Troubleshooting

Unknown track alias

from plotnado import GenomicFigure

GenomicFigure.available_track_aliases()

Check Track Aliases if the alias comes from YAML or config.

Empty plots

  • Confirm the region overlaps your data.
  • Check chromosome naming consistency such as chr1 versus 1.
  • Validate required columns for in-memory tables.
  • For file-backed tracks, confirm paths are visible from the process running PlotNado.

Overlay panel looks squashed

Put autoscale_group on the overlay track itself when the entire panel should match sibling signal tracks.

fig.autoscale(True)
fig.overlay(
    [signal_a, signal_b],
    title="Overlay",
    autoscale_group="signal-panels",
)

If two series need fundamentally different y-ranges, split them into separate panels.

Docs build fails with Python version errors

PlotNado requires Python 3.12+.

uv run python --version
uv sync --extra dev --extra docs
QUARTO_PYTHON=.venv/bin/python quarto render

If Quarto reports that Jupyter or PyYAML is missing from a system Python, it is not using the uv environment. Set QUARTO_PYTHON=.venv/bin/python.

CLI command is missing

Check the installed command surface:

uv run plotnado --help
uv run plotnado init --help
uv run plotnado validate --help
uv run plotnado plot --help

There is no plotnado track-options command. Use the Python runtime helpers instead.

I cannot find a track option

from plotnado import GenomicFigure

GenomicFigure.track_options("overlay")
GenomicFigure.track_options_markdown("bigwig")

Then compare with Compact Options and Reference.