2d:null 2e:["$","title",null,{"children":"Let's talk about seeds! | Max Brown | Observable"}] 33:Tf90,plot_1 = { const svg = d3 .create("svg") .attr("width", width) .attr("height", height) .attr("font-family", "sans-serif") .attr("font-size", 10); const group2 = svg.append('g'); group2 .selectAll("rect") .data(series) .join("g") .attr("fill", d => color(d.key)) .selectAll("rect") .data(d => d) .join("rect") .attr("x", d => xScale2(d[0])) .attr("y", (d, i) => yScale2(d.data.Family)) .attr("width", d => xScale2(d[1]) - xScale2(d[0])) .attr("height", yScale2.bandwidth()) // tooltip .on('mouseover', function(d, i) { tooltip .html( `

Family: ${d.data.Family}

Category: ${ d.key } - ${Math.round(d[1] * 100 - d[0] * 100)}%

#Species measured: ${ d.data.N }

` ) .style('visibility', 'visible'); d3.select(this) .transition() .attr('fill', hoverColor); }) .on('mousemove', function() { tooltip .style('top', d3.event.pageY + 10 + 'px') .style('left', d3.event.pageX + 10 + 'px'); }) .on('mouseout', function() { tooltip.html(``).style('visibility', 'hidden'); d3.select(this) .transition() .attr('fill', d => color(d.key)); }); // add a group for the y-axis group2 .append("g") .call(yAxis) .selectAll('text') .style("font-size", 12) .style("cursor", "pointer") .on( "click", d => window.open(`https://en.wikipedia.org/wiki/${d}`) // this link takes you to the Kew SID //window.open(`https://data.kew.org/sid/SidServlet?Clade=&Order=&Family=${d.toUpperCase()}&APG=off&Genus=&Species=&StorBehav=0&DsFlag=on`) ); // add a group for the x-axis group2 .append("g") // we have to move this group down to the bottom of the vis .attr("transform", `translate(0, ${height})`) .call(xAxis) //add a label for the x-axis .append("text") .attr("fill", "black") .attr("font-family", "sans-serif") .attr("x", width / 2) .attr("y", 40) .style("font-size", 15) .text("Seed dispersal mode proportion"); // LEGEND // Legend as a group const legend = svg .append("g") // Apply a translation to the entire group .attr("transform", `translate(${250}, ${0})`); const size = 30; const border_padding = 15; const item_padding = 60; const text_offset = 20; // Boxes legend .selectAll("boxes") .data(legend_) .enter() .append("rect") .attr("y", border_padding) .attr("x", (d, i) => border_padding + i * (size + item_padding)) .attr("width", size) .attr("height", size) .style("fill", d => colours(d)); // Labels legend .selectAll("labels") .data(legend_) .enter() .append("text") .attr("y", border_padding + 16) .attr( "x", (d, i) => border_padding + i * (size + item_padding) + size / 2 + text_offset ) .text(d => d) .attr("text-anchor", "left") .style("alignment-baseline", "middle") .style("font-family", "sans-serif") .style("font-size", 15); // ORDER LINES const orders = svg.append("g"); orders .selectAll("orderLines") .data(lineOrders) .join("line") .attr("x1", d => d.Dist) .attr("y1", d => yScale2(d.O1)) .attr("x2", d => d.Dist) .attr("y2", d => yScale2(d.O2) + yScale2.bandwidth()) .attr("stroke-width", 3) .attr("stroke", "black"); orders .selectAll("orderText") .data(lineOrders) .join("text") .attr("x", d => d.Dist + 6) .attr( "y", d => yScale2.bandwidth() + yScale2(d.O1) + (yScale2(d.O2) - yScale2(d.O1)) / 2 ) .text(d => d.Order) .style("font-family", "sans-serif") .style("font-size", 12); return svg.node(); }34:T22fa,treestring = "(((((((Atherospermataceae:0.00487804878,Siparunaceae:0.00487804878):0.01463414634,(Monimiaceae:0.009756097561,(Hernandiaceae:0.00487804878,Lauraceae:0.00487804878):0.00487804878):0.009756097561):0.01951219512,((Magnoliaceae:0.009756097561,(Annonaceae:0.00487804878,Erythroxylaceae:0.00487804878):0.00487804878):0.00487804878,Myristicaceae:0.01463414634)Magnoliales:0.0243902439):0.01951219512,((Winteraceae:0.00487804878,Canellaceae:0.00487804878)Canellales:0.009756097561,(Piperaceae:0.00487804878,Aristolochiaceae:0.00487804878)Piperales:0.009756097561):0.04390243902)Magnoliids:0.00487804878,Chloranthaceae:0.06341463415):0.9317073171,(((((((((Misodendraceae:0.00487804878,Loranthaceae:0.00487804878):0.009756097561,(Santalaceae:0.00487804878,Opiliaceae:0.00487804878):0.009756097561):0.009756097561,Balanophoraceae:0.0243902439,Olacaceae:0.0243902439)Santalales:0.3170731707,((((((((Gentianaceae:0.009756097561,(Loganiaceae:0.00487804878,Apocynaceae:0.00487804878):0.00487804878):0.00487804878,Rubiaceae:0.01463414634)Gentianales:0.06829268293,((Convolvulaceae:0.00487804878,Solanaceae:0.00487804878):0.05365853659,(((((((Bignoniaceae:0.01463414634,Pedaliaceae:0.01463414634,Lentibulariaceae:0.01463414634,Acanthaceae:0.01463414634):0.00487804878,Verbenaceae:0.01951219512):0.009756097561,(Paulowniaceae:0.00487804878,Lamiaceae:0.00487804878):0.0243902439):0.00487804878,Scrophulariaceae:0.03414634146):0.00487804878,Plantaginaceae:0.03902439024):0.00487804878,Gesneriaceae:0.04390243902):0.00487804878,Oleaceae:0.0487804878):0.009756097561):0.0243902439,Boraginaceae:0.08292682927):0.009756097561,Garryaceae:0.09268292683,Icacinaceae:0.09268292683)Lamiids:0.05365853659,((((((Cyperaceae:0.00487804878,Asteraceae:0.00487804878)Asteraceae:0.00487804878,Goodeniaceae:0.009756097561):0.00487804878,Menyanthaceae:0.01463414634):0.00487804878,Campanulaceae:0.01951219512)Asterales:0.0243902439,((Caprifoliaceae:0.00487804878,Adoxaceae:0.00487804878)Dipsacales:0.01463414634,((Apiaceae:0.00487804878,Araliaceae:0.00487804878):0.00487804878,Pittosporaceae:0.009756097561):0.009756097561):0.0243902439):0.00487804878,Aquifoliaceae:0.0487804878)Campanulids:0.09756097561):0.07317073171,(((((((Ericaceae:0.00487804878,Rhizophoraceae:0.00487804878)Ericaceae:0.00487804878,Clethraceae:0.009756097561):0.00487804878,Actinidiaceae:0.01463414634):0.01463414634,Theaceae:0.02926829268,(Styracaceae:0.00487804878,Symplocaceae:0.00487804878):0.0243902439):0.01951219512,((Primulaceae:0.00487804878,Ebenaceae:0.00487804878):0.00487804878,Sapotaceae:0.009756097561):0.03902439024,Pentaphylacaceae:0.0487804878):0.009756097561,Lecythidaceae:0.05853658537,Polemoniaceae:0.05853658537):0.009756097561,(Tetrameristaceae:0.00487804878,Marcgraviaceae:0.00487804878):0.06341463415)Ericales:0.1512195122)Ericales_to_asterales:0.01463414634,((Hydrangeaceae:0.00487804878,Loasaceae:0.00487804878):0.00487804878,Cornaceae:0.009756097561):0.2243902439)Asterids:0.07804878049,((Simmondsiaceae:0.04390243902,((((Portulacaceae:0.00487804878,Cactaceae:0.00487804878):0.00487804878,Molluginaceae:0.009756097561):0.01463414634,((Nyctaginaceae:0.00487804878,Phytolaccaceae:0.00487804878):0.00487804878,Aizoaceae:0.009756097561):0.01463414634):0.01463414634,((Euphorbiaceae:0.00487804878,Amaranthaceae:0.00487804878)Amaranthaceae:0.00487804878,Caryophyllaceae:0.009756097561):0.02926829268):0.00487804878):0.02926829268,((Tamaricaceae:0.009756097561,(Plumbaginaceae:0.00487804878,Polygonaceae:0.00487804878):0.00487804878):0.01463414634,((Ancistrocladaceae:0.00487804878,Nepenthaceae:0.00487804878):0.00487804878,Droseraceae:0.009756097561):0.01463414634):0.0487804878)Caryophyllales:0.2390243902):0.02926829268):0.3756097561,(((((((((Melastomataceae:0.00487804878,Penaeaceae:0.00487804878):0.009756097561,(Vochysiaceae:0.00487804878,Myrtaceae:0.00487804878):0.009756097561):0.009756097561,(Onagraceae:0.00487804878,Lythraceae:0.00487804878):0.01951219512):0.00487804878,Combretaceae:0.02926829268)Myrtales:0.00487804878,Geraniaceae:0.03414634146):0.1073170732,((((((Sapindaceae:0.01463414634,(Rutaceae:0.009756097561,Simaroubaceae:0.009756097561,Meliaceae:0.009756097561):0.00487804878):0.009756097561,(Anacardiaceae:0.00487804878,Burseraceae:0.00487804878):0.01951219512):0.00487804878,Nitrariaceae:0.02926829268):0.06341463415,(((((Malvaceae:0.01951219512,(Cistaceae:0.00487804878,Dipterocarpaceae:0.00487804878):0.01463414634,Muntingiaceae:0.01951219512