epiviz / epiviz

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Epiviz

Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

For more information, visit - http://epiviz.github.io/

Using any PHP supported webserver

Copy the Epiviz directory to the webserver configured directory. Navigate to /epiviz/index.php on your browser.

Using PHP

PHP (http://php.net/) lets your run local webservers. Navigate to localhost:8181 on your browser. To run epiviz use:

php.exe -S localhost:8181 -t <location of the epiviz directory>

Using Docker

This repository includes a Dockerfile to run a webserver that serves the epiviz web application. It includes a site-settings.js file that sets up data backends pointing to the University of Maryland. Update that file to use a different backend. It is registered in the DockerHub registry: (https://hub.docker.com/r/epiviz/epiviz/)[https://hub.docker.com/r/epiviz/epiviz/]. To run it use:

docker pull epiviz/epiviz
docker run --name epiviz-app -d -p 80:80 epiviz/epiviz

To Compile closure

java -jar compiler.jar --js_output_file=epiviz-compiled-jar.js --js 'src/epiviz/**' --js '!src/epiviz/default-settings.js' --js '!src/epiviz/epivizr-settings.js' --js '!src/epiviz/standalone-settings.js' --entry_point=goog:epiviz.main

epiviz's Issues

Add transparency to line plots to clean up plots with multiple series

add functionality for changing order of charts

Currently, charts are added one after another, and their order cannot be interchanged except by removing and adding them again in a different order. Add functionality to allow this.

investigate how we could integrate EpiViz with Wolfram language

find a solution to process sparse data

Currently, EpiViz only handles continuous sequences of data (consecutive global indices). It would be extremely useful, however, if some filtering were done on the data provider side, and only filtered data were sent up to the UI.

Use hierarchical clustering on the rows of heatmap plots

workspace save/open/delete dialog

Add a dialog for workspace management, instead of the text box and buttons.

cache measurements for the add measurements dialog

Currently, every time the dialog is shown, the table with the measurements is re-generated, which makes it take a while until it loads.

google oauth login

EpiViz currently supports log in with either Facebook or Twitter. Google is a better variant and more commonly used in the research community.

simplify the process of plugging Gist/Github scripts into EpiViz

Currently, when a user wants to plug a Gist/Github script into EpiViz, he has to retrieve the raw version of the script. However, Github renders those as:

X-Content-Type-Options: nosniff
Content-Type: text/plain

To get around to that and use them as Content-Type: text/javascript, we ask the users to use the rawgit service.

Create a feature to handle Gist/Github links internally.

add access lists and permissions to workspaces

Currently, anyone with a link to a workspace can view that workspace. It would be great to have a way of sharing some workspaces with only a set of users, and also allow multiple users to have write permissions for some workspaces.

Entering inverse coordinates in the search box enable to use navigation tools, but the views don't change.

For example if you enter "1,000-500" in the search box, and then use "slide right", the search box generates "801 - -194". Inverse coordinates should not be enable, and maybe an error message could be displayed.

I tested on Chrome 38, and Safari 7 on Mac OS X Mavericks 10.9.5. All the same result.

multiple object selection in visualizations

Currently, objects in the visualizations can be selected only one at a time. Allow for Ctrl+Click, Shift+Click, and selection by mouse drag-drop.

when UI is on one server, and data on another, because index.php is on the UI side, the session user is not preserved!

When UI is on one server, and data on another, because index.php is on the UI side, the session user is not preserved!

change code occurrences where we use MeasurementSet/Array.<Measurement> to Iterable.<Measurement>

Where applicable, change code occurrences where we use epiviz.measurements.MeasurementSet or Array.<epiviz.measurements.Measurement> to epiviz.utils.Iterable.<epiviz.measurements.Measurement>.

add exception handling code at data provider level

Currently, EpiViz assumes all data provider responses are 100% correct, not allowing for errors.

make events asynchronous

Currently, EpiViz events are synchronous by default. Add functionality to optionally make them asynchronous (via setTimeout()).

load and navigate using genome events

Add events to data that allow users to jump from one event location to another.

minify javascript code

The code is documented such that it follows the guidelines of the Google Closure compiler. Use this compiler to minify and optimize it further.

add functional unit tests for code

EpiViz implements a simple unit testing framework, used for running basic performance tests. This framework can be used to test various EpiViz features as well.

If the range of the coordinates is less than 3 base pairs, epiviz doesn't enable navigation along the genome.

The options "slide left", "slide right", "zoom in" and "zoom out" don't work.
I tested on Chrome 38, and Safari 7 on Mac OS X Mavericks 10.9.5. All the same result.

epivizr console

Create a chart type that contains a text box where users can type R commands that are send through the WebSocket protocol to the R connection. (Same applies with Python connections, etc.)

log user actions for quality assurance

Currently, the data server only stores minimal information about users, and nothing about their actions. It would be useful to track user actions in order to discover usage patterns and catch bugs.

allow users to add annotation to individual data objects

add code to handle web request errors

Currently, the UI code assumes that all web requests are fulfilled correctly, not allowing for request timeouts or GET/POST server errors. Add exception handling functionality for this issue.

epiviz as genome viewer

Is it possible to load the bam file? I am trying to create publication quality figure for a manuscript. I have assembly data and want to show a specific locus with the assembled transcript and the reads in that locus. The image from IGV and UCSC genome browser isn't looks good. I just came across this tool and liked the presentation.

splash screen

While EpiViz loads, it would improve user experience if there were a splash screen

Use getBBox() to compute where legend text should be drawn

In epiviz.ui.charts.Track.prototype._drawTitle, use the following code to detect where to draw each of the chart entries:

/**
 * @private
 */
epiviz.ui.charts.Track.prototype._drawTitle = function() {
  var textLength = 0;
  var title = '';

  var measurements = this.measurements().toArray();

  var self = this;
  this._svg.selectAll('.chart-title').remove();
  var titleEntries = this._svg
    .selectAll('.chart-title')
    .data(measurements)
    .enter()
    .append('text')
    .attr('class', 'chart-title')
    .attr('font-weight', 'bold')
    .attr('fill', function(m, i) { return self.colors().get(i); })
    .attr('y', self.margins().top() - 5)
    .text(function(m, i) { return m.name(); });

  var textLength = 0;
  var titleEntriesStartPosition = [];

  $('#' + this.id() + ' .chart-title')
    .each(function(i) {
      titleEntriesStartPosition.push(textLength);
      textLength += this.getBBox().width + 3;
    });

  titleEntries.attr('x', function(m, i) {
    return self.margins().left() + titleEntriesStartPosition[i];
  });
};

replace current computed measurements dialog with a wizard

Use epiviz.ui.controls.Wizard for the Computed Measurements dialog

clear workspace / new empty workspace

Add functionality for clearing the current workspace or creating a new empty one.

Trigger chart remove when a measurement used in chart is removed

create information pane

Implement information pane, that displays selected data from all charts.