https://github.com/pseudogene/genetic-mapper
SVG Genetic Map Drawer
https://github.com/pseudogene/genetic-mapper
bioinformatics genetic-maps genetics perl-script svg
Last synced: 4 months ago
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SVG Genetic Map Drawer
- Host: GitHub
- URL: https://github.com/pseudogene/genetic-mapper
- Owner: pseudogene
- Archived: true
- Created: 2015-12-07T15:02:44.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2020-05-22T07:54:31.000Z (about 5 years ago)
- Last Synced: 2025-01-24T02:19:30.044Z (5 months ago)
- Topics: bioinformatics, genetic-maps, genetics, perl-script, svg
- Language: Perl
- Homepage:
- Size: 46.9 KB
- Stars: 10
- Watchers: 2
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
Awesome Lists containing this project
README
Genetic-mapper - Vectorial Genetic Map Drawer
[](https://travis-ci.org/pseudogene/genetic-mapper) [](https://www.codacy.com/manual/pseudogene/genetic-mapper?utm_source=github.com&utm_medium=referral&utm_content=pseudogene/genetic-mapper&utm_campaign=Badge_Grade)
# Genetic-mapper
Genetic-mapper is a perl script able to draw publication-ready vectorial genetic maps.
## Description
Perl script for creating a publication-ready vectorial genetic/linkage map in Scalable Vector Graphics (SVG) format. The resulting file can either be submitted for publication and edited with any vectorial drawing software like [Inkscape](https://inkscape.org/) and [Abobe Illustrator(R)](http://www.adobe.com/uk/products/illustrator.html).
The input file must be a text file with at least the marker name (ID), linkage group (LG) and the position (POS) separeted by tabulations. Additionally a logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.
```plaintext
map.tsv
IDLGPOSLOD
13519 12 0 0.250840894
2718 12 1.0 0.250840893
11040 12 1.6 0.252843341
...
```
## How to cite Genetic-mapper
>**Genetic-Mapper: vectorial genetic map drawer**.
>Bekaert M.
>_F1000Research_. 2016, 5:1301 (poster).
[](http://dx.doi.org/10.7490/f1000research.1112266.1)
## Installation (optional)
You can directly use the script `script/genetic_mapper.pl` or install it in your system using:
```sh
git clone https://github.com/pseudogene/genetic-mapper.git
cd genetic-mapper
perl Makefile.pl
make
make test
sudo make install
```
## Usage
```plaintext
..:: Vectorial Genetic Map Drawer ::..
Usage: ./genetic_mapper.pl [options] --map=
Options
--map
The input file must be a text file with at least the marker name (ID), linkage
group (LG) and the position (POS) separeted by tabulations. Additionally a
logarithm of odds (LOD score) can be provided. Any extra parameter will be ignored.
ID LG POS LOD
M19 12 0.01 0.45068
M18 12 1.14 0.00014
M40 12 11.48 0.25284
--chr
Draw only the specified chromosome/linkage group.
--delim
Use as the field delimiter character instead of the tab character.
--bar
Use a coloured visualisation with a dark bar at the marker position.
--plot
Rather than a list of marker names, it plots a circle. If the LOD-score is provided
a dark disk fills the circle proportionality to its value.
--species
Rather than a list of marker names, it plots a coloured circle. The option --col
must be used to specify the species name (incompatible with --plot or --bar).
--var
If specified with --bar or --plot the size of the bar/circle is proportional to the
number of markers.
--col
If --plot is specified and if more that one LOD-score column is available specify
the column number [default 1 (first LOD-score column)].
--square
Small squares are used rather than names (incompatible with --plot).
--pos
The marker positions are indicated on the left site of the chromosome.
--compact
A more compact chromosome is used (incompatible with --bar).
--karyotype=
Specify a karytype to scale the physical chromosme. Rather than using genetic
distances, expect nucleotide position in the map file.
FORMAT: "chr - ID LABEL START END COMMENT"
--scale= ]0,+oo[
Change the scale of the figure [default x10].
--split
If multiple markers have the same position, split the markers on multiple links
rather than on a long list on name.
--horizontal
Rotate the figure by 90 degrees.
--verbose
Become chatty.
```
## Examples
```sh
# compact (stylish)
./genetic_mapper.pl --var --compact --plot --map=map.tsv > lg.svg
# Classic publication style
./genetic_mapper.pl --pos --chr=13 --map=map.tsv > lg13.svg
```
## License
The content of this project itself is licensed under the [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/), and the source code presented is licensed under the [GPLv3 license](http://www.gnu.org/licenses/gpl-3.0.html).