,Bixaceae:0.01951219512):0.00487804878,Thymelaeaceae:0.0243902439):0.00487804878,Neuradaceae:0.02926829268)Malvales:0.01951219512,((Brassicaceae:0.00487804878,Resedaceae:0.00487804878):0.009756097561,(Moringaceae:0.00487804878,Caricaceae:0.00487804878):0.009756097561):0.03414634146)Malvales_to_brassicales:0.009756097561,(Dipentodontaceae:0.00487804878,Tapisciaceae:0.00487804878):0.05365853659)Huerteales_to_brassicales:0.03414634146):0.00487804878,Picramniaceae:0.09756097561):0.00487804878,Staphyleaceae:0.1024390244):0.03902439024)Malvids:0.1853658537,((((((Cucurbitaceae:0.009756097561,(Tetramelaceae:0.00487804878,Begoniaceae:0.00487804878):0.00487804878):0.0243902439,(((Myricaceae:0.00487804878,Juglandaceae:0.00487804878):0.009756097561,(Casuarinaceae:0.00487804878,Betulaceae:0.00487804878):0.009756097561):0.00487804878,Fagaceae:0.01951219512):0.01463414634):0.03414634146,(((((Moraceae:0.00487804878,Urticaceae:0.00487804878):0.00487804878,Cannabaceae:0.009756097561):0.00487804878,Ulmaceae:0.01463414634):0.009756097561,(Rhamnaceae:0.00487804878,Elaeagnaceae:0.00487804878):0.01951219512):0.00487804878,Rosaceae:0.02926829268)Rosales:0.03902439024):0.009756097561,(Polygalaceae:0.00487804878,Fabaceae:0.00487804878):0.07317073171):0.09756097561,((((Oxalidaceae:0.00487804878,Connaraceae:0.00487804878):0.009756097561,(Elaeocarpaceae:0.00487804878,Cunoniaceae:0.00487804878):0.009756097561):0.07317073171,(Ochnaceae:0.06829268293,Putranjivaceae:0.06829268293,((Goupiaceae:0.01951219512,(Salicaceae:0.00487804878,Lacistemataceae:0.00487804878):0.01463414634,(Violaceae:0.00487804878,Passifloraceae:0.00487804878):0.01463414634):0.00487804878,Achariaceae:0.0243902439):0.04390243902,(Chrysobalanaceae:0.00487804878,Dichapetalaceae:0.00487804878):0.06341463415,Clusiaceae:0.06829268293,Malpighiaceae:0.06829268293,Humiriaceae:0.06829268293,Caryocaraceae:0.06829268293,Linaceae:0.06829268293)Malpighiales:0.01951219512):0.00487804878,Celastraceae:0.09268292683)Celastrales_to_malpighiales:0.08292682927):0.00487804878,Zygophyllaceae:0.1804878049)Fabids:0.1463414634):0.00487804878,Vitaceae:0.3317073171)Rosids:0.03414634146,((Paeoniaceae:0.01463414634,(Altingiaceae:0.009756097561,(Hamamelidaceae:0.00487804878,Daphniphyllaceae:0.00487804878):0.00487804878):0.00487804878):0.01463414634,((Saxifragaceae:0.00487804878,Grossulariaceae:0.00487804878):0.00487804878,Crassulaceae:0.009756097561):0.01951219512):0.3365853659):0.3512195122,Dilleniaceae:0.7170731707):0.00487804878,Buxaceae:0.7219512195)Trochodendrales_to_asterales:0.01951219512,(Nelumbonaceae:0.009756097561,(Proteaceae:0.00487804878,Platanaceae:0.00487804878):0.00487804878)Proteales:0.7317073171,Sabiaceae:0.7414634146)Sabiales_to_asterales:0.01951219512,((Menispermaceae:0.009756097561,(Berberidaceae:0.00487804878,Ranunculaceae:0.00487804878):0.00487804878):0.00487804878,Papaveraceae:0.01463414634):0.7463414634)Eudicots:0.1658536585,(((((((((Asparagaceae:0.00487804878,Amaryllidaceae:0.00487804878):0.00487804878,Iridaceae:0.009756097561):0.00487804878,Tecophilaeaceae:0.01463414634):0.00487804878,Hypoxidaceae:0.01951219512):0.00487804878,Orchidaceae:0.0243902439)Asparagales:0.05853658537,(Arecaceae:0.05365853659,((Typhaceae:0.00487804878,Bromeliaceae:0.00487804878):0.01463414634,(Juncaceae:0.009756097561,(Poaceae:0.00487804878,Restionaceae:0.00487804878):0.00487804878):0.009756097561)Poales:0.03414634146,((((Costaceae:0.00487804878,Zingiberaceae:0.00487804878):0.00487804878,Marantaceae:0.009756097561):0.00487804878,Heliconiaceae:0.01463414634)Zingiberales:0.009756097561,(Commelinaceae:0.00487804878,Pontederiaceae:0.00487804878)Commelinales:0.01951219512):0.02926829268)Commelinids:0.02926829268):0.0243902439,((Melanthiaceae:0.009756097561,(Colchicaceae:0.00487804878,Alstroemeriaceae:0.00487804878):0.00487804878):0.009756097561,(Liliaceae:0.00487804878,Smilacaceae:0.00487804878):0.01463