init

init

1

.github/workflows/publish.yml

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+on:
+  push:
+    branches:
+      - main
+      - 'releases/**'
+
+jobs:
+  publish:
+    environment: cloudflare_secrets
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      deployments: write
+    name: Publish to Cloudflare Pages
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Get the JSON files
+        shell: bash
+        run: |            
+             wget https://github.com/chasemc/temp3/releases/download/a/socialgene_mibig_refseq_search_json.tar.gz
+             wget https://github.com/chasemc/temp3/releases/download/a/md5
+             md5sum -c md5
+             tar -xf socialgene_mibig_refseq_search_json.tar.gz
+             rm socialgene_mibig_refseq_search_json.tar.gz
+      - name: Publish to Cloudflare Pages
+        uses: cloudflare/pages-action@v1
+        with:
+          apiToken: ${{ secrets.CLOUDFLARE_API_TOKEN }}
+          accountId: ${{ secrets.CLOUDFLARE_ACCOUNT_ID }}
+          projectName: bgcatlas
+          directory: .
+          # Optional: Enable this if you want to have GitHub Deployments triggered
+          # Optional: Switch what branch you are publishing to.
+          # By default this will be the branch which triggered this workflow
+          branch: production
+          # Optional: Change the working directory
+          workingDirectory: .
+          # Optional: Change the Wrangler version, allows you to point to a specific version or a tag such as `beta`
+          wranglerVersion: '3'

LICENSE

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+MIT License
+
+Copyright (c) 2024 Chase Clark (modified clustermap.js code is MIT Licensed from https://github.com/gamcil/clinker/blob/a53bb9e26856e32b573eb1f59197fb0960734934/LICENSE)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1 +1 @@
-# bgcatlas
+# bgc_atlas

