Cytoscape - Data Visualization Toolbox

What is this tool?

A browser tool for creating network (graph) diagrams from table data, GEXF, or GraphML. You visualize relationships as nodes (points) and edges (lines), style them with metrics such as degree and community, and export a figure with a legend.

You can paste an edge list from Excel and finish a co-occurrence network in a short time. It uses Cytoscape.js, from the same family as the desktop Cytoscape application, and is also useful for social and complex network visualization.

Features

Data import — Upload GEXF, GraphML, or CSV/TSV. Paste from Excel and map source, target, and weight columns
Sample datasets — Social networks such as Les Misérables and Game of Thrones, scientific networks, and a co-occurrence CSV
Directed / undirected — Hide arrows for undirected co-occurrence networks. Switch edge shape (Bezier / straight / Haystack)
Computed metrics — Degree, weighted degree, and Louvain communities are calculated automatically. After load, size maps to degree, color to community, and edge width to weight
Styling — Switch categorical/sequential scales, choose palettes (including colorblind-safe), adjust size range, and control labels (all / top N / selected / none)
Readable figures — Legend, hover attributes, neighbor highlight on click, title and source
Layouts — Cose (physics simulation, default), Circle, Concentric, Breadthfirst, Grid, and Random. Fit the graph to the viewport
Export — PNG (with title, legend, and source) and SVG
Project save/load — Save projects to the server and restore them later

How to use

Choose a file from “Load Data File”, paste a table with “Paste CSV”, or pick a sample
For CSV, confirm the source, target, and weight columns; aggregate duplicate edges if needed, then create the graph
Adjust direction (directed/undirected) and layout, then use “Fit” to show the whole graph
Assign node color, size, and labels, and edge color and thickness, using attributes or computed metrics
Add a title and source
Save as PNG or SVG from “Export”

Data formats

GEXF / GraphML

XML formats designed for graphs. They can richly describe node and edge attributes (categories, weights, coordinates, etc.). They can be exported from many tools such as Gephi and NetworkX.

CSV / TSV (edge list)

A format that can be easily created from spreadsheets or Excel. You can upload a file or paste a table.

A header row is required
Specify source and target columns. source / from / 始点 and target / to / 終点 are detected automatically (case-insensitive)
A weight column (weight / value / 重み, etc.) can be used for edge thickness
Duplicate source–target pairs can be aggregated by summing weights
All other columns are imported as edge attributes
Nodes are generated automatically from the edge list
After load, node size defaults to degree and color to community

source,target,weight,type
Alice,Bob,1.0,friends
Bob,Carol,2.5,colleagues
Alice,Dave,0.8,family

Japanese headers are also supported.

始点,終点,重み
Alice,Bob,1.0
Bob,Carol,2.5
Alice,Dave,0.8