Skip to main content

Command-line tool to make beautiful and reproducible genome browser snapshots

Project description

PyPI Version bioconda-badge bioconda-badge Build Status Coverage

pyGenomeTracks

Standalone program and library to plot beautiful genome browser tracks

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:

  • bigwig
  • bed/gtf (many options)
  • bedgraph
  • epilogos
  • narrow peaks
  • links (represented as arcs)
  • Hi-C matrices

pyGenomeTracks can make plots with or without Hi-C data. The following is an example output of pyGenomeTracks from Ramírez et al. 2017

pyGenomeTracks example

Table of content

Installation

pyGenomeTracks works with python >=3.6.

The recommended way to install pyGenomeTracks is via conda

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7

To get a specific version, one can specify it. For example:

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7

Also, pyGenomeTracks can be installed using pip

$ pip install pyGenomeTracks

If the latest version wants to be installed use:

$ pip install  git+https://github.com/deeptools/pyGenomeTracks.git

Usage

To run pyGenomeTracks a configuration file describing the tracks is required. The easiest way to create this file is using the program make_tracks_file which creates a configuration file with defaults that can be easily changed. The format is:

$ make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini

make_tracks_file uses the file ending to guess the file type.

Then, a region can be plotted using:

$ pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 --outFileName nice_image.pdf

The ending --outFileName defines the image format. If .pdf is used, then the resulting image is a pdf. The options are pdf, png and svg.

Description of other possible arguments:

optional arguments:
  -h, --help            show this help message and exit
  --tracks TRACKS       File containing the instructions to plot the tracks.
                        The tracks.ini file can be genarated using the
                        `make_tracks_file` program.
  --region REGION       Region to plot, the format is chr:start-end
  --BED BED             Instead of a region, a file containing the regions to
                        plot, in BED format, can be given. If this is the
                        case, multiple files will be created using a prefix
                        the value of --outFileName
  --width WIDTH         figure width in centimeters (default is 40)
  --height HEIGHT       Figure height in centimeters. If not given, the figure
                        height is computed based on the heights of the tracks.
                        If given, the track height are proportionally scaled
                        to match the desired figure height.
  --title TITLE, -t TITLE
                        Plot title
  --outFileName OUTFILENAME, -out OUTFILENAME
                        File name to save the image, file prefix in case
                        multiple images are stored
  --fontSize FONTSIZE   Font size for the labels of the plot (default is 0.3 *
                        figure width)
  --dpi DPI             Resolution for the image in case the ouput is a raster
                        graphics image (e.g png, jpg) (default is 72)
  --trackLabelFraction TRACKLABELFRACTION
                        By default the space dedicated to the track labels is
                        0.05 of the plot width. This fraction can be changed
                        with this parameter if needed.
  --trackLabelHAlign {left,right,center}
                        By default, the horizontal alignment of the track
                        labels is left. This alignemnt can be changed to right
                        or center.
  --decreasingXAxis     By default, the x-axis is increasing. Use this option
                        if you want to see all tracks with a decreasing
                        x-axis.
  --version             show program's version number and exit

Citation

If you use pyGenomeTracks in your analysis, you can cite the following paper :

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications (2018) doi:10.1038/s41467-017-02525-w

Documentation

Our documentation provide examples, as well as the full list of possible parameters and guidelines for developers who would like to add a new track type.

External users

  • CoolBox is an interactive genomic data explorer for Jupyter Notebooks
  • Galaxy integration offers a graphical user-interface to create PGT plots. It is also possible to include PGT into workflows and automatic pipelines.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyGenomeTracks-3.5.tar.gz (66.1 kB view details)

Uploaded Source

Built Distribution

pyGenomeTracks-3.5-py2.py3-none-any.whl (92.8 kB view details)

Uploaded Python 2 Python 3

File details

Details for the file pyGenomeTracks-3.5.tar.gz.

File metadata

  • Download URL: pyGenomeTracks-3.5.tar.gz
  • Upload date:
  • Size: 66.1 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.2.0.post20200712 requests-toolbelt/0.9.1 tqdm/4.48.0 CPython/3.6.10

File hashes

Hashes for pyGenomeTracks-3.5.tar.gz
Algorithm Hash digest
SHA256 177d94152b66bfa857238448f38d36f785b0b8b7ad7e1a50107507f6c4abfad0
MD5 98feb09328b6940d3ac580efe768cc38
BLAKE2b-256 502c7e40fc5746852b604fbc963470498abe2b1f705c8b3d5b8c73eb80d73ad3

See more details on using hashes here.

Provenance

File details

Details for the file pyGenomeTracks-3.5-py2.py3-none-any.whl.

File metadata

  • Download URL: pyGenomeTracks-3.5-py2.py3-none-any.whl
  • Upload date:
  • Size: 92.8 kB
  • Tags: Python 2, Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.2.0.post20200712 requests-toolbelt/0.9.1 tqdm/4.48.0 CPython/3.6.10

File hashes

Hashes for pyGenomeTracks-3.5-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 271b3794a7c67534d8666c53879a98a84b2c31290029dfc5556fbb0df0ad0bec
MD5 0f99c6864845b1ee6b1943272779cdd1
BLAKE2b-256 1d2bd24b2ccfe44e80d31167c806beaa1fd1091aa8982aca4fcfff846058a604

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page