HPA-UMAP-Nucleolus.imjoy.html

<docs>
[TODO: write documentation for this plugin.]
</docs>

<config lang="json">
{
  "name": "HPA-UMAP-Nucleolus",
  "type": "web-worker",
  "tags": [],
  "ui": "",
  "version": "0.1.2",
  "cover": "",
  "description": "Displaying the HPA UMAP with the ImJoy Chart Editor",
  "icon": "extension",
  "inputs": null,
  "outputs": null,
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": ["https://cdn.jsdelivr.net/npm/[email protected]/papaparse.min.js"],
  "dependencies": []
}
</config>
<script lang="javascript">
function loadCSV(url) {
  return new Promise((resolve, reject) => {
    Papa.parse(url, {
      download: typeof url === "string" && url.startsWith('http'),
      header: true,
      dynamicTyping: true,
      skipEmptyLines: true,
      error: (err, file, inputElem, reason) => {
        alert("Falied to load the table: " + reason.toString());
        reject(reason);
      },
      complete: (results) => {
        resolve(transpose(results.data));
      },
    });
  });
}

function transpose(data) {
  let result = {};
  for (let row of data) {
    for (let [key, value] of Object.entries(row)) {
      result[key] = result[key] || [];
      result[key].push(value);
    }
  }
  return result;
}
    
async function convertUniprot2Ensembl(query){
 const url = 'https://www.uniprot.org/uploadlists/'

 const params = {
    'from': 'ID',
    'to': 'ENSEMBL_ID',
    'format': 'tab',
    'query': query.join('\t')
 }
 const formData = [];
 for(let k in params){
    formData.push(`${k}=${encodeURIComponent(params[k])}`)
 }
 const response = await fetch(url, {method: "POST", headers: {'Content-Type': 'application/x-www-form-urlencoded'}, body: formData.join('&') })
 const data = await response.text()
 const ret = []
 for(let line of data.split('\n').slice(1)){
     if(line.length>0)
     ret.push(line.split('\t'))
 }
 const mapping = Object.fromEntries(ret);
 return query.map(u=> mapping[u])
}
    
async function insertQueryData(data, queryFile){
    await api.showMessage('Parsing file '+ queryFile.name)
    const queryFull = await loadCSV(queryFile);
    if(queryFull.Uniprot) queryFull.Ensembl = await convertUniprot2Ensembl(queryFull.Uniprot)
    
    if(!queryFull.Ensembl){
        const matchingColumn = await api.prompt(`Please select a maching column name (options: ${JSON.stringify(Object.keys(queryFull))})`, "")
        if(matchingColumn){
            if(!queryFull[matchingColumn]){
                await api.alert(`Column ${matchingColumn} not found`)
                return
            }
            queryFull.Ensembl = queryFull[matchingColumn]
        }
        else{
            return
        }
    }
    await api.showMessage('Merging columns...')
    for(let col in queryFull){
        data[col] = []
    }
    for(let i=0;i<data['gene_ensembl_id'].length;i++){
        const id = data['gene_ensembl_id'][i]
        if(id){  
            const index = queryFull.Ensembl.indexOf(id)
            if(index>=0){
                for(let col in queryFull){
                    data[col][i] = queryFull[col][index]
                }
            }
        }
    }
    await api.showMessage('New columns are ready!')
}

class ImJoyPlugin {
  async setup() {
    await api.showMessage("Loading data...")
    this.data = await loadCSV("https://dl.dropbox.com/s/k9ekd4ff3fyjbfk/umap_results_fit_all_transform_all_sorted_20190422.csv");
    await api.log('initialized')
  }
  async loadDataHandler(file){
     await insertQueryData(this.data, file)
      debugger
     await this.editor.loadDataSource(this.data)
  }
  async run(ctx) {
    const editor = await api.createWindow({src: 'https://chart.imjoy.io',
                                           name: 'HPA UMAP Studio',
                                           fullscreen: true,
                                          config:{_rintf: true, loadDataHandler: this.loadDataHandler.bind(this)}}) // 'https://imjoy-team.github.io/imjoy-chart-editor/', name: 'HPA UMAP Studio', fullscreen: true})
    this.editor = editor;
    await editor.loadDataSource(this.data)
    await api.showMessage("Data loaded.")
    await editor.addWidget({
        type:'html',
        name: 'Details',
        body: ''
    })
    await editor.addWidget({
        type:'html',
        name: 'Overview',
        body: ''
    })

    await editor.addListener({_rintf: true, event:'plotly_hover', callback: async (points)=>{
        const metadata = points[0].customdata;
        const id = metadata.id
        const image_base_url = id.includes('_')?'https://images.proteinatlas.org/' + id.split('_')[0] + '/' + id.split('_')[1] +'_' + id.split('_')[2] + '_'+ id.split('_')[3] : null
        const thumbnail_url = image_base_url && image_base_url + '_blue_red_green_yellow_thumb.jpg'
        await editor.updateWidget({
            type:'html',
            name: 'Overview',
            body: `<p>Gene: ${metadata.gene}</p> <p>Location: ${metadata.location}</p> <br> <img style="width:100px" src="${thumbnail_url}"></img>`
        })
    }})

    await editor.addListener({_rintf: true, event:'plotly_click', callback: async (points)=>{
        const metadata = points[0].customdata;
        const id = metadata.id
        const image_base_url = id.includes('_')?'https://images.proteinatlas.org/' + id.split('_')[0] + '/' + id.split('_')[1] +'_' + id.split('_')[2] + '_'+ id.split('_')[3] : ''
        const full_url = image_base_url + '_blue_red_green.jpg'
        await editor.updateWidget({
            type:'html',
            name: 'Details',
            body: `<p>ID: ${metadata.id}</p> <p>Gene: ${metadata.gene}</p> <p>Location: ${metadata.location}</p> <br> <a target="_blank" href="${full_url}"><img style="width:100%" src="${full_url}"></img></a>
<br><a target="_blank" href="https://www.proteinatlas.org/${metadata.gene_ensembl_id}-${metadata.gene}/cell/">Open HPA Page</a>`
        })
    }})
  }
}

api.export(new ImJoyPlugin())
</script>