 0 ${largeArcFlag} ${sweepFlag} ${p1.x} ${p1.y}`;
|
|
6
36
|
}
|
|
7
37
|
|