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Revised

wigExplorer, a BioJS component to visualise wig data

[version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]
PUBLISHED 09 Aug 2016
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Abstract

Summary: wigExplorer is a BioJS component whose main purpose is to provide a platform for visualisation of wig-formatted data. Wig files are extensively used by genome browsers such as the UCSC Genome Browser. wigExplorer follows the BioJS standard specification, requiring a simple configuration and installation. wigExplorer provides an easy way to navigate the visible region of the canvas and allows interaction with other components via predefined events.
Availability: http://biojs.io/d/biojs-vis-wigexplorer;http://dx.doi.org/10.5281/zenodo.8516

Keywords

BioJS, data visualisation, genome browsers

Revised Amendments from Version 2

In the new version we have updated the availability sources, and some reference details based on the referees' comments.

See the authors' detailed response to the review by Stefan Thomas Lang
See the authors' detailed response to the review by Robert Buels
See the authors' detailed response to the review by Phil Lord

Introduction

Numerous web applications exist for visualisation of biological data. Data can be prepared for visualisation using a variety of formats, one of which is the widely used wiggle (wig) file. A wiggle file contains text that defines either a feature or a data track. The wiggle format was developed by the UCSC genome browser1 and then quickly adopted by other initiatives2,3. Web applications such as genome browsers rely heavily on JavaScript, a popular language for processing and rendering client-side information in a web browser. Despite their widespread use in bioinformatics, biological web applications are usually implemented with no standard reutilisation guidelines in mind, hence BioJS was developed4. BioJS code contains proper guidelines on how to use the components and how the API can be implemented to interact with other components.

BioJS is an open source JavaScript library of components for the visualisation of biological data on the web. Here we present wigExplorer, a standard, portable BioJS component designed to easily render wig data format files. wigExplorer can be integrated and controlled from other applications. To our knowledge, this is the first modular component to visualise wig data that complies with BioJS standards.

The wigExplorer component

wigExplorer is fully integrated in the BioJS project. It follows the standards set by the BioJS registry5, a centralised repository of BioJS components hosted at the European Bioinformatics Institute (EBI). Having wigExplorer in the BioJS registry is advantageous because it promotes i) easy discoverability for the component, ii) collaborative development with other members of the BioJS community and iii) reutilisation by third party applications. In the BioJS registry, component APIs are exposed, i.e., events and methods are defined and documented so that other BioJS components can interact with each other. By following these conventions, wigExplorer is able to interact with other components on the same web page, enriching the overall experience for the user. The code below shows how to incorporate wigExplorer into a web application. Only three configuration elements are needed: the target HTML element in which the component will be rendered, the background colour of the component, and the file path containing the wig data. Wig files contain minimalistic information of genomic data wigExplorer and can handle a large genomic region such as a chromosome (tested with a single file containing 12 chromosome with average length of 60 Mb), but this depends on the richness of the data rather than the length of the genomic region.

var instance = new Biojs.wigExplorer({
     target: "YourOwnDivId",
     selectionBackgroundColor: ’<background-colour>’,
     dataSet: "<path–to–file>"
});

wigExplorer uses D3.js, the data-driven documents JavaScript library6, to generate graphical representations from wig data. D3.js handles the manipulation of the data documents, the reading of wig data as text format and their conversion to an area chart format. On the top right side, wigExplorer contains a dropdown to toogle between different references from the wig file. To control the visual aspect of the wig data, wigExplorer contains simple controls for zooming and panning. It is also possible to zoom and pan using provided API.

instance._updateDraw(start, end)

Application

wigExplorer can be used to visualise genomic data in different ways. An application is shown in Figure 1, depicting single nucleotide polymorphism (SNP) density data from a genomic annotation in the tomato genome. Here chromosome 2 is zoomed in to show the genomic interval contained between position 2.5M and 47.5M. The SNP density data contained in the wig data file are presented as bins, where the Y axis indicates the number of SNPs contained in each bin. The screenshot shows a dramatic change in the density of SNPs just after the 24M bin mark of the chromosome, suggesting a potential boundary for an introgression segment introduced from a closely related tomato species. Other potential applications of wigExplorer may involve the visualisation of gene expression and alignment data.

4dada545-e358-4f08-a893-f772ebdc1a85_figure1.gif

Figure 1. wigExplorer view of tomato variety Heinz chromosome 2.

The top controls are designed to toogle between different references as well as zoom and pan. Peaks show SNP density of 1kb size bins. A change of SNP density can be observed around the 24M mark, with a slightly greater density of SNPs on the right, indicative of a potential introgression segment from another related species.

Third party browsers are also using wigExplorer. A screenshot of the TGAC Browser7 is shown in Figure 2 using wigExplorer to depict Myzus spp. scaffold 1 zoomed in between regions 714K and 727K. Here strandspecific RNA-Seq paired-end read coverage is shown as a wig track. The track below shows a closely related annotated species gene set for comparison. This comparison suggests a potential gene extension in both forward and reverse orientation.

4dada545-e358-4f08-a893-f772ebdc1a85_figure2.gif

Figure 2. An example of wigExplorer integration using the TGAC Browser.

The wigExplorer track shows read coverage in Myzus spp. for scaffold 1. Forward and backward strands are depicted in red and blue respectively. Evidence genes from a closely related species are displayed in the track below.

Conclusions

The wigExplorer component provides a platform to visualise biological data in wig format. wigExplorer can be easily integrated with other web components or extended to provide new functionality. We expect this component to be particularly useful for visualisation in a variety of data types such as SNP density, alignments and gene expression. Like any other BioJS component, wigExplorer requires little technical knowledge for its utilisation.

