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Visualization Grammar

Genome browser applications 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 concept was first introduced in The Grammar of Graphics and developer further in ggplot2 and Vega-Lite.

TODO: Quick introduction to view specifications. Meanwhile, have a look at Vega-Lite's view specification documentation to get the general idea.

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 visualization and analysis of large datasets that contain genomic coordinates. GenomeSpy tries to faithfully follow Vega-Lite's grammar where practical. Thus, this documentation has many references to its documentation.