CLI

PlotNado’s CLI is a YAML-template workflow:

  1. plotnado init infers a template from data files.
  2. plotnado validate checks the template before plotting.
  3. plotnado plot renders one or more regions.

Run commands through uv in the source tree:

uv run plotnado --help

plotnado init

uv run plotnado init sample1.bw sample2.bw peaks.narrowpeak --auto --output template.yaml

Useful options:

Option Purpose
--output, -o Write the YAML file to a specific path.
--genome, -g Set a default genome such as hg38 or mm10.
--group-by Group files by a built-in strategy or regex.
--auto Use inferred defaults without interactive prompts.
--no-genes Do not add the genes guide track.

Example template:

genome: hg38
guides:
  genes: true
tracks:
  - path: sample1.bw
    type: bigwig
    title: sample1
    group: sample
  - path: peaks.narrowpeak
    type: narrowpeak
    title: peaks

plotnado validate

uv run plotnado validate template.yaml

Validation checks YAML parsing, local file existence, group references, and template compilation.

plotnado plot

uv run plotnado plot template.yaml --region chr1:1,000,000-1,100,000 --output output.png

Useful options:

Option Purpose
--region, -r Genomic region or gene name; repeat for multiple outputs.
--output, -o Explicit output path for a single region.
--format, -f Output format such as png, pdf, svg, or jpg.
--width, -w Override template width in inches.
--dpi Output resolution.

Examples:

uv run plotnado plot template.yaml --region chr1:1,000,000-2,000,000
uv run plotnado plot template.yaml --region GNAQ
uv run plotnado plot template.yaml --region chr1:1,000,000-2,000,000 --region chr2:5,000,000-6,000,000
uv run plotnado plot template.yaml --region chr1:1,000,000-2,000,000 --output plot.pdf --dpi 300

Gene-name resolution requires genome in the template.

Python bridge

The template format is shared with the Python API:

from plotnado import GenomicFigure

fig = GenomicFigure.from_template("template.yaml")
fig.save("output.png", region="chr1:1,000,000-1,100,000")

See Template Schema for the compact field reference.