5.2 HiGlass

iGlass

1. Distinguished features

2. Get Started

   2.1. Concept1: Anatomy of HiGlass view board

   2.2. Concept2: Track types

HiGlass is a web-based tool for exploring genomic contact matrices and tracks.HiGlass is a viewer for HiC and other genomic data. It can be used online or run locally with private data(docker). It uses a client-server architecture to allow users to view large contact matrices in a web browser. Publication

Distinguished features

• smooth navigation, continuous interface

• multiple datasets, map link, auto sync, optional sync(by loc or zoom)

• various representations (horizontal triangular, vertical triangular, 2D heatmap, 1D track)

• highly configurable

• diff scale of data (linear, log)

• export (SVG, JSON config) with metadata rather than lengthy url records everything

• share data local net or publicly

• locally or web databased

Get Started

We will unfold the main features of Higlass as follows: 1. Show anatomy of HiGlass view board. 2. Show the category of tracks which represents multi-omics data. 3. Show how to upload your own datasets, which is the most important part.

Just a reminder, all the information illustrated here can be learned from: [1] [2] We're trying our best to walk you through the gist of this software within the least of your time by our understanding and reorganized materials :D

Concept1: Anatomy of HiGlass view board

"Tracks" and "Views" are the two most basic ingredients of a Higlass view. Each view is composed of a set of tracks which share common axes. All view operations can be found here.

• A view is simply the area with a gray bar at the top. A view can be understood as a canvas, and tracks are figures on this canvas. There is nothing else. Tracks are of various types and will be elaborated later.

Operations for Views includes:

a) Resize views before adding(copying) new views.

We want to create four views in total showing two different data sets. To start, we'll resize the current view and replicate it twice

b) Cross-view operations

transferring or linking parameters (such as scaling factor and location) between two separate views. Examples: Let's make sure the top two rows and the bottom two rows always show the same locations as each other.

c) View synchronization

location or zoom or both(just for two views at a time, if you want to sync many views, you have to do it pair by pair).

d) Go to interesting location

e) Project viewport

f) Unclock and close

Concept2: Track types

Common feeatures for every track:

• Label (Positions, color, opacity, background color).

• Color mmap:from matplotlib or custom defined. Configure Series --> Color map.

• Zoom limit.

Different tracks( Icon | Higlass-wiki | Special-features):

	Rectangular heatmap	Transforms(ICE,KR,etc)-see Chap3.2Value scaling(linear,log)Zoom limit(5k-20M)
	Horizontal and vertical heatmaps	45° roatate of 2D heatmapCan be added lef,right,top,bottomDefault faces: down & right(can be fpliiped)
	Line	Scaling(linear,log)Label positionAxis positionStroke color
	Chromosome grid	Grid on chromosome scaleUser can define the scale
	Chromosome axis	Diff scale for zoom in&outUser can define the scale
	Viewport projection	show one dataset with two different resolutionsOpen from view
	Gene annotations	Developer docs

Upload your own data

In most cases, people would like to upload their own data for different tracks. To embed your own data and present them on your own browser, you should follow these steps.

• Download docker

• Install python package: cooler and clodius

• Capsule your data into docker container

Install docker:

Docker is a computer program that performs operating-system-level virtualization also known as containerization. It resembles VM in some ways but much thinner. Instead of virtualizing hardware, containers rest on top of a single Linux instance. This means you can leave behind the useless elements, leaving you with a small, neat capsule containing your application. Higlass also embrace docker.

To install docker, you can first download and install it on your local machine or server docker CE(community edition). Win and Mac users can directly use it by openning it. Linux users need to start the service by running the following command with root privileges.

service docker start

Install & Run higlass container

Next, pull down the higlass-container from higlass-docker repository (tutorial). After that, you can try to create an instance on that container and open your own higlass website in your own browser (tutorial). However, you may get confused about some commands if you're new to Docker. To solve this, you can refer to docker's docs or to make life easier: Docker cheat sheet.

docker pull gehlenborglab/higlass 
# If no version tag is specified, docker will download the latest.

One important thing is that you can not change parameters of an already setup container, you have to stop it first, remove that and create a new one. This also suggests that we'd better not put your data into a container, instead, we store the data locally and map it to a different container by docker --run -volume.

docker stop higlass-container
docker rm higlass-container

docker run --detach \ # start the container background, it will last until you rm your container
           --publish 8888:80 \  # map a container’s port(80) to the host(8880) so that you can visit it with localhost:8888
           --volume ~/hg-data:/data \   # map local data dir ~/hg-data to container dir /data
           --volume ~/hg-tmp:/tmp \
           --name higlass-container \  # name of your container
           gehlenborglab/higlass

Here you go, if you intsall docker on your own computer then you can visit your higlass by localhost:8888.com. If you install docker on a server with IP:AA:BBB:CC:DD, then with url AA:BBB:CC:DD:8888 you can see your own viewer on your browser.

Create your own tracks data

You can use your own data to substitute tracks with specific format and datatype. Refer to here for more details.

Tracks	Tools	Filetype
Contact matrix	cooler	cool
Line	clodius	BigWig\bedGraphs
TAD annotation	clodius	bed-like
Gene annotation	clodius	bed-like

Tools: Cooler

Cooler is a support library for a sparse, compressed, binary persistent storage format, called cool, used to store genomic interaction data, such as Hi-C contact matrices. To get started you can try this walkthrough. Basically, this tool includes some useful functions listed below (not all included).

• Do contact matrix balancing

• Create and load contact matrix

• generate zoom levels for Higlass viewer

• Display a contact matrix

• ...