414634):0.08780487805):0.01463414634,((Pandanaceae:0.00487804878,Cyclanthaceae:0.00487804878):0.00487804878,Dioscoreaceae:0.009756097561):0.112195122):0.03902439024,(((Scheuchzeriaceae:0.01951219512,((Cymodoceaceae:0.009756097561,(Potamogetonaceae:0.00487804878,Zosteraceae:0.00487804878):0.00487804878):0.00487804878,Aponogetonaceae:0.01463414634):0.00487804878):0.009756097561,(Hydrocharitaceae:0.00487804878,Alismataceae:0.00487804878):0.0243902439):0.00487804878,Araceae:0.03414634146)Alismatales:0.1268292683):0.7658536585)Poales_to_asterales:0.06829268293)Magnoliales_to_asterales:0.00487804878,Nymphaeaceae:1)Nymphaeales_to_asterales;"35:T4c1,// should probably have made a function to extract this data for me but hey. lineOrders = [ { O1: 'Atherospermataceae', O2: 'Piperaceae', Order: 'Magnoliids', Dist: 900 }, { O1: 'Asparagaceae', O2: 'Araceae', Order: 'Monocots', Dist: 900 }, { O1: 'Asparagaceae', O2: 'Orchidaceae', Order: 'Asparagales', Dist: 806 }, { O1: 'Misodendraceae', O2: 'Papaveraceae', Order: 'Eudicots', Dist: 900 }, { O1: 'Bignoniaceae', O2: 'Oleaceae', Order: 'Lamiales', Dist: 806 }, { O1: 'Bignoniaceae', O2: 'Oleaceae', Order: 'Lamiales', Dist: 806 }, { O1: 'Clethraceae', O2: 'Marcgraviaceae', Order: 'Ericales', Dist: 806 }, { O1: 'Simmondsiaceae', O2: 'Droseraceae', Order: 'Caryophyllales', Dist: 806 }, { O1: 'Sapindaceae', O2: 'Nitrariaceae', Order: 'Sapindales', Dist: 806 }, { O1: 'Moraceae', O2: 'Rosaceae', Order: 'Rosales', Dist: 806 }, { O1: 'Ochnaceae', O2: 'Linaceae', Order: 'Malphigiales', Dist: 806 }, { O1: 'Paeoniaceae', O2: 'Crassulaceae', Order: 'Saxifragales', Dist: 806 }, { O1: 'Menispermaceae', O2: 'Papaveraceae', Order: 'Ranunculales', Dist: 806 }, { O1: 'Scheuchzeriaceae', O2: 'Araceae', Order: 'Alismatales', Dist: 806 } ]36:[{"id":"ed1d721d7b86b188bd9b02c47ea9ad71f46cae4448a9e491030bec519918464399f5e6640931c37b521459a4356959bdf6486373a4eb0d515a00d8c8eb6c27cf","href":"https://static.observableusercontent.com/files/ed1d721d7b86b188bd9b02c47ea9ad71f46cae4448a9e491030bec519918464399f5e6640931c37b521459a4356959bdf6486373a4eb0d515a00d8c8eb6c27cf","name":"observable2@3.csv","type":"text/csv","lastModified":1595958365008.207,"size":10298}] 31:{"id":"d9b20e58072dd95e","slug":"lets-talk-about-seeds","title":"Let's talk about seeds!","thumbnail":"f5dc0aba24f2382bfe6cd770e7355a404655ef7ce9989e0ec07929d33b9f6938","access_level":"public","create_time":"$D2020-07-26T13:44:20.507Z","update_time":"$D2020-08-23T14:11:56.797Z","view_time":null,"first_public_time":"$D2020-07-29T10:47:45.117Z","has_unpublished_edits":null,"fork":false,"stars":3,"starred":false,"owner":{"type":"team","id":"8736e7a8f8672f04","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":"starter_2024"},"version":643,"publish_version":643,"role":null,"authored":false,"authors":[{"type":"individual","id":"448dbf923c3ebf2f","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":null}],"members":[{"type":"individual","id":"448dbf923c3ebf2f","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":{"id":"86dad9ec2738f6cc","slug":"kew-seed-information-database","title":"Kew Seed Information Database","owner":{"id":"8736e7a8f8672f04","login":"euphrasiologist","name":"Max Brown"}},"type":"notebook","body":{"title":"Let's talk about seeds!","cells":[{"id":0,"value":"md`# Let's talk about seeds!`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":364,"value":"md`In between writing up my PhD thesis, I thought it would be fun to download the entire Kew Seed Information Database (SID), and see what secrets we can learn. Seeds are remarkable really, they are what define the seed plants. These include conifers and all flowering plants, and exclude plants such as ferns and mosses. Seeds are formed from the ovaries and outer coat of the ovaries (integument). They are a critical innovation in severing the dependence of plants on water for reproduction, and have allowed plants to colonise almost every part of the planet.