igvteam / spacewalk

SpaceWalk is an application for displaying and interacting with super-resolution chromatin tracing data in 3D. SpaceWalk includes igv.js and juicebox.js instances for rapid and intuitive visual comparison and interaction between 3D data and 1D genomic data.

SpaceWalk

SpaceWalk is an application for displaying and interacting with super-resolution chromatin tracing data in 3D. SpaceWalk includes igv.js and juicebox.js instances for rapid and intuitive visual comparison and interaction between 3D data and 1D genomic data.

Requirements

• Node >= v10.13.0
• NPM >= v6.9.0

Supported Browsers

SpaceWalk require a modern web browser with support for Javascript ECMAScript 2015.

Installation

• Clone this repository.

git clone [email protected]:igvteam/spacewalk.git

• Install

npm install

Build the app

npm run build

Run the app

npm run start

• Open a browser and enter the follow url to run the app

localhost:8080/index.html

Getting Started

After launching the app. You will see a blank 3D space. Use one of the dropdown menus in the navbar to load either a point cloud or a segment list dataset.

SpaceWalk supports loading files of various types:

• Point Cloud - Each file contains a list of point clusters. Each cluster corresponds to a genomic range.
• Segment List - Each file contains a list of traces. Each trace contains a list of segments. Each segment is a genomic range.
• IGV Tracks - Track files consumed by the IGV panel. Refer to the track section of the igv.js wiki
• Juicebox Contact Maps - Refer to the Aiden Lab website for details.

Three rendering styles are supported. All rely on the use of color to map genomic location to 3D.

Noodle

A tube is rendered that interpolates between a list of chromatin centroids. Color along the length of the tube corresponds to genomic location. The genomic navigator - described above - is used to identify and highlight genomic regions.

Ball & Stick

A list of chromatin centroids are rendered as balls. Each ball is colored according to it's genomic location. Sticks (cylinders) connect balls in the order they appear in the genomic range. The genomic navigator - described above - is used to identify each ball and highlight genomic regions. Alternatively, mouse over a ball to see it's genomic location in the genomic navigator's color ramp.

Point Cloud

Centroid point clouds are rendered as 3D points. Points associated with a particular genomic range are colored based on the genomic navigator color ramp. Mouse over the genomic navigator to isolate clusters of points for that genomic range.

Click the gear icon at upper left to show/hide a panel. Panels can be repositioned by dragging.

These task-specific interaction panels support analysis of the 3D data.

The panels include:

• Trace Select. A widget to navigate between the set of traces that comprise an ensemble.

• Genomic Navigator. The genomic range for a given trace is represented by a color ramp. Mouse over this color ramp to highlight the corresponding genomic location in the 3D trace structure.

  • Noodle highlighting. A sub-section of the noodle corresponding to the genomic region is isolated

  

  • Ball & Stick highlighting. The ball corresponding to the genomic region is highlighted.

  

  • Point Cloud highlighting. The point cloud cluster corresponding to the genomic region remains colored all other clusters are deemphasized. The size of the highlight in the genomic navigator corresponds to the relative size of the genomic region.

  

• IGV. A fully functional IGV.js application. The app has been extended to enable interaction with the 3D model. On the left, mousing across a track behaves similar to the genomic navigator. On the right we have selected a track. The features are automatically mapped to the 3D model. Now mousing across the mapped track shows a sliding red ring on the 3D model indicating genomic location.

• Juicebox. A fully functional Juicebox.js application. The app has been extended to enable interaction with the 3D model. Mouse over the contact map to highlight the corresponding genomic locations on the 3D model.

• Distance Map. An ensemble level and trace level distance map created on the fly when an ensemble file is loaded.

• Contact Frequency Map. An ensemble level and trace level contact frequency map created on the fly when an ensemble file is loaded.

spacewalk's Issues

Walking along the IGV tracks doesn't work in the shared links

Hello @turner and @jrobinso,

I've noticed that if I load a track bed file from a URL, I can move my mouse along that track and the corresponding area will show on the spacewalk trace. But, when I share this view with my collaborators, they can't do so with the link I shared with them
Here is an example
Guy

Map track feature colors to pointcloud

Map track feature colors to pointcloud

Support toggling the ground plane on and off.

Support toggling the ground plane on and off.

Point cloud format

A question came up as to the format for point cloud; can this be explained in the README? Or is there other documentation or tutorials? If so can it be linked?

Trace number

Hi Team,

A tiny issue - My *.sw file has six traces, starting from trace 0. At the top, spacewalk has this box that tells the trace number out of how many traces in total. For this file, it shows '0 out of 6'. But it should start from one, that is, the first trace should be '1 out of 6'. Currently, the last trace will be '5 out of 6'.

Thank you,
Guy

Gray localizations hiding highlighted localizations

Hi @turner,

I have a point cloud sw file and I'm looking at the localizations in my traces. When I'm trying to look at one segment of the trace the other localizations are shown in gray. However, these gray localizations are 'hiding' my highlighted localizations. I think, you should have the option to not show the not-selected localizations or have them transparent.

Thank you,
Guy

PointClouds: Implement live distance and contact maps

Implement live distance and contact maps for pointclouds.

