CLI

PlotNado includes a template-driven CLI for users who prefer a file-based workflow.

The standard flow is:

1. plotnado init to infer a YAML template from track files
2. plotnado validate to catch missing files or bad group references
3. plotnado plot to render one or more regions from that template

plotnado init

Generate a starting template from track files:

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

Useful options:

• --output / -o: where to write the YAML file
• --genome / -g: set a default genome such as hg38 or mm10
• --group-by: group tracks by a predefined strategy or regex
• --auto: skip interactive prompts and use inferred defaults
• --no-genes: do not add a genes guide track by default

Examples:

plotnado init *.bw --auto
plotnado init sample1_H3K27ac.bw sample1_H3K4me3.bw sample2_H3K27ac.bw --group-by sample
plotnado init control_r1.bw control_r2.bw treat_r1.bw treat_r2.bw --group-by '([^_]+)_r[0-9]'

The generated template is plain YAML and intended to be edited. A typical file looks like:

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

plotnado validate

Validate a template before rendering:

plotnado validate template.yaml

Validation checks:

• template can be loaded as YAML
• local track files exist
• group references resolve against track name or title
• the template compiles into a render plan cleanly

plotnado plot

Render a template for one or more regions:

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

Useful options:

• --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:

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

Gene-name resolution requires genome to be defined in the template.

Python bridge

The CLI template format is not separate from the Python API. The same template can be loaded directly in Python:

from plotnado import GenomicFigure

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