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":384,"value":"md`Seeds can be dispersed in many ways, so that plants can spread and inhabit new areas. Sometimes the seed itself is the dispersal agent. In the well known weed, Fireweed (Chamaenerion angustifolium) for example, the seeds have fine hairs which catch the wind. In other plants, for example Dandelions (Taraxacum), the seed is actually enclosed in the fruit, which is ornamented with a parachute. It is sometimes important to make these distinctions, so we can be sure of a structure's homology. This is so that we can make statements about how these plants evolved.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":388,"value":"md`The graph below shows for each family of plants, what proportion of species are dispersed either by animals, wind, water, or are unassisted in their travels. I realise that family names are not so helpful, so click on them to get taken to Wikipedia to learn more! I've also highlighted some higher order clades on the right.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":25,"value":"$33","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":433,"value":"md`In the above plot, plant families are ordered phylogenetically, with sister lineages in adjacent rows. This is interesting from the perspective that there may be some correlation between relatedness of families, and their dispersal modes. This would have to be tested in a model however!`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":453,"value":"md`There is much more information locked up in the Kew Seed Information Database however. I think three more seed traits may be of general interest: the seed weight (g), the protein content of seeds (% of total seed mass), and the oil content (% of total seed mass). The first (mass), can give an indication as to the life history of a plant species - do they produce many, small seeds? Or few large? Secondly, protein content and oil content may give an indication as to how and where plant species establish - large protein and oil reserves facilitate early development and growth, but are costly for parental plants to produce. Update to follow!`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":467,"value":"md`## Plot 1 - seed dispersal modes`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":242,"value":"md`### Legend`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":245,"value":"colours = d3.scaleOrdinal(seed_colours).domain(legend_)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":220,"value":"legend_ = [\"Animal\", \"Wind\", \"Water\", \"Unassisted\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":206,"value":"md`### Tooltip`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":207,"value":"tooltip = d3\n .select('body')\n .append('div')\n .attr('class', 'd3-tooltip')\n .style('position', 'absolute')\n .style('z-index', '10')\n .style('visibility', 'hidden')\n .style('padding', '10px')\n .style('background', 'rgba(0,0,0,0.6)')\n .style('border-radius', '4px')\n .style('color', '#fff')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"hoverColor = \"#eec42d\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":214,"value":"staticColor = \"#437c90\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"md`### Scales`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":288,"value":"leftAdj = margin.left + 110","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":95,"value":"yScale2 = d3\n .scaleBand()\n .domain(assoc_data2.map(d => d.Family))\n .range([margin.bottom + 50, height - 57])\n .padding(0.2)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":93,"value":"xScale2 = d3\n .scaleLinear()\n // was d.N before\n .domain([0, 1])\n // range here will need fixing\n .range([leftAdj, width - 200])","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":91,"value":"xAxis = g =>\n g\n .attr('transform', `translate(0, ${height - 57})`)\n .call(d3.axisBottom(xScale2))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":89,"value":"yAxis = g =>\n g.attr(\"transform\", `translate(${leftAdj},0)`).call(d3.axisLeft(yScale2))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":85,"value":"color = d3\n .scaleOrdinal()\n .domain(series.map(d => d.key))\n // light blue = animal -> water\n // dark blue = wind\n // light green = water -> animal\n // dark green = unassisted\n .range(seed_colours)\n //.range(d3.schemeGreens[4])\n .unknown(\"#ccc\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":193,"value":"seed_colours = [\"#b2df8a\", \"#1f78b4\", \"#a6cee3\", \"#33a02c\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":275,"value":"md`### Phylogeny groupings`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":633,"value":"md`The phylogenetic data was calculated from the R package brranching (ref), using the XX tree (ref). Branch lengths were then calculated using the R package ape::compute.brlen()`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":146,"value":"phylogenySorted = {\n \n const filterAndSort = lw\n .rectangleLayout(lw.readTree(treestring))\n .horizontal_lines.map(d => d.thisLabel)\n .filter(d => d !== \"\")\n .filter(d => d.indexOf('aceae') !== -1);\n\n filterAndSort.splice(41, 1);\n\n return filterAndSort;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":53,"value":"tree_df = lw.rectangleLayout(lw.readTree(treestring))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":35,"value":"md`### Margins and dimensions`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":"margin = ({top: 0, right: 10, bottom: 10, left: 10})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":46,"value":"width = 1000","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":48,"value":"height = 2500","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":39,"value":"md`### Data`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"// note the NA's from csv have been changed to zero (+)\n// also note on the original file, that the FamN columns are *wrong*!\nassoc_data = d3.csvParse(\n await FileAttachment('observable2@3.csv').text(),\n function(object) {\n return {\n Order: object.Order,\n Family: object.Family,\n Animal: +object.Animal,\n Unassisted: +object.Unassisted,\n Water: +object.Water,\n Wind: +object.Wind,\n N: +object.FamN\n };\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":172,"value":"// there are a couple of mis-placed families?\n// just remove them, I can't be bothered to reorder: 7, 40, 52, 76\nassoc_data2 = {\n const x = assoc_data.slice().sort(function(a, b) {\n return (\n phylogenySorted.indexOf(a.Family) - phylogenySorted.indexOf(b.Family)\n );\n });\n return x.filter(function(value, index) {\n return [7, 40, 52, 76].indexOf(index) == -1;\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":97,"value":"series = d3\n .stack()\n .keys([\"Animal\", \"Wind\", \"Water\", \"Unassisted\"])(assoc_data2)\n .map(d => (d.forEach(v => (v.key = d.key)), d))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":484,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":42,"value":"md`## Global Imports`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"d3 = require(\"d3@v5\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"lw = import(\"https://cdn.jsdelivr.net/gh/euphrasiologist/lwPhylo@1.0.4/dist/lwPhylo.min_mod.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":626,"value":"import {\n parseRefer,\n createBib\n} from \"@euphrasiologist/refer-database-to-javascript-object\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":634,"value":"md`## Bibliography`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W36","stdlib":"1","titling":"auto"}} 32:"$31:body"