Dash Bio

Dash Bio is a suite of bioinformatics components built to work with Dash.

Announcement: https://medium.com/@plotlygraphs/announcing-dash-bio-ed8835d5da0c

Demo: https://dash-gallery.plotly.host/Portal/?search=Bioinformatics

Documentation: https://dash.plotly.com/dash-bio

Components

The Dash Bio components each fall into one of three categories:

Custom chart types
Sequence analysis tools
3D rendering tools

Custom chart types

Dash Circos
Dash Clustergram
Dash Manhattan Plot
Dash Needle Plot
Dash Volcano Plot

Sequence analysis tools

Dash Alignment Chart
Dash Onco Print
Dash Forna Container
Dash Sequence Viewer

Visualization tools

Dash Mol2D
Dash Mol3D
Dash Speck
Dash Ngl

Using Dash Bio

It's easy to add a fully interactive chromosomal, molecular or genomic visualization to your Dash app by simply including the Dash Bio component into your app layout as follows:

import urllib.request as urlreq
from dash import Dash, html
import dash_bio as dashbio

app = Dash(__name__)

data = urlreq.urlopen(
    'https://raw.githubusercontent.com/plotly/dash-bio-docs-files/master/alignment_viewer_p53.fasta'
).read().decode('utf-8')

app.layout = html.Div([
    dashbio.AlignmentChart(
        id='my-default-alignment-viewer',
        data=data
    )
])

if __name__ == '__main__':
    app.run_server(debug=True)

See the Dash Bio documentation for more components and examples.

Run Dash Bio in a JupyterLab environment

Create a virtual environment:

The following steps require a virtual environment tool to be installed on your computer: pip install virtualenv

a. On macOS and Linux: python3 -m venv env

b. On Windows, enter: py -m venv env
Activate your new environment:

a. On macOS and Linux, enter: source env/bin/activate

b. On Windows, enter: .\env\Scripts\activate
Install required libraries (make sure you have pip installed with pip help):
```
pip install dash dash-bio pandas numpy Jupyterlab
```
To run Dash inside Jupyter lab:

a. Install jupyter-dash: pip install jupyter-dash

b. Enter jupyter lab build

(Note: This step requires Node.js and NPM installed on yourcomputer. To check if Node and NPM are installed, enter node -v and npm -v in your terminal. For install instructions see nodejs.org.

To display Plotly figures in JupyterLab:

pip install jupyterlab "ipywidgets>=7.5”
jupyter labextension install jupyterlab-plotly@4.14.3

Start JupyterLab by typing: jupyter lab

Important: JupyterLab must be run within the virtual environment that was previously activated.

For more on running a Dash app in Jupyter Lab visit Getting Started with Jupyter Dash.

Dash

Learn more about Dash at https://plotly.com/products/dash/.

Consulting and OEM

For inquiries about Dash app development, advanced OEM integration, and more, please reach out.

Contributing and Local Development

If you would like to contribute to this repository, or run demo apps and tests, please refer to the contributing guidelines.

plotly / dash-bio

readme