GRAL is a library for creating high quality plots and charts in Java. Many plot types are available like scatter plot, bubble plots, line plots, area plots, pie charts, and bar charts. Additionally, GRAL can exchange and process data (smoothing), and various plug-ins allow the import and export of data and graphics to formats like CSV, JPEG, PNG, EPS, PDF, or SVG.
VectorGraphics2D can export Java painting operations to Encapsulated PostScript (EPS), Scalable Vector Graphics (SVG), or Portable Document Format (PDF) files. It supports the rendering of all geometric shapes provided by the Java language. More advanced features like transparency or clipping paths can be used as well. It has a very small footprint and can be easily used as a replacement for Java's java.awt.Graphics2D class.
VisIt is an interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. It was designed to interactively handle very large data set sizes in the terascale range, and works well down to small data sets in the kilobyte range.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
JGraph is a free, mature, and robust Java diagramming library. It contains all the graph visualization, layout, and interaction functionality you might expect in a graph library, including multiple views, layering, zoom, drag and drop, undo, automatic expanding and collapsing, routing, and layouts. You can create workflow editors, BPMN, CAD tools, network diagrams, database visualization tools, and more. It is fully documented, including examples, and has an active support community.