Peax

A Visual Pattern Explorer For Epigenomic Data Using Unsupervised Deep Representation Learning

Epigenomic data expresses a rich body of diverse patterns that help to identify regulatory elements like promoter, enhancers, etc. But finding these patterns reliably genome wide is challenging. Peax is a tool for interactive visual pattern search and exploration of epigenomic patterns based on unsupervised representation learning with convolutional autoencoders. The visual search is driven by manually labeled genomic regions for actively learning a classifier to reflect your notion of interestingness.

Citation: Lekschas et al., Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning, Computer Graphics Forum, 2020, doi: 10.1111/cgf.13971.

More background information is available at peax.lekschas.de.

Installation

Requirements:

• Conda >= 4.8

git clone https://github.com/Novartis/peax peax && cd peax
conda env create -f environment.yml && conda activate px
make install

Do not fear, make install is just a convenience function for setting up conda and installing npm packages.

Notes:

• If you're a macOS user you might need to brew install libpng and openssl for the pybbi package (see here) and xz for pysam (if you see an error related to lzma.h).

Overview

Peax consists of three main parts:

1. A server application for serving genomic and autoencoded data on the web. [/server].
2. A user interface for exploring, visualizing, and interactively labeling genomic regions. [/ui].
3. A set of examples showing how to configure Peax and build your own. [/examples]

Data

We provide 6 autoencoders trained on 3 kb, 12 kb, and 120 kb window sizes (with 25, 100, and 1000 bp binning) on DNase-seq and histone mark ChIP-seq data (H3K4me1, H3K4me3, H3K27ac, H3K9ac, H3K27me3, H3K9me3, and H3K36me).

You can find detailed descriptions of the autoencoders at zenodo.org/record/2609763. When you follow the Quick Start instructions, you will automatically download the related autoencoders.

Quick start

Peax comes with 6 autoencoders for DNase-seq and histone mark ChIP-seq data and several example configurations for which we provide convenience scripts to get you started as quickly as possible.

For instance, run one of the following commands to start Peax with a DNase-seq track for 3 kb, 12 kb, and 120 kb genomic windows.

Command	Window Size	Step Freq.	Chromosomes
make example-3kb	3 kb	2	21
make example-12kb	12 kb	3	20-21
make example-120kb	120 kb	6	17-21

Note: The first time Peax is started it will precompute the datasets for exploration. This can take a few minutes depending on your hardware. Also, these demos will only prepare the above mentioned chromosomes, so don't try to search for patterns on another chromosome. It won't work! For your own data you can freely configure this of course.

The scripts will download test ENCODE tracks and use the matching configuration to start the server. More examples are described in /examples.

Get Started

In the following we describe how you can configure Peax for your own data.

Configure Peax with your data

Next, you need to configure Peax with your data to tell it which tracks you want to visualize in HiGlass and which of those tracks are encodable using an (auto)encoder.

The fastest way to get started is to copy the example config:

cp config.json.sample config.json

The config file has 10 top level properties:

Field	Description	Dtype
encoders	List of encoders.	list
datasets	List of tracks.	list
coords	Genome coordinates. Peax currently supports hg19, hg38, mm9, and mm10	str
chroms	Chromosomes to to be searched. If omitted all chromosomes will be prepared for searching.	list
step_freq	Step frequency of the sliding window approach. E.g., given an encoder with window size 12 kb, a step frequency of 6 means that every 2 kb a 12 kb window will be extracted from the bigWig.	int
db_path	Relative path to the sqlite db for storing searches.	str
normalize_tracks	If true the y-scale of tracks within a window will be normalized to the minimum and maximum value. This is useful for exploring differential signal.	bool
variable_target	If true the window with the highest prediction probability will be shown in the query view.	bool
classifier	The class name of an SciKit Learn Classifier	str
classifier_params	A dictionary of parameters to customize the classifier	obj

The main parts to adjust are encoders and datasets. encoders is a list of (auto)encoder definitions for different datatypes.T here are two ways to configure an (auto)encoder: (a) point to a pre-defined autoencoder or (b) configure from scratch.

Assuming you want to use a predefined autoencoder all you have to do is

Field	Description	Dtype
content_type	Unique string identifying the autoencoder in the configuration file	str
from_file	Relative path to the encoder configuration file.	str

Example:

{
  "content_type": "histone-mark-chip-seq-3kb",
  "from_file": "examples/encoders.json"
}

The encoder configuration file is a dictionary with the top level keys acting as the identifier and need to match content_type above. Given the example from above the file could look like this:

{
  "histone-mark-chip-seq-3kb": {},
  "dnase-seq-3kb": {}
}

See [encoders.json](encoders.json) for an example. The specific definition if an autoencoder is the same as described in the following.