clinker.js

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+function serialise(svg) {
+  /* Saves the figure to SVG in its current state.
+   * Clones the provided SVG and sets the width/height of the clone to the
+   * bounding box of the original SVG. Thus, downloaded figures will be sized
+   * correctly.
+   * This function returns a new Blob, which can then be downloaded.
+  */
+  let node = svg.node()
+    .cloneNode(true)
+
+  // Remove all hidden elements
+  d3.select(node)
+    .selectAll(".hidden")
+    .remove()
+
+  // Draw filtered node in hidden <div> to calculate real bounding box
+  let container = svg.node().parentNode
+  let div = d3.select(container)
+    .append("div")
+    .attr("visibility", "hidden")
+  div.append(() => node)
+  let bbox = div.select("g.clusterMapG").node().getBBox()
+  div.remove()
+
+  const xmlns = "http://www.w3.org/2000/xmlns/"
+  const xlinkns = "http://www.w3.org/1999/xlink"
+  const xhtml = "http://www.w3.org/1999/xhtml"
+  const svgns = "http://www.w3.org/2000/svg"
+
+  node.setAttribute("width", bbox.width);
+  node.setAttribute("height", bbox.height);
+  node.setAttributeNS(xmlns, "xmlns", svgns);
+  node.setAttributeNS(xmlns, "xmlns:xlink", xlinkns);
+  node.setAttributeNS(xmlns, "xmlns:xhtml", xhtml);
+
+  // Adjust x/y of <g> to account for axis/title position.
+  // Replaces the transform attribute, so drag/zoom is ignored.
+  d3.select(node)
+    .select("g.clusterMapG")
+    .attr("transform", `translate(${Math.abs(bbox.x)}, ${Math.abs(bbox.y)})`)
+
+  const serializer = new window.XMLSerializer;
+  const string = serializer.serializeToString(node);
+  return new Blob([string], { type: "image/svg+xml" });
+}
+
+function download(blob, filename) {
+  /* Downloads a given blob to filename.
+   * This function appends a new anchor to the document, which points to the
+   * supplied blob. The anchor.click() method is called to trigger the download,
+   * then the anchor is removed.
+  */
+  const link = document.createElement("a");
+  link.href = URL.createObjectURL(blob);
+  link.download = filename;
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+}
+
+function plot(data) {
+  const div = d3.select("#plot")
+  const chart = ClusterMap.ClusterMap()
+    .config({
+      scaleFactor: 30,
+      cluster: {
+        spacing: 50,
+        alignLabels: true,
+      },
+      gene: {
+        label: {
+          show: false,
+        }
+      },
+    })
+
+  let plot = d3.select("#plot")
+    .data([data])
+    .call(chart)
+
+  d3.select("#btn-save-svg")
+    .on("click", () => {
+      const svg = div.select("svg.clusterMap")
+      const blob = serialise(svg)
+      download(blob, "clinker.svg")
+    })
+
+  /**
+   * Saves current chart config and data to JSON.
+   * Can be loaded back into the clinker webapp using loadData().
+   */
+  function saveData() {
+    const obj = { config: chart.config(), data: chart.data() }
+    const blob = new Blob(
+      [JSON.stringify(obj, null, 2)],
+      { type: "application/json" }
+    );
+    download(blob, "clinker.json")
+  }
+
+  /**
+   * Loads JSON generated by saveData() into clinker webapp.
+   * Should contain config and data properties.
+   */
+  function loadData(event) {
+    const files = event.target.files
+    const file = files[0]
+    if (!file) return
+    const reader = new FileReader()
+    reader.readAsText(file)
+    reader.onload = function () {
+      let newData = JSON.parse(reader.result)
+      chart.config(newData.config)
+      plot.selectAll("*").remove()
+      plot.data([newData.data])
+      plot.call(chart)
+    }
+    reader.onerror = function () {
+      console.log("Failed to load data", reader.error)
+    }
+  }
+
+  // Bind save/load
+  d3.select("#btn-save-data")
+    .on("click", () => saveData("clinker.json"))
+  d3.select("#input-load-data")
+    .on("change", loadData)
+
+  function update(opts) {
+    chart.config(opts)
+    plot.call(chart)
+  }
+
+  // Populate label type multi select and bind change handler
+  let labelTypes = new Set()
+  data.clusters.forEach(cluster => {
+    cluster.loci.forEach(locus => {
+      locus.genes.forEach(gene => Object.keys(gene.names).forEach(type => labelTypes.add(type)))
+    })
+  })
+  const changeLabel = event => {
+    const type = event.target.value
+    d3.selectAll("text.geneLabel")
+      .each(d => d.label = d.names[type] ? d.names[type] : d.label)
+    update({})
+  }
+  let select = d3.select("#select-label-type")
+    .on("change", changeLabel)
+  select.selectAll("option")
+    .data(labelTypes)
+    .join("option")
+    .attr("value", d => d)
+    .text(d => d)
+
+  // Figure layout
+  d3.select("#input-scale-factor")
+    .on("change", function () { update({ plot: { scaleFactor: +this.value } }) })
+  d3.select("#input-cluster-spacing")
+    .on("change", function () { update({ cluster: { spacing: +this.value } }) })
+  d3.select("#input-scale-genes")
+    .on("change", function () { update({ plot: { scaleGenes: d3.select(this).property("checked") } }) })
+
+  // Cluster
+  d3.select("#input-cluster-align-labels")
+    .on("change", function () { update({ cluster: { alignLabels: d3.select(this).property("checked") } }) })
+  d3.select("#input-cluster-hide-coords")
+    .on("change", function () { update({ cluster: { hideLocusCoordinates: d3.select(this).property("checked") } }) })
