2b:null 2c:["$","title",null,{"children":"Characterizing Rubisco Distances and Orientations within Fibrils | lametskas | Observable"}] 31:T6bf,{ const bandwidth = 0.3 const use = [] const groupBy = 'innerConcentration' const effectiveAngles = angles.distWithinChain .filter(d => d.length > 2).flat() //.filter(d => math.abs(d.theta) < 100 ) const realData = vl.markLine({ opacity: 0.75}) .data(effectiveAngles) .transform( vl.filter(`${use.length > 0 ? use.map(d => "datum.carbIndex === " + d).join('|') : "datum.carbIndex !== -1"}`), vl.calculate(`datum.d*${pixelSizeNm}`).as(`distNm`), //vl.filter(`datum.dist < ${params.maxDistance}`), //vl.filter(`datum.theta < 100`), //vl.calculate(`datum.numRubInner/datum.volume`).as('concentration'), vl.groupby([groupBy]) .density('distNm') .counts(false) .bandwidth(bandwidth) // .cumulative(false) // .groupby(['carbIndex']), ) .encode( vl.x({axis:{grid: false}}).fieldQ('value').title('Distance to next RuBisCO in the chain (pixel)'),//.bin({maxbins: 300, anchor: 0.5}), //.sort(vl.field('count').order('descending')), //.order('descending'), vl.y({axis:{grid: false}}).fieldQ('density'),//count(), //('count').field('angle'),//.sum().field('angle'),//.scale({type: 'log'}), // vl.x().fieldQ('value'), ////vl.y().fieldQ('density'), // .scale({type: 'log'}), vl.color().fieldQ('innerConcentration').title([`Inner Rubisco Concentration (µM)`]).scale({scheme: 'plasma'}).sort('descending').legend({orient: 'bottom', titleLimit: 300, width: 400}), // vl.strokeWidth().fieldQ('count') vl.tooltip([groupBy]) //.fieldN('reg') ) return vl .layer(realData) .width(750) .height(400) .config({view: {stroke: "transparent"}}) .render({renderer: 'svg'}) }32:T4bc,{ const bandwidth = 1 const use = [] const groupBy = 'l' const effectiveAngles = angles.distWithinChain .filter(d => d.length > 2).flat() const realData = vl.markBar({ opacity: 0.75}) .data(effectiveAngles) .encode( vl.x({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15, } }).fieldQ('twist').bin({maxbins: 20, anchor: 0 }).title(['Rotation angle between neighboring', 'RuBisCOs within a chain (deg)']), //.sort(vl.field('count').order('descending')), //.order('descending'), vl.y({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15 } }).count().title('Counts').scale({domain: [0, 400]}), vl.color().fieldQ('innerConcentration').title([`Inner Rubisco Concentration (µM)`]).scale({scheme: 'viridis', domain: [200, 600]}).sort('descending').legend({orient: 'bottom', titleLimit: 300, width: 400, titleFontSize: 15, labelFontSize: 15, tickCount: 5, padding: 10}), vl.tooltip(['twist']) ) return vl .layer(realData) .width(350) .height(200) .config({view: {stroke: "transparent"}}) .render({renderer: 'svg'}) }33:T4fb,{ const bandwidth = 0.5 const use = [] const effectiveAngles = angles.distWithinChain .filter(d => d.length > 2).flat() //.filter(d => math.abs(d.theta) < 100 ) const realData = vl.markBar({ opacity: 0.75}) .data(effectiveAngles) .transform( vl.filter(`${use.length > 0 ? use.map(d => "datum.carbIndex === " + d).join('|') : "datum.carbIndex !== -1"}`), vl.filter(`datum.l > 2`), ) .encode( vl.x({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15, tickCount: 4, } }).fieldQ('bend').title('Bending angle to next RuBisCO in the chain (deg)').bin({maxbins: 25}), vl.y({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15 } }).count().title('Counts'), vl.color().fieldQ('innerConcentration').title([`Inner Rubisco Concentration (µM)`]).scale({scheme: 'viridis', domain: [200, 600]}).sort('descending').legend({orient: 'bottom', titleLimit: 300, width: 400, titleFontSize: 15, labelFontSize: 15, tickCount: 5, padding: 10}), ) return vl .layer(realData) .width(350) .height(200) .config({view: {stroke: "transparent"}}) .render({renderer: 'svg'}) }34:T78c,{ const bandwidth = 0.5 const use = [] const effectiveAngles = angles.distWithinChain .filter(d => d.length > 2).flat() //.filter(d => math.abs(d.theta) < 100 ) const realData = vl.markPoint({ opacity: 0.75, filled: true}) .data(effectiveAngles) .transform( vl.filter(`${use.length > 0 ? use.map(d => "datum.carbIndex === " + d).join('|') : "datum.carbIndex !