---
name: "Bio::Tradis::TradisPlot"
section: "3pm"
platform: "linux"
package: "bio-tradis"
version: "1.4.5+dfsg2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tradis::TradisPlot"
---

# Bio::Tradis::TradisPlot(3pm)

Generate plots as part of a tradis analysis

## NAME

Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis

## VERSION

version 1.4.5

## SYNOPSIS

Generate insertion plots for Artemis from a mapped fastq file and a reference in GFF format

```
   use Bio::Tradis::TradisPlot;

   my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc');
   $pipeline->plot();
```

## PARAMETERS

### Required

`"mappedfile"` - mapped and sorted BAM file

### Optional

- •

  `"outfile"` - base name to assign to the resulting insertion site plot. Default = tradis.plot

- •

  `"mapping_score"` - cutoff value for mapping score. Default = 30

## METHODS

`"plot"` - create insertion site plots for reads in \`mappedfile\`. This file will be readable by the Artemis genome browser \<http://www.sanger.ac.uk/resources/software/artemis/\>

## AUTHOR

Carla Cummins \<path-help@sanger.ac.uk\>

## COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

```
  The GNU General Public License, Version 3, June 2007
```