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CytoscapeFunction introduction
1. Supports multiple analysis methods, and you can choose to analyze the network.
2. Cytoscape software supports analyzing subsets of nodes, batch analysis, and loading network statistics.
3. Draw parameters and generate styles from statistical information
4. Display network statistics using an extensible dialog interface
5. Store node parameters in the node table and edge parameters in the edge table
6. Bright color mapping standard ameters, dark color mapping standard ameters, intermediate color mapping standard ameters
7. NetworkAnalyzer, Cytoscape web browser
8. Merge process, job status monitor, command line dialog box, execution command file
9. Selected node, selected node with options, command line parameters
10. Cytoscape’s quick tour, network creation, and nested networks
11. Supported network file formats, node and edge data
12. Style, application manager, command tool, rendering engine, export data
13. Cytoscape and OpenCL, Cytoscape.js and Cytoscape automation
CytoscapeSoftware features
Cytoscape software uses a scalable user interface to navigate and view the network. ZUIs use two navigation mechanisms: zooming and panning. Zoom increases or decreases the magnification of the view depending on how much or how little of the content the user wants to see
Node and edge column data
Interaction networks are useful as stand-alone models. However, they are most effective for answering scientific questions when combined with other information. Cytoscape allows users to add arbitrary node, edge and network information into Cytoscape as node/edge/network data columns
Cytoscape functionality is not fixed. They can be extended via apps. They can extend Cytoscape in various ways. An application can import data from an online database. Another application could provide a new way to analyze networks. You can install the application after installing Cytoscape. Most applications are developed by Cytoscape users like you.
If you are familiar with Cytoscape2. You may know that fine Cytoscape applications are called plug-ins. Starting from Cytoscape3.0, we call it application.
CytoscapeInstructions for use
1. Input file
Supports multiple input formats, can save project files, supports multiple layout methods, supports exporting images, can make rich adjustments to styles, and intelligently selects and filters.
1. edge file format:
tsv (tab-delimited txt is the same), csv (comma-delimited), xls, xlsx files, etc. Generally, two tsv files are enough for us to use. The following is a typical three-column tsv format file example. The first column is the original node, the third column is the target node, and the second column is the interaction relationship between the two. The interaction relationship here indicates different types. In the following You can see the beauty of it in the network settings, and the source and target here are both numbers. How to convert it into the gene name we want to see? Here is a question first, which will be explained later.
2. node properties file
It can be imported and can be used to solve our above problem by replacing the numbers in the edge file with simple visual gene names.
2. Import data
You can click on the species name above to select an example to study, or you can directly select an empty network to import data. For example, if I selected Arabidopsis, the following interface will appear. The diagram shows an example of a completed network:
user interface
1. Import data
2. Import the properties file
3. Layout
3. Advanced functions
1. Adjust the style
(1)Basic style
(2)Node style
(3) Side style
2. Change the node name
3. Change the color of the edge
4. Statistics on various indicators of the control network
The result will appear in a new panel:
5. Change node size
An important point to emphasize here is that before changing the node size here, if you want to set the gradient through the number of edges connected by the node, you must perform the statistical analysis in the fourth step above, otherwise No Degree option appears:
Double-click the gradient setting area above to bring up the control panel for modification:
4. Select filter
1. Selection of nodes
2. Selection and separation of subnetworks
6. Export pictures
The export of data can be a network file, a table file or an image file. Image files include a variety of image formats and pdf formats. Comparing the shapes of icons, the two left icons shown in the figure below are icons for quickly importing files:
Biological information analysis software (Cytoscape) 7. Expression analysis
Cytoscape can also import the expression values of genes and display different expression values in color gradients. Since my analysis does not have this part of the data, I made a few screenshots of the pictures I learned on the Internet:
8. Others
Cytoscape provides many external databases. Right-click on the corresponding node and select externallinks from the options that appear. There are the following connected databases:
In addition, based on the development of a large number of powerful plug-ins, the following functions are also very comprehensive:
GO analysis: BiNGO
Pathway analysis: CytoKegg, KEGGscape, etc.
Module and complex analysis: jActiveModules+BiNGO
Cytoscape update log
1. Fixed other bugs;
2. Optimized software compatibility.
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