+  d3.select("#input-cluster-name-size")
+    .on("change", function () { update({ cluster: { nameFontSize: +this.value } }) })
+  d3.select("#input-locus-name-size")
+    .on("change", function () { update({ cluster: { lociFontSize: +this.value } }) })
+  d3.select("#input-locus-spacing")
+    .on("change", function () { update({ locus: { spacing: +this.value } }) })
+
+  // Gene polygon shape
+  d3.select("#input-body-height")
+    .on("change", function () { update({ gene: { shape: { bodyHeight: +this.value } } }) })
+  d3.select("#input-tip-height")
+    .on("change", function () { update({ gene: { shape: { tipHeight: +this.value } } }) })
+  d3.select("#input-tip-length")
+    .on("change", function () { update({ gene: { shape: { tipLength: +this.value } } }) })
+  d3.select("#input-gene-stroke-colour")
+    .on("change", function () { update({ gene: { shape: { stroke: this.value } } }) })
+  d3.select("#input-gene-stroke-width")
+    .on("change", function () { update({ gene: { shape: { strokeWidth: +this.value } } }) })
+
+  // Gene labels
+  d3.select("#input-gene-labels")
+    .on("change", function () { update({ gene: { label: { show: d3.select(this).property("checked") } } }) })
+  d3.select("#input-label-rotation")
+    .on("change", function () { update({ gene: { label: { rotation: +this.value } } }) })
+  d3.select("#input-label-start")
+    .on("change", function () { update({ gene: { label: { start: +this.value } } }) })
+  d3.select("#select-label-anchor")
+    .on("change", function () { update({ gene: { label: { anchor: this.value } } }) })
+  d3.select("#input-label-size")
+    .on("change", function () { update({ gene: { label: { fontSize: +this.value } } }) })
+  d3.select("#input-label-spacing")
+    .on("change", function () { update({ gene: { label: { spacing: +this.value } } }) })
+  d3.select("#select-label-position")
+    .on("change", function () { update({ gene: { label: { position: this.value } } }) })
+
+  // Scale bar
+  d3.select("#input-scalebar-fontsize")
+    .on("change", function () { update({ scaleBar: { fontSize: +this.value } }) })
+  d3.select("#input-scalebar-height")
+    .on("change", function () { update({ scaleBar: { height: +this.value } }) })
+  d3.select("#input-scalebar-basepair")
+    .on("change", function () { update({ scaleBar: { basePair: +this.value } }) })
+  d3.select("#input-scalebar-margin-top")
+    .on("change", function () { update({ scaleBar: { marginTop: +this.value } }) })
+
+  // Colour bar
+  d3.select("#input-colourbar-fontsize")
+    .on("change", function () { update({ colourBar: { fontSize: +this.value } }) })
+  d3.select("#input-colourbar-height")
+    .on("change", function () { update({ colourBar: { height: +this.value } }) })
+  d3.select("#input-colourbar-margin-top")
+    .on("change", function () { update({ colourBar: { marginTop: +this.value } }) })
+
+  // Legend
+  d3.select("#input-legend-fontsize")
+    .on("change", function () { update({ legend: { fontSize: +this.value } }) })
+  d3.select("#input-legend-entryheight")
+    .on("change", function () { update({ legend: { entryHeight: +this.value } }) })
+  d3.select("#input-legend-margin-left")
+    .on("change", function () { update({ legend: { marginLeft: +this.value } }) })
+
+  // Links
+  d3.select("#input-link-show")
+    .on("change", function () { update({ link: { show: d3.select(this).property("checked") } }) })
+  d3.select("#input-link-best-only")
+    .on("change", function () { update({ link: { bestOnly: d3.select(this).property("checked") } }) })
+  d3.select("#input-link-as-line")
+    .on("change", function () { update({ link: { asLine: d3.select(this).property("checked") } }) })
+  d3.select("#input-link-straight")
+    .on("change", function () { update({ link: { straight: d3.select(this).property("checked") } }) })
+  d3.select("#input-link-group-colour")
+    .on("change", function () { update({ link: { groupColour: d3.select(this).property("checked") } }) })
+  d3.select("#input-link-stroke-width")
+    .on("change", function () { update({ link: { strokeWidth: +this.value } }) })
+  d3.select("#input-link-threshold")
+    .on("change", function () { update({ link: { threshold: +this.value } }) })
+  d3.select("#input-link-fontsize")
+    .on("change", function () { update({ link: { label: { fontSize: +this.value } } }) })
+  d3.select("#input-link-label-pos")
+    .on("change", function () { update({ link: { label: { position: +this.value } } }) })
+  d3.select("#input-link-label-show")
+    .on("change", function () { update({ link: { label: { show: d3.select(this).property("checked") } } }) })
+  d3.select("#input-link-labelbg-show")
+    .on("change", function () { update({ link: { label: { background: d3.select(this).property("checked") } } }) })
+}
+
+
+
+function switchit() {
+
+  z = d3.select("#inputfile").property("value")
+  d3.json("./jsons/" + z).then(plot)
+
+}
+
+d3.select("#inputfile")
+  .on("click", switchit)
+

filenames.py

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+from pathlib import Path
+
+a=[i.name for i in Path("jsons").glob("*.json")]
+a.sort()
+
+with open('filenames.js', 'w') as f:
+    _=f.write('var filenames=[')
+    for i in a:
+        _=f.write(f"'{i}',")
+    _=f.write(']')