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functree-ng's Introduction

FuncTree 2

MIT License

FuncTree is a web application that allows users to map omics data onto a pre-defined radial tree (e.g. based on the KEGG brite functional hierarchy) to help them quickly and comprehensively understand the functional potential of their data, and to develop further hypothesis and scientific insights.

Installation

Clone this repository and change directory to functree-ng:

$ git clone --recursive https://github.com/yamada-lab/functree-ng.git
$ cd functree-ng

Building and running the application

Using Docker and Docker Compose (preferred and supported way)

Execute the command below. docker-compose will automatically set up Docker containers:

$ docker-compose build
$ docker-compose up

Then open http://localhost:8080 in your web browser.

Automatic transpilation, for dev mode only (optional)

To enable automatic transpilation of ECMAScript and SCSS in dev mode, enter the docker instance

docker exec -it functree-ng_app_1 /bin/bash

then issue the following commands

yarn babel:watch
yarn sass:watch

Manual installation (unsupported, use at your own risk)

Requirements
  • Python 3
  • Node.js
  • MongoDB

Install dependencies and build the application:

$ pip3 install -r requirements.txt
$ npm install yarn --global
$ yarn run install-depends
$ yarn run install-devDepends
$ yarn run bower install
$ yarn run build

Start up the application:

$ uwsgi --ini uwsgi.ini

Then open http://localhost:8080 in your web browser.

Configuration

To configure the behavior of the application, create instance/config.py with the same format as functree/config.py.

Loading of functional annotations from external sources (optional)

  1. Download generate-external-mapping.sh and edit LIST_HOME to match the location of your local KEGG distribution.
  2. Run the script to generate the external_annotation.map file.
  3. Add external_annotation.map to /app/functree/static/data/ortholog_mapping/ (See the docker-compose