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Visualization tools

Ralonso edited this page Apr 8, 2015 · 64 revisions

Babelomics implements two new advanced options for visualization of omics data. These include:

  • Network viewer, for the representation of the results of network analysis, which allows users to customize the results and to produce high quality figures for papers
  • Genome browser, to represent SNPs or variants in their genomic context.

Network Viewer

Network viewer tool takes advantage of CellMaps and provides a fast and easy to use environment to visualize and edit networks. It comprises 3 components (from the top to the bottom):

  1. Menu bar, which has the menus for the three main CellMaps functions.
  2. Tool bar, which includes the options for commonly used functions like editing and configuring the network layouts and its elements.
  3. Viewer panel, the visualization window that displays the network.

NV tool

Menu bar

The menu bar has three elements, which takes the three general function menus:

  • The File menu contains the basic functionality for file exporting data like downloading networks and snapshots of the current network viewer as an image. file menu bar
  • The Network menu allows you to edit your network, to select network elements or change the network layout. file menu bar
  • The Attributes menu allows the users to add and edit additional information of the network and its elements. These attributes can be created through the edit attributes box. The attributes assigned to the network elements can be used to custom the visual parameters through the visualization settings box.
    attributes menu bar

Tool bar

The toolbar includes the commonly used functions for editing and configuring the network, nodes and edges. To see the description of each button, put the mouse pointer over the corner of the button and wait momentarily for a tooltip. The following table describes each of the toolbar buttons.

Icon Name Description
select mode Nodes/edges mode Select nodes and edges
network mode Network mode Move the whole network along the canvas
background mode Background mode Select and move the background images
add Add mode Add nodes
Join Join mode Join nodes by an edge
delete Delete mode Delete the selected node / edges
Layout Layout Render the whole graph using different algorithms. Default: force directed
select Select Select nodes, vertices or both
background Background Change the color of the background, select a predefined image or upload your own image
Zoom Zoom Increase or decrease the network view
node name Node Name Show and edit the name of the selected node
edge name Edge Name Show and edit the name of the selected edge
node shape Node Shape Change the shape of the selected node(s)
edge shape Edge Shape Change the shape of the selected edge(s)
size Node fill color & size Change the color and size of the selected node(s)
Stroke size Node stroke color & size Change the border color and size of the selected node(s)
Edge size Edge fill color & size Change the color and size of the selected edge(s)
Opacity Opacity Changes the transparency of the selected node/edge(s)
label size Label size Change the font size of the node/edge(s) labels
search Search Search nodes or edges according the node id or an attribute (ex. node name). Also you can choose the color used to highlight your search (orange by default)

Viewer panel

The Network Viewer panel displays all the nodes and edges of the network and it is used to arrange and navigate around the elements of the network.

networkviewer

NOTE: For a detailed tutorial of CellMaps functionalities, see CellMaps wiki. Note that Network Viewer integrated in Babelomics only takes the minimum set of functionalities provided by CellMaps to allow a basic visualization and edition of the network. For an advanced use of the networks provided by Babelomics, you can download the network and attributes from the result form in Babelomics and go to http://cellmaps.babelomics.org/


Genome browser

Babelomics integrates GenomeMaps as the genome browser for genomic data visualization. Users can navigate through the chromosomes and explore variants in the context of genomic features (genes, transcripts, SNPs, etc.).

If you are using Firefox take into account that you can't use this component when using private window mode. Also, if in your Firefox preferences under privacy tab in the history section, you don't have "Remember history selected" the genome browser won't work well.

When analysing genomic data with Babelomics, results will generally show a table containing the significant variants from your analysis (a) and the genome browser (b):

results

  • The table view will show a list of the significant variants obtained in your analysis and some other relevant information such as position, statistic, p-value and odds ratio.
  • The genome browser will show you these variants in the genomic context.

Both panels are connected and synchronized so that clicking in a variant listed in the table view will locate the genome browser in this exact position.

The genome browser can be divided in different sections:

  1. Tool bar, containing functions to configure the visialization, navigate through the genome, zoom and activate and inactivate panels.
  2. Region overview, a distant representation of the region of interest.
  3. Region in detail, a close visualization of the region of interest and other relevant information.

results

Tool bar

The Tool bar contains the necessary functions to tune the visualization. The available functions are described in the following table:

Icon Name Description
karyotype Karyotype Activate or inactivate Karyotype view
chromosome Chromosome Activate or inactivate Chromosome view
region Region overview Activate or inactivate Region overview
zoom Zoom Zoom in or out. Click on the middle bar to set zoom at the desired level. Click + or - to slowly increase or decrease the level of zoom. Select 100 to set the zoom at the maximum level (sequence view) or 0 to set the zoom a the farthest view
window size Window size Specify how big must be the detailed region window in bp
position Region box Specify the region or position to examine. Format: Chr:Start-End for regions or Chr:Position for positions
move Move Move across the region. Use < or > to move slowly upstream or downstream respectively. Use << or >> to move faster. Alternatively, users can use the mouse to move the region by clicking and draging
collapse Collapse/Expand Collapse or expand tracks to fit contents

Region overview

In this track users can see a distant representation of the region they are exploring. Only genes are shown in this panel. The name of every gene is specified together with the corresponding strand, indicated with the sign < for reverse or > for forward, and its biotype between brackets. Genes are coloured by biotype.

Dragging and dropping in the Region overview will update the Region in detail panel.

region overview

Region in detail

This panel contains detailed genetic information for the explored region. An orange vertical stripe indicates the centre of the region. When a variant is clicked in the Table view the vertical stripe indicates the exact position for this variant. This panel is divided into three different sections or tracks:

  1. Sequence track, when using high levels of zoom, it shows the genomic sequence where every base is coloured differently, otherwise, it will only show the bp corresponding to the first and the last position showed in the region and the one in the middle.
  2. Gene track, shows genes and transcripts in detail. Solid rectangles represent genes which are coloured by biotype. transcripts are drawn below the gene as small rectangles (exons) and lines (introns). Coloured exons represent coding regions.
  3. SNP track, when using high levels of zoom, it indicates the location of known single nucleotide variants (SNPs), otherwise, it shows a histogram summarising the amount of SNPs in this region.

region in detail

Citing Genome Maps

Medina I., Salavert F., Sanchez R., de Maria A., Alonso R., Escobar P., Bleda M., Dopazo J. Genome Maps, a new generation genome browser. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6. doi: 10.1093/nar/gkt530 - NAR - PubMed - Google Scholar

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