It is quite simple using Cytoscape . What you need to do is create two files
- File containing node and edge information (File1)
- File containing tooltip information (File2)
File1
These are just 3 columns (sourceNode, destinationNode, edgeLabel) And then you can go File → Import → Network from the table (Text / MS Excel). Select the source of the node, the destination of the node, and the type of interaction.
Do not forget to change the display settings in VizMapper
File2
Node and edge attribute files are simply formatted: the node attribute file starts with the attribute name in the first line (note that it cannot contain spaces). Each next line contains the name node, followed by an equal sign and the value of this attribute. Numbers and text strings are the most common attribute types. All values for this attribute must be of the same type. For example:
FunctionalCategory YAL001C = metabolism YAR002W = apoptosis YBL007C = ribosome
The edge attribute file has the same structure, except that the edge name is the source name of the node, followed by the type of interaction in parentheses, followed by the target name of the node. The directionality is calculated, so switching the source and target will relate to another (or possibly nonexistent) edge. The following is an example of an edge attribute file:
InteractionStrength YAL001C (pp) YBR043W = 0.82 YMR022W (pd) YDL112C = 0.441 YDL112C (pd) YMR022W = 0.9013
Since Cytoscape treats boundary attributes as directed, the attribute values of the second and third edges refer to two different edges (the source and target objects are reversed, although the nodes involved are the same).
Each attribute is stored in a separate file. node and edge attribute files are used in the same format. node attribute file names often use the suffix ".noa", and attribute names of boundary attributes use the suffix ".eda". Cytoscape recognizes these suffixes when viewing attribute files.
Node, and edge attributes can be loaded on the command line using the -n and -e options or via the File → Import menu.
When expression data is loaded using an expression matrix, it is automatically loaded as node attribute data, unless explicitly stated otherwise.
Node, and edge attributes are tied to nodes and edges and therefore are independent of networks. The attributes for this node or edge will be applied to all copies of this node or edge in all downloaded network files, regardless of whether the attribute file or network file is imported.
Note. To import network attributes in Cytoscape 2.4, go to File → Import → Attribute from a table (text / MS Excel) ... or encode them in an XGMML network file
Each line that has passed the first line identifies the name of the object (a node in the node attribute file or an edge in the face attribute file) along with a String representation of the attribute value. The delimiter is always equal to the sign; spaces (spaces and / or tabs) before and after the equal sign is ignored.
Object names must be node ID or Edge ID, as shown in the leftmost column of the attribute browser, if the attribute should display anything. These names must be reproduced accurately, including case, or they will not match.
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