Visualization Grammar

Genome browsers typically couple the visual representations to specific file formats and provide few customization options. GenomeSpy has a more abstract approach to visualization, providing combinatorial building blocks such as marks, transforms, and scales. Users can author novel visualizations that display the underlying data more effectively. The variety of building blocks is still rather limited, but already allows for many useful visualizations.

Ggplot2 and Vega-Lite are two widely used grammar-based visualization tools.

TODO: Quick introduction to view specifications.

A subset of Vega-Lite

The visualization grammar of GenomeSpy is a subset and a dialect of Vega-Lite. However, the goals of GenomeSpy and Vega-Lite are different – GenomeSpy is more domain specific and is intended for visualizing genomic coordinates. In its current form, the grammar of GenomeSpy is limited to specifying the visual encoding and certain data transformations. GenomeSpy tries to faithfully follow Vega-Lite's grammar where practical. Thus, this documentation has many references to its documentation.