Interactively Query, Transform and Visualize Genomic data from flat files using Epiviz

1.Instructions.md

Interactively Query and Visualize Genomic data from flat files using Epiviz

• Define data sets (available locally or publicly) as a json configuration file - data.json

• Run the Epiviz File Server

  Install package through PyPI

  $ pip install epivizfileserver

  or using conda conda

  $ conda create -n epiviz python=3.7

  $ pip install epivizfileserver

  The epiviz python script allows users to load data from the configuration file and define transformations

  $ python epiviz.py

  more information on the file server is available at - Documentation or GitHub

• Epiviz Components allows users to interactively visualize and embed tracks on most web based platforms that support HTML.

  • First create a directory

  $ mkdir epiviz && cd

  • Use bower to install dependencies

  $ bower init

  $ bower install epiviz/epiviz-chart

  • Create an index.html file to add Epiviz Components that query data from the Epiviz file server, more information on components is available at GitHub

• Use Caddy or any web server to serve the Components

  $ cd epiviz && caddy

2.data.json

[
    {
        "url": "http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/E070-H3K9me3.pval.signal.bigwig",
        "file_type": "bigwig",
        "datatype": "feature",
        "name": "Brain Germinal Matrix - H3k9me3 signal",
        "id": "E070-H3K9me3",
        "annotation": {
          "group": "H3K9me3",
          "tissue": "Brain Germinal Matrix"
        },
        "metadata": []
      },
      {
        "url": "http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/E071-H3K9me3.pval.signal.bigwig",
        "file_type": "bigwig",
        "datatype": "feature",
        "name": "Brain Hippocampus Middle - H3k9me3 signal",
        "id": "E071-H3K9me3",
        "annotation": {
          "group": "H3K9me3",
          "tissue": "Brain Hippocampus Middle"
        },
        "metadata": []
      },
      {
        "url": "http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/E070-H3K27me3.pval.signal.bigwig",
        "file_type": "bigwig",
        "datatype": "feature",
        "name": "Brain Germinal Matrix - H3K27me3 signal",
        "id": "E070-H3K27me3",
        "annotation": {
          "group": "H3K27me3",
          "tissue": "Brain Germinal Matrix"
        },
        "metadata": []
      },
      {
        "url": "http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/E071-H3K27me3.pval.signal.bigwig",
        "file_type": "bigwig",
        "datatype": "feature",
        "name": "Brain Hippocampus Middle - H3K27me3 signal",
        "id": "E071-H3K27me3",
        "annotation": {
          "group": "H3K27me3",
          "tissue": "Brain Hippocampus Middle"
        },
        "metadata": []
      }
]

3.epiviz.py

from epivizfileserver import setup_app, create_fileHandler, MeasurementManager
import os
import numpy
import pickle

if __name__ == "__main__":
    # create measurements manager
    mMgr = MeasurementManager()

    # create file handler
    mHandler = create_fileHandler()
    
    # add genome annotation
    genome = mMgr.add_genome("hg19")

    # define datasets/files available to the File server instance
    fmeasurements = mMgr.import_files(os.getcwd() + "/data.json", mHandler)

    # define computations over files
    ms = [m for m in fmeasurements if m.annotation["group"] == "H3K9me3"]
    cms = mMgr.add_computed_measurement("computed", "diff_brain_H3K9me3_signal", "Diff Brain H3K9me3 Signal", measurements=ms, 
                    computeFunc=numpy.mean, annotation={"group": "computed_atac"})

    ms = [m for m in fmeasurements if m.annotation["group"] == "H3K27me3"]
    cms = mMgr.add_computed_measurement("computed", "diff_brain_H3K27me3_signal", "Diff Brain H3K27me3 Signal", measurements=ms, 
                    computeFunc=numpy.mean, annotation={"group": "computed_atac"})

    # run the app
    app = setup_app(mMgr)
    app.run(host="0.0.0.0", port=8000)

4.bower.json

{
    "name": "epiviz-app",
    "authors": ["Jayaram Kancherla <jayaram.kancherla@gmail.com>"],
    "license": "MIT",
    "dependencies": {
      "polymer": "Polymer/polymer#^2.0.0",
      "webcomponentsjs": "webcomponents/webcomponentsjs#^1.0.0",
      "epiviz-charts": "epiviz/epiviz-chart"
    },
    "resolutions": {
      "polymer": "^2.0.0",
      "lodash": "^4.17.10"
    },
    "private": true
  }

5.index.html

<!doctype html>
<html lang="en">

<head>
    <title>epiviz Charts Demo</title>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, minimum-scale=1.0, initial-scale=1, user-scalable=yes">
    <script src="bower_components/jquery/dist/jquery.js"></script>
    <script src="bower_components/jquery-ui/jquery-ui.js"></script>
    <script src="bower_components/webcomponentsjs/webcomponents-lite.js"></script>
    <script src="bower_components/epiviz-charts/src/renderingQueues/renderingQueue.js"></script>

    <link rel="import" href="bower_components/epiviz-data-source/epiviz-data-source.html">
    <link rel="import" href="bower_components/epiviz-charts/epiviz-charts.html">
</head>

<body>

    <!-- Let the components know where the epiviz file server is running -->
    <epiviz-data-source provider-type="epiviz.data.WebServerDataProvider" provider-id="fileapi"
        provider-url="http://localhost:8000">
    </epiviz-data-source>

    <!-- initiliaze navigation to a gene location or genomic region -->
    <epiviz-navigation
        chr="chr18"
        start=32254012
        end=42505003
    >
    <!-- add a genes track for hg19 -->
        <epiviz-genes-track slot="charts" dim-s='["hg19"]'></epiviz-genes-track>

        <!-- add signal tracks for brain tissues -->
        <epiviz-line-track slot="charts" dim-s='["E070-H3K9me3", "E071-H3K9me3"]'></epiviz-line-track>
        <epiviz-line-track slot="charts" dim-s='["E070-H3K27me3", "E071-H3K27me3"]'></epiviz-line-track>

        <!-- add signal tracks computed diff in histone modification across tissues  -->
        <epiviz-line-track slot="charts" dim-s='["diff_brain_H3K9me3_signal", "diff_brain_H3K27me3_signal"]'></epiviz-line-track>
    </epiviz-navigation>

    <noscript>
        Please enable JavaScript to view this website.
    </noscript>
</body>

</html>