The network viewer

By default, the Network viewer displays the regulatory elements that have obtained a significant p-value in the test, showing as targets the genes introduced by the user. However, it has many other functionalities:

  • Search for any node/gene in the network using either the HGNC symbol as any other identifier.
  • Selection:
    • all nodes, connections, or both
    • of adjacent nodes
    • Neighborhood: nodes and edges adjacent to a node.
    • Connected component: a group of nodes connected to each other and separated from the rest.
  • Editing and manipulation of the network:
    • Layout: Different renderings for the same graph (dot, born, twopi, circus, pdf, SFDP, random, circle, square)
    • Move, select, add, delete, creating connections between nodes, etc..
    • Format: color, shape, border, size, label, etc.
    • Background: We import a picture to have as background on the network.
  • Export and import:
    • Save the network created and edited to import it and load it in a new session.
    • Download an image of the network in PNG, JPG or SVG.
    • Import networks in SIF format (nodeA <relationship type> NodeB)


Viewer interface: the tool bar

Tool bar

The available operations are described here:

Icon Name Description
Collapse Collapse Place the selected nodes close to each other.
Layout Layout Render the whole graph using different algorithms. Default: neato.
Label size Label size Change the font size of the node labels.
Advanced select Advanced select Select all nodes, all vertices or both.
Adjacent: nodes adjoining a node.
Neighborhood: nodes and edges adjacent to a node.
Connected component: a group of nodes connected to each other and separated from the rest.
Zoom in Zoom in Magnify the network.
Zoom out Zoom out Decrease magnification to obtain a more distant view of the network.
Select Select Define selection area.
Drag Drag Click on the empty area and move the whole network.
Add Add Add node.
Join Join Place the selected nodes close to each other.
Delete Delete Delete the selected node(s).
Node shape Node shape Change the shape of the selected node(s).
Resize Resize Change the dimensions of the selected element(s) (nodes or edges).
Color Color Change the color of the selected node(s).
Stroke size Stroke size Change the border size of the selected node(s).
Stroke color Stroke color Change the border color of the selected node(s).
Opacity Opacity Changes the transparency of the selected element(s).
Edge type Edge type Modify the type of the selected edge(s). Every option makes reference to a different type of interaction (see SBGN).
Background Background Change the color of the background, select a predefined image or upload your own image.


Tutorial

Find extra information about your genes and their regulatory elements

The network viewer is not a simple graph editor. Behind RENATO's interface much genetic and regulatory information has been stored and can be accessed though the network viewer. Just by clicking on a gene or regulator label, an information widget appears containing information about this element.

Widgets

network_viewer.txt · Last modified: 2012/05/03 17:46 by mbleda
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