User guide

The user guide begins with the general visualization grammar and then adds GenomeSpy’s composition and genomic concepts.

If declarative visualization is new to you, begin with data and chart inputs, then continue through the Foundations pages in order. If you already use Altair or Vega-Lite, start with chromosomes and locus scales to learn GenomeSpy’s genomic extensions.

Foundations

• Data and chart inputs explains records, tables, URLs, and inherited data.

• Charts and marks introduces the shapes that represent rows.

• Encodings and channels maps fields to position, color, size, and other visible properties.

• Scales, axes, and legends controls those mappings and their guides.

• Transforms filters, derives, and summarizes rows before they are drawn.

Larger and genomic views

• Composition layers charts and arranges linked panels.

• Import remote view specifications reuses published JSON views by URL.

• Configuration sets dimensions, titles, and shared visual defaults.

• Chromosomes and locus scales introduces assemblies and genomic coordinates.

• Large and indexed genomic data loads only the visible part of an indexed file.

• Linked genome tracks combines tracks on one zoomable genomic axis.

• Label points and genomic coordinates adds selected point callouts and scored gene tracks.

Interaction and output

• Parameters and interaction covers zooming, controls, overview brushes, selections, and cursor rulers.

• Create and update charts in notebooks covers display, dataframe transport, and live dataset updates without remounting.

• Display controls and embed options covers image export, the Inspector, and rendering-time settings.

• Save and inspect charts writes specifications and standalone HTML.