> ## Documentation Index
> Fetch the complete documentation index at: https://primerlab-genomic.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# primerlab plot

> CLI reference for the primerlab plot command

Generate visualizations from primer design results.

## Synopsis

```bash theme={null}
primerlab plot <result> [options]
```

## Arguments

| Argument | Required | Description              |
| -------- | -------- | ------------------------ |
| `result` | Yes      | Path to result.json file |

## Options

| Option       | Short | Description                       |
| ------------ | ----- | --------------------------------- |
| `--sequence` | `-s`  | Path to sequence file (required)  |
| `--type`     | `-t`  | Plot type (default: gc-profile)   |
| `--theme`    |       | Color theme: light, dark          |
| `--output`   | `-o`  | Output path (PNG/SVG)             |
| `--window`   | `-w`  | Sliding window size (default: 20) |

## Plot Types

| Type         | Description                |
| ------------ | -------------------------- |
| `gc-profile` | GC content across amplicon |

## Examples

### Basic GC Profile

```bash theme={null}
primerlab plot result.json --sequence input.fasta
```

### Dark Theme

```bash theme={null}
primerlab plot result.json --sequence input.fasta --theme dark
```

### Custom Window Size

```bash theme={null}
primerlab plot result.json --sequence input.fasta --window 50
```

### Save to File

```bash theme={null}
primerlab plot result.json --sequence input.fasta --output gc_profile.png
```

## Output

* Interactive plot displayed (if no --output)
* PNG/SVG file saved (if --output specified)
* Primer positions highlighted on plot