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Command line

The tree-annotated-plot command pairs a saved Vega-Lite chart spec (JSON or HTML) with an Auspice JSON tree and writes the combined plot to disk.

The configuration options below are auto-generated from PlotConfig, so descriptions and CLI --help text are guaranteed to match.

Quickstart

tree-annotated-plot \
    --tree h3n2.auspice.json \
    --chart titers.json \
    --output combined.html \
    --chart-strain-field axis_label \
    --tree-strain-field derived_haplotype \
    --branch-length div

The output's format is dispatched on the file extension: .html, .json, .png, .svg, .pdf are all accepted.

Reference

::: mkdocs-click :module: tree_annotated_plot.cli :command: main