To configure an autoencoder from scratch you need to provide a dictionary with the following required format:

Field	Description	Defaults	Dtype
autoencoder	Relative path to your pickled autoencoder model. (hdf5 file)		str
encoder	Relative path to your pickled encoder model. (hdf5 file)		str
decoder	Relative path to your pickled decoder model. (hdf5 file)		str
content_type	Unique string describing the content this autoencoder can handle. Data tracks with the same content type will be encoded by this autoencoder.		str
window_size	Window size in base pairs used for training the autoencoder.		int
resolution	Resolution or bin size of the window in base pairs.		int
latent_dim	Number of latent dimensions of the encoded windows.		int
input_dim	Number of input dimensions for Keras. For 1D data these are 3: samples, data length (which is window_size / resolution), channels.	3	int
channels	Number of channels of the input data. This is normally 1.	1	int

Note that if you have specified an autoencoder you do not need to provide separate encoder and decoder models.

Example:

{
  "encoder": "path/to/my-12kb-chip-seq-encoder.h5",
  "decoder": "path/to/my-12kb-chip-seq-decoder.h5",
  "content_type": "histone-mark-chip-seq",
  "window_size": 12000,
  "resolution": 100,
  "channels": 1,
  "input_dim": 3,
  "latent_dim": 12
}

Datasets require the following format:

Field	Description	Dtype
filepath	Relative path to the data file (bigWig or bigBed).	str
content_type	Unique string describing the content this dataset. If you want to search for patterns in this track you need to have an autoencoder with a matching content type.	str
id	A unique string identifying your track. (Optional)	str
name	A human readable name to be shown in HiGlass. (Optional)	str

Example:

{
  "filepath": "data/chip-seq/my-fancy-gm12878-chip-seq-h3k27ac-fc-signal.bigWig",
  "content_type": "histone-mark-chip-seq",
  "uuid": "my-fancy-gm12878-chip-seq-h3k27c-track",
  "name": "My Fancy GM12878 ChIP-Seq H3k27c Track"
}

Start Peax

First, start the Peax server to serve your data.

Note: The first time you run Peax on a new dataset all the data will be prepared! Depending on your machine this can take some time. If you want to track the progress activate the debugging mode using -d.

python start.py

Now go to http://localhost:5000.

To start.py script supports the following options:

usage: start.py [-h] [-c CONFIG] [--clear] [--clear-cache]
                [--clear-cache-at-exit] [--clear-db] [-d] [--host HOST]
                [--port PORT] [-v]

Peak Explorer CLI

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        path to your JSON config file
  --clear               clears the cache and database on startup
  --clear-cache         clears the cache on startup
  --clear-cache-at-exit
                        clear the cache on shutdown
  --clear-db            clears the database on startup
  -d, --debug           turn on debug mode
  --host HOST           customize the hostname
  --port PORT           customize the port
  -v, --verbose         turn verbose logging on

The hostname defaults to localhost and the port of the backend server defaults to 5000.

In order to speed up subsequend user interaction, Peax initially prepapres all the data and caches that data under /cache. You can always remove this directory manually or clear the cache on startup or at exist using the --clear as specified above.

---

Development

Handy commands to keep in mind:

• make install installs the conda environment and npm packages and builds the UI
• make update updates the conda environment and npm packages and rebuilds the UI
• make build builds the UI
• python start.py starts the Flask server application for serving data
• [/ui]: npm install installs and updates all the needed packages for the frontend
• [/ui]: npm build creates the production built of the frontend
• [/ui]: npm start starts a dev server with hot reloading for the frontend

To start developing on the server and the ui in parallel, first start the backend server application using ./start.py and then start the frontend server application from ./ui using npm start. Both server's watch the source code, so whenever you make changes to the source code the servers will reload.

Configuration

There are 2 types of configuration files. The backend server configuration defines the datasets to explore and is described in detail above.

Additionally, the frontend application can be configured to talk to a different backend server and port if needed. Get started by copying the example configuration:

cd ui && cp config.json.sample config.json

By default the server is dynamically set to the hostname of the server running the frontend application. I.e., it is assumed that the backend server application is running on the same host as the frontend application. The port of the server defaults to 5000.

Start the backend and frontend apps

For development the backend and frontend applications run as seperate server applications.

# Backend server
./start.py --debug --config path/to/your/config.json

# Frontend server
cd ui && npm start