Ball & Stick, ball radius cannot be changed

When rendering Ball & Stick, ball radius cannot be changed.

GSDB (JSON) Menu Item

GSDB Dataset

Link:
http://calla.rnet.missouri.edu/genome3d/GSDB/GSDB_JSON_URL_LIST.txt

Source:
Jianlin Cheng
University of Missouri - Columbia

Select multiple genomic segments.

Use the genomic navigator to select multiple genomic extents. Highlight the corresponding regions in the 3D structure.

Incorrect behavior when loading a local bed file into IGV

Hi, I ran into an issue when loading a local bed file onto IGV where the color-coded annotations specified in the bed file aren't displaying correctly. It seems that one chromosome is highlighted in gray and the rest of the chromatin is shaded blue. I'm using this shared session:

https://aidenlab.org/spacewalk/?spacewalkSessionURL=blob:dVTbbpwwEP0XPwNrgzGwUtWHpI2aXhI1VV6qKjLGsG69NjFms5so_96xN2kjkYBk4XNmztxsHtDsNFqjjffjtF6t7u7uss7ZsbX7TNjtalo1rRi66Q.bqbpVGJBRS2lu.lnrTJlO7mWXCdO17zv9DqMEaSvmCa0fkNg4EIaVADpIY7dKXHnuPFqTf8AH06F1ThscHvKYIO.4kJ_lAVyDmhp2l9xIDY5eAmaskQA7CZHdlT_oAB536RS2qVNtaw3YjMHvWk2qVVr5Q0jp09l1VAsFq66Twex8VkJCuQviVE2eGyG_8nHBnVjjufAfnbydpRGHpQ2UMkCF1rzM4L_AkTux2rqQmDv2JK4trMHb2dl0lxpk35CIBmMweKmDswY3NS6anJSsZnlFo_BrcPsaDKEF30rHv6hh45UZvqshSG.l5x33PHzvpJsUNHlNsxJGdhjDFC7a31L446zB3YeMnsDiNPP2_OriW2iLPdqBzDwrmD5iLe5xm5OUEYZTWvYs5ZiItCh4RbHsctKHI_QU5hJijyCgdvIk5gmUgQ.grGuV5_pGPOOaH8A6dnXLvVN7tP5JEvz0kiRlGW6g9rquaooLRnOZkiqSrzPROSsKgmtGyroqc0oJTUhWkaLCDBNWUlxSkuR5mRUlrirWMFZQ6G5CfiWotzvIhmQAkNjtpoEYMIp7a7cxTyN5HCItSU0aTHFdM0pABJwDE_DsBVEF0XjjCE4Qj62JQr3S2zM.D9CYojxuL_p.ksBimMJoJ.XjDB_QPgRcFIXgtC0LQ_dwXxfFhYvL3SDjWP0ben4pmFcF4CCZ4qwEU1rQCo5hxaqyfgwncXnPnq_lj42T08bq8P8o2eNf&sessionURL=blob:pZNRa9swFIX_ShB92MCVLSddZsMYbA_Zw9ggpXRjjHLtyLaYJbmSbDcN.e.7kpJthb1sNeQESzqfrnWPDmTixgqtSElyyjLKSEJsp.drkEPPP4HklpQN9JYnxPCGG65qTsoDETu0dC0r0KBwGb59GCWoxYvN9n23XKd.7iVONmAd3Gw_.uXODbZMU9FOtOWKD.AcN4pq06b4rnGz1PL7YA1CgxkhQu34w7MgqAJB9d7pCtTuP1je.g6t1D04JEEvwD7F2CUFCY9awWxprWXgIoueWb9qugtu6qDyNXVGS21xxWez4waBOMKSBWoedBl0FfQq6Kug66CvgxZBWRb_optFO4t.FgEsElhEsMhgEcIiJY.U_FRDpHwJ.pUcE9LresRYEFayy3xVJFmW4c9Hxxmof.DUtwNx.8GHAo9vDJlJiI5fd1lk2ZoVRX61Wq.yomDH5HCO0JY3aFhssBfWZ0cbCQ7HMXq.Pz4J59zdtadFo.n_uQeqrgTudc3vqdXG8dBU2j7.PWrPY1JX.eRNwopK9MLtb3ELPeNBMLxr4zDgYnvb6Z5vAu6P.yb1BFX_e.R0giwLj6.10U9LneeZ.kKo6iVVoqOtnnyUefoWky3fXFz4LsXWgFLagfO3__j9.BM-

I'm using this bed file for testing:
http://genome.compbio.cs.cmu.edu:8008/~kxiong/data/sniper/annotations/hg19/GM12878_track_hg19.bed

If I'm not using this correctly, could you provide some advice for properly loading the bed file?
Any help is greatly appreciated. Thanks!

• Kyle

Bed/bedgraph file not recognized

Hello team,

I tried uploading a bed file (Features exported from IGV) to go along with my cloud point data (in a separate file) and the bed file wasn't recognized. I converted the bed to bedgraph but it didn't help.

Please contact me if you need the spacewalk or bed files.

Thank you,
Guy