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 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):
- Menu bar, which has the menus for the three main CellMaps functions.
- Tool bar, which includes the options for commonly used functions like editing and configuring the network layouts and its elements.
- Viewer panel, the visualization window that displays the network.
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.
- The Network menu allows you to edit your network, to select network elements or change the network layout.
- 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.
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.
|Nodes/edges mode||Select nodes and edges|
|Network mode||Move the whole network along the canvas|
|Background mode||Select and move the background images|
|Add mode||Add nodes|
|Join mode||Join nodes by an edge|
|Delete mode||Delete the selected node / edges|
|Layout||Render the whole graph using different algorithms. Default: force directed|
|Select||Select nodes, vertices or both|
|Background||Change the color of the background, select a predefined image or upload your own image|
|Zoom||Increase or decrease the network view|
|Node Name||Show and edit the name of the selected node|
|Edge Name||Show and edit the name of the selected edge|
|Node Shape||Change the shape of the selected node(s)|
|Edge Shape||Change the shape of the selected edge(s)|
|Node fill color & size||Change the color and size of the selected node(s)|
|Node stroke color & size||Change the border color and size of the selected node(s)|
|Edge fill color & size||Change the color and size of the selected edge(s)|
|Opacity||Changes the transparency of the selected node/edge(s)|
|Label size||Change the font size of the node/edge(s) labels|
|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)|
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.
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/
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):
- 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:
- Tool bar, containing functions to configure the visialization, navigate through the genome, zoom and activate and inactivate panels.
- Region overview, a distant representation of the region of interest.
- Region in detail, a close visualization of the region of interest and other relevant information.
The Tool bar contains the necessary functions to tune the visualization. The available functions are described in the following table:
|Karyotype||Activate or inactivate Karyotype view|
|Chromosome||Activate or inactivate Chromosome view|
|Region overview||Activate or inactivate Region overview|
|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||Specify how big must be the detailed region window in bp|
|Region box||Specify the region or position to examine. Format:
|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/Expand||Collapse or expand tracks to fit contents|
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 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:
- 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.
- 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.
- 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.
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