`_.
.. |higlass-python| replace:: **higlass-python**
.. _higlass-python: https://github.com/higlass/higlass-python
|higlass-docker|_ - Our docker
container consists all packages that are required to run HiGlass as a persistent server to make the installation process easier.
An update in any of the above repositories will be reflected in an update in
the docker container. The versions of all the components is accessible at
https://higlass.io/version.txt
.. |higlass-docker| replace:: **higlass-docker**
.. _higlass-docker: https://github.com/higlass/higlass-docker
Track types
~~~~~~~~~~~
HiGlass supports both 1D and 2D track types that can be arranged in views to show desired
combinations of data.
.. raw:: html
.. figure:: img/bedlike-track-thumb.png
:height: 72px
:align: center
:figwidth: 100px
Bed-like intervals
.. figure:: img/gene-annotations-track-thumb.png
:height: 72px
:align: center
:figwidth: 100px
Gene annotations
.. figure:: img/chromosome-labels-thumb.png
:align: center
:figwidth: 100px
Chromosome labels
.. figure:: img/line-track-thumb.png
:align: center
:figwidth: 100px
Line
.. figure:: img/point-track-thumb.png
:align: center
:figwidth: 100px
Point
.. figure:: img/horizontal-heatmap-thumb.png
:align: center
:figwidth: 100px
Horizontal heatmap
.. figure:: img/horizontal-2d-rectangle-domains-thumb.png
:align: center
:figwidth: 100px
Horizontal rectangle domains
.. figure:: img/heatmap-track-thumb.png
:height: 72px
:align: center
:figwidth: 100px
Heatmap
.. figure:: img/chromosome-grid-thumb.png
:height: 72px
:align: center
:figwidth: 100px
Chromosome grid
.. raw:: html
It can be used to display a variety of `track types `_ populated with data from
different file formats.
.. figure:: img/higlass-heatmap-screenshot.png
:align: right
:figwidth: 300px
A screenshot of HiGlass displaying a Hi-C contact matrix along with tracks
for gene annotations chromosome labels.
.. figure:: img/higlass-dual-genome-browser-screenshot.png
:align: right
:figwidth: 300px
A screenshot of HiGlass displaying a context-detail type view of two
regions of the mouse genome. The locations of the two detail regions on the
bottom are highlighted in the context view on top.
Technology
~~~~~~~~~~
HiGlass is built with a variety of different open source components. The most
crucial are listed below.
- `D3.js `_ - an outstanding library for online data
visualization. We make heavy use of D3's `scales
`_, `zoom behavior
`_ and `brush behavior
`_.
- `Pixi.js `_ - a fast, easy to use and most
importantly, well-documented library for drawing scene graphs on html
canvases. Oh, and it has WebGL support. We use Pixi to quickly render track
data and perform updates on zooming and panning.
- `React `_ - a widely used library for
managing state within web applications. We use React to manage the
user-interface components and lay out the positions of the views and tracks.
.. toctree::
:hidden:
:glob:
tutorial
javascript_api
jupyter
data_preparation
track_types
views
higlass_server
higlass_docker
view_config
plugin_track
plugin_datafetcher
available_to_plugins
developer
troubleshooting
.. toctree::
:hidden:
:glob:
:titlesonly:
releasenotes