== -1"}`), vl.filter(`datum.l > 2`), //${params.maxDistance}`), //vl.filter(`datum.theta < 100`), //vl.calculate(`datum.numRubInner/datum.volume`).as('concentration'), //vl.groupby([groupBy]) // .density('bend') //.counts(false) //.bandwidth(bandwidth) // .cumulative(false) // .groupby(['carbIndex']), ) .encode( vl.x({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15, tickCount: 4, } }).fieldQ('bend').title('Bending angle to next RuBisCO in the chain (deg)'), //.sort(vl.field('count').order('descending')), //.order('descending'), vl.y({ axis:{ grid: false, labelFontSize: 15, titleFontSize: 15 } }).fieldQ('twist').title('Twist (deg)'), //('count').field('angle'),//.sum().field('angle'),//.scale({type: 'log'}), // vl.x().fieldQ('value'), ////vl.y().fieldQ('density'), // .scale({type: 'log'}), vl.color().fieldQ('innerConcentration').title([`Inner Rubisco Concentration (µM)`]).scale({scheme: 'viridis', domain: [200, 600]}).sort('descending').legend({orient: 'bottom', titleLimit: 300, width: 400, titleFontSize: 15, labelFontSize: 15, tickCount: 5, padding: 10}), // vl.strokeWidth().fieldQ('count') //vl.tooltip([groupBy]) //.fieldN('reg') ) return vl .layer(realData) .width(750) .height(400) .config({view: {stroke: "transparent"}}) .render({renderer: 'svg'}) }35:T1012,angles = { const results = [] const allDistances = [] const twistedAngles = [] const distWithinChain = [] for (const carbChains of chainData.results) { const leadingVectors = leadingVector.filter(d => d.carbIndex === carbChains.carb.carbIndex) const N = leadingVectors.length if (N > chainParams.minNumberOfChains) { const rubs = allDataWithVectors.filter(d => d.reg === carbChains.carb.carbIndex) for (let i = 0; i < N - 1; i++) { const chain1 = leadingVectors[i].leadVector const chain1Normed = math.dotDivide(chain1, math.norm(chain1)) const chainData = leadingVectors[i].chain .map(d => rubs.find( r => r.tag === d)) .map(r => { const pos = math.matrix([r.x, r.y, r.z]) const posUnit = math.dotDivide(pos, math.norm(pos)) const p = math.dot(pos, chain1Normed) return { ...r, p } }) .sort((a, b) => a.p - b.p) .map(r => { const narot = math.dot(chain1, r.vec) > 0 ? r.narot : -r.narot return { ...carbChains.carb, narot: narot < 0 ? (90 + (narot % 90) ) % 90 : narot % 90, originalNarot: narot, tag: r.tag, p: r.p, pos: math.matrix([r.x, r.y, r.z]), vec: r.vec } })// twistedAngles.push(chainData) const distsInChain = [] for (let z = 0; z < chainData.length - 1; z++) { const rub1Orientation = math.dotDivide(chainData[z].vec, math.norm(chainData[z].vec)) const rub2Orientation = math.dotDivide(chainData[z+1].vec, math.norm(chainData[z+1].vec)) const tmpBend = math.dot(rub1Orientation, rub2Orientation) const bend = tmpBend > 0 ? tmpBend : math.dot(rub1Orientation, math.dotMultiply(rub2Orientation, -1)) const dAngle = chainData[z+1].narot - chainData[z].narot distsInChain.push({ d: math.norm(math.subtract(chainData[z].pos, chainData[z+1].pos)), rub1: chainData[z+1], rub2: chainData[z], bend: 180 * math.acos(bend) /Math.PI, twist: dAngle > 45 ? 90 - dAngle : (dAngle < -45 ? 90 + dAngle : dAngle), l: chainData.length, ...carbChains.carb }) } distWithinChain.push(distsInChain) for (let j = i + 1; j < N; j++) { const comDist = math.norm(math.subtract(leadingVectors[i].centerOfMass, leadingVectors[j].centerOfMass)) const distance = distBetweenChains(leadingVectors[i], leadingVectors[j]) distance.allDists.forEach(d => { allDistances.push({ i: leadingVectors[i].chainId, j: leadingVectors[j].chainId, minDist: distance.dist, dist: d }) }) const chain2 = leadingVectors[j].leadVector const chain2Contrary = math.dotMultiply(-1, chain2) const chain2Normed = math.dotDivide(chain2, math.norm(chain2)) const chain2ContraryNormed = math.dotMultiply(-1, chain2Normed) const dot1 = math.dot(chain1Normed, chain2Normed) const dot2 = math.dot(chain1Normed, chain2ContraryNormed) const c2 = dot1 > dot2 ? chain2Normed : chain2ContraryNormed const dot = Math.max(dot1, dot2) const cross = math.cross(chain1Normed, c2) const theta = math.dot(cross, distance.direction) results.push( { ...carbChains.carb, dot, angle: 180 * math.acos(dot) /Math.PI, comDist, dist: distance.dist, direction: distance.direction, theta, chainId1: leadingVectors[i].chainId, chainId2: leadingVectors[j].chainId, chain1: leadingVectors[i], chain2: leadingVectors[j] } ) } } } } return { results, allDistances, twistedAngles, distWithinChain } }36:T49c,leadingVector = { const results = [] let i = 0 for (const chain of chainData.results) { for (const seq of chain.s.chains) { if (seq.length < chainParams.minChainSize) { continue } let leadVector = math.matrix([0,0,0]) let centerOfMass = math.matrix([0,0,0]) const rubs = seq.map(i => allDataWithVectors.find(d => d.tag === i)).flat() const pos = [] for (const rub of rubs) { //const thisVec = math.matrix([Math.abs(rub.vec.x), Math.abs(rub.vec.y), Math.abs(rub.vec.z)]) const contrary = math.dotMultiply(-1, rub.vec) const thisVec = math.dot(leadVector, rub.vec) > math.dot(leadVector, contrary) ? rub.vec : contrary leadVector = math.add(leadVector,thisVec) centerOfMass = math.add(centerOfMass, math.matrix([rub.x, rub.y, rub.z])) pos.push(math.matrix([rub.x, rub.y, rub.z])) } centerOfMass = math.dotDivide(centerOfMass, rubs.length) results.push({ carbIndex: chain.carb.carbIndex, chain: seq, leadVector, centerOfMass, rubs, pos, chainId: i }) i++ } } return results }37:[] 2f:{"id":"80a485d7b02964ff","slug":null,"title":"Characterizing Rubisco Distances and Orientations within Fibrils","thumbnail":null,"access_level":"public","create_time":"$D2023-05-23T21:45:50.353Z","update_time":"$D2023-05-24T15:03:57.877Z","view_time":null,"first_public_time":"$D2023-05-23T21:45:50.353Z","has_unpublished_edits":null,"fork":{"id":"c5b3ca38b33e2f3b","slug":"chain-stats","title":"Chain 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Rubisco Distances and Orientations within Fibrils","cells":[{"id":0,"value":"# Characterizing Rubisco Distances and Orientations within Fibrils","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":970,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1785,"value":"dataForNextRubInChain = angles.distWithinChain.filter(d => d.length > 2).flat()\n .map(d => {\n return {\n distNm: d.d*pixelSizeNm,\n reg: d.carbIndex,\n innerConcentration: d.innerConcentration,\n }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1261,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1797,"value":"dataForTwistBetweenNeighbRubsWithinChain = angles.distWithinChain.filter(d => d.length > 2).flat()\n .map(d => {\n return {\n twist: d.twist,\n reg: d.carbIndex,\n innerConcentration: d.innerConcentration,\n }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1628,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1802,"value":"dataForBendingBetweenNeighbRubsWithinChain = angles.distWithinChain.filter(d => d.length > 2).flat()\n .filter( d => d.l > 2) \n.map(d => {\n return {\n bend: d.bend,\n reg: d.carbIndex,\n innerConcentration: d.innerConcentration,\n }\n })","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":1743,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2124,"value":"## Major Computations","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":27,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":7,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2072,"value":"## Helper Functions and Parameters","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2075,"value":"pixelSizeNm = math.multiply(pixelSize,1e9)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2082,"value":"minChainLength = 4","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2105,"value":"meanTwistBetweenRubs = math.mean(dataForTwistBetweenNeighbRubsWithinChain.map(d => d.twist))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2109,"value":"stdTwistBetweenRubs = math.std(dataForTwistBetweenNeighbRubsWithinChain.map(d => d.twist))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2115,"value":"meanBendingAngleBetweenRubs = math.mean(dataForBendingBetweenNeighbRubsWithinChain.map(d => d.bend))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2119,"value":"stdBendingAngleBetweenRubs = math.std(dataForBendingBetweenNeighbRubsWithinChain.map(d => d.bend))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2070,"value":"## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":2143,"value":"math = require(\"mathjs@9\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2146,"value":"import { vl } from \"@vega/vega-lite-api-v5\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2077,"value":"import { pixelSize } from 'af0568b05533fb86' \n// From NewBaseAnalysis","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2093,"value":"import { chainParams, chainData, allDataWithVectors } from 'b22e7bd264cfacaf'\n//Identify Rubiscos within Fibrils","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2130,"value":"import { distBetweenChains } from '2b7eb09d08e8d862'\n//Exploring the spatial relationship between chains notebook","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W37","stdlib":"1","titling":"auto"}} 30:"$2f:body"