Skip to content
This repository has been archived by the owner on Oct 31, 2024. It is now read-only.

Latest commit

 

History

History
114 lines (91 loc) · 4.53 KB

README.md

File metadata and controls

114 lines (91 loc) · 4.53 KB
Raw

Genetic-mapper - Vectorial Genetic Map Drawer

Build Status Codacy Badge

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 and Abobe Illustrator(R).

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.

map.tsv

ID<tab>LG<tab>POS<tab>LOD
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).

DOI

Installation (optional)

You can directly use the script script/genetic_mapper.pl or install it in your system using:

git clone https://github.com/pseudogene/genetic-mapper.git
cd genetic-mapper
perl Makefile.pl
make
make test
sudo make install

Usage

..:: Vectorial Genetic Map Drawer ::..

Usage: ./genetic_mapper.pl [options] --map=<map.tsv>

Options
 --map <genetic map file>
       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 <string>
       Draw only the specified chromosome/linkage group.
  --delim <character>
       Use <character> 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=<karyotype.file>
       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

# 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

LG13

License

The content of this project itself is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License, and the source code presented is licensed under the GPLv3 license.