Software availability

Zenodo: wigExplorer, a BioJS component to visualise wig data_v2, doi: 10.5281/zenodo.85168

GitHub: BioJS, http://github.com/biojs/biojs/releases/tag/v1.0;

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Version 3
VERSION 3 PUBLISHED 13 Feb 2014
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CITE
how to cite this article
Thanki AS, Jimenez RC, Kaithakottil GG et al. wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.12688/f1000research.3-53.v3)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 3
VERSION 3
PUBLISHED 09 Aug 2016
Revised
Views
17
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Reviewer Report 05 Oct 2016
Chunlei Wu, Scripps Research Institute, La Jolla, CA, USA 
Jiwen Xin, The Scripps Research Institute, La Jolla, CA, USA 
Approved with Reservations
VIEWS 17
This manuscript decribed a useful BioJS component for visualizing genomic tracks from a wig-formatted file. There are some major concerns raised by the reviewer:
  • Demo code show “Unknown format detected” error. When clicking the demo code
... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Wu C and Xin J. Reviewer Report For: wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.5256/f1000research.10145.r16472)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Version 2
VERSION 2
PUBLISHED 30 May 2014
Revised
Views
18
Cite
Reviewer Report 07 Jun 2016
Stefan Thomas Lang, Department of Molecular Hematology, Lund University, Lund, Sweden 
Approved with Reservations
VIEWS 18
I am no JavaScript developer myself and I have not tested the described functionality, but I already can think of applications in my own work if the package is able to not only show predefined chromosomes in a wig file, but ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Lang ST. Reviewer Report For: wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.5256/f1000research.4634.r14186)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 09 Aug 2016
    Anil Thanki, The Genome Analysis Centre, UK
    09 Aug 2016
    Author Response
    Dear Stefan

    We would like to thank you for reviewing the manuscript and making some positive comments that could be used for your application.

    Please find below our ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 09 Aug 2016
    Anil Thanki, The Genome Analysis Centre, UK
    09 Aug 2016
    Author Response
    Dear Stefan

    We would like to thank you for reviewing the manuscript and making some positive comments that could be used for your application.

    Please find below our ... Continue reading
Views
14
Cite
Reviewer Report 01 Mar 2016
Phil Lord, School of Computing Science, University of Newcastle, Newcastle, UK 
Approved
VIEWS 14
The authors have provided ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Lord P. Reviewer Report For: wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.5256/f1000research.4634.r4977)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Version 1
VERSION 1
PUBLISHED 13 Feb 2014
Views
65
Cite
Reviewer Report 07 Mar 2014
Phil Lord, School of Computing Science, University of Newcastle, Newcastle, UK 
Approved with Reservations
VIEWS 65
I have tried this piece of software and it does appear to do what it says and running the software was not too difficult. The link to the software on Zenodo in the Software Availability section (Zenodo: wigExplorer, a BioJS ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Lord P. Reviewer Report For: wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.5256/f1000research.3732.r3697)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 23 May 2014
    Anil Thanki, The Genome Analysis Centre, UK
    23 May 2014
    Author Response
    We would like to thank Phil for taking the time to review the manuscript. 

    Please find below our responses to your comments

    1) The link to the software on Zenodo in the ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 23 May 2014
    Anil Thanki, The Genome Analysis Centre, UK
    23 May 2014
    Author Response
    We would like to thank Phil for taking the time to review the manuscript. 

    Please find below our responses to your comments

    1) The link to the software on Zenodo in the ... Continue reading
Views
148
Cite
Reviewer Report 25 Feb 2014
Robert Buels, JBrowse, University of California, Berkeley, CA, USA 
Not Approved
VIEWS 148
The manuscript is well written, but it does not accurately describe the software in question.

I installed the software on my machine, and evaluated its behavior under several scenarios that I think would be commonly encountered by people using it. The major ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Buels R. Reviewer Report For: wigExplorer, a BioJS component to visualise wig data [version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]. F1000Research 2016, 3:53 (https://doi.org/10.5256/f1000research.3732.r3699)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Reader Comment 26 Feb 2014
    Anil Thanki, The Genome Analysis Centre, UK
    26 Feb 2014
    Reader Comment
    Hi Robert,

    I thank you for your useful comments, and I fully understand your concerns about the code and the performance of the tool. I have already started working on fixes ... Continue reading
  • Author Response 28 May 2014
    Anil Thanki, The Genome Analysis Centre, UK
    28 May 2014
    Author Response
    Dear Robert
     
    We would like to thank you for taking the time to review the manuscript.
     
    Please find below our responses to your comments.
     
    1) wigExplorer does not provide any useful error messages when ... Continue reading
COMMENTS ON THIS REPORT
  • Reader Comment 26 Feb 2014
    Anil Thanki, The Genome Analysis Centre, UK
    26 Feb 2014
    Reader Comment
    Hi Robert,

    I thank you for your useful comments, and I fully understand your concerns about the code and the performance of the tool. I have already started working on fixes ... Continue reading
  • Author Response 28 May 2014
    Anil Thanki, The Genome Analysis Centre, UK
    28 May 2014
    Author Response
    Dear Robert
     
    We would like to thank you for taking the time to review the manuscript.
     
    Please find below our responses to your comments.
     
    1) wigExplorer does not provide any useful error messages when ... Continue reading

Comments on this article Comments (0)

Version 3
VERSION 3 PUBLISHED 13 Feb 2014
Comment
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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