7 network mapping i
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This document provides instructions for generating a network map using Cytoscape. It describes creating an edge list and node attributes files with the necessary information to define the network. Steps are outlined for importing these files into Cytoscape, mapping node and edge attributes, adjusting the layout, and exporting the final network map. The overall goal is to map relationships between topics in a name to generate a visual representation of the connections.
7 network mapping i
- 1. Biology Chemistry Informatics Introduction to network mapping Network Mapping Goal: Generate a mapped “name” network Topics: 1. Edge list 2. Node attributes 3. Network Mapping 4. Cytoscape
- 2. Network Mapping Biology Chemistry Network Mapping Informatics Steps: 1.Make Edge list 2.Make Node attributes 3.Generate Network 4.Map node attributes 5.Final touches See Items in “Network” folder for results
- 3. Edge List Biology Chemistry Informatics Network Mapping Minimum Requirements: •2 column matrix with source (start) and target (end) nodes (e.g. letters) •extra columns can be used to set edge (connection) aesthetics (e.g. width, color, etc.) •See file “name edge list.xlsx” for an example edge list defining how the letters in my name (Dmitry Grapov) are connected with an extra column identifying consonants
- 4. Node Attributes Biology Chemistry Network Mapping Informatics Minimum Requirements: •ID for nodes (rows) must match the edge ID •Extra columns can be used to set each nodes properties (e.g. color, size, image, etc.) •See file “node attributes.xlsx” for an example node attributes file
- 5. Network Generation Biology Chemistry Informatics Network Mapping Use Cytoscape to generate network (v2.83) (http://www.cytoscape.org/ ) •Import Edge list (this can be many forms) 1 2
- 6. Network Generation (cont.) Biology Chemistry Network Mapping Informatics 1. Select file for edge list 2. Identify columns for edge (connection) source and target. Double click column to enable edge attributes. Hint: Show Text File Import Options>>Transfer first line….. 1 3 2 4 5 6
- 7. Node Layout Biology Chemistry Informatics 1 Cytoscape provides many options to help auto-optimize the node (letters) layout Network Mapping 2 (3 default add-ins) 3
- 8. Global Defaults Biology Chemistry Informatics Set defaults to modify global node, edge and other options. Double-click on Defaults image Network Mapping 1 3 2
- 9. Modify Edge Attributes Biology Chemistry Informatics Network Mapping Use the VizMapper to map “extra columns” in edge list (attributes) to aesthetics. 1
- 10. Node Attributes Biology Chemistry Informatics Select file for the node attributes. Extra options can be used to select node ID (must match edge list), change the file delimiter, etc. 1 Network Mapping 2 4 5 6 3
- 11. Modify Node Attributes Biology Chemistry Informatics Network Mapping Use the VizMapper to map node attributes. 1
- 12. Add node images Biology Chemistry Informatics Network Mapping New columns can be added to the node attributes and change the mapping in existing networks. Here I’ll add a url for a .png to use as a custom node image. Custom images can also be defined as local file path (e.g. windows: file:///C:.....)
- 13. Override mapped attributes Biology Chemistry Informatics Right-click on an edge or node to manually change their aesthetics Network Mapping 1 2 3
- 14. Export Network as Image Biology Chemistry Informatics Export as .pdf or .svg to further modify (and beautify) the network. 1 Network Mapping 2
- 15. Final Touches Biology Chemistry Informatics Network Mapping Use irfanview (http://www.irfanview.com/) for minor edits or inkscape (http://www.inkscape.org/en/) for complete control of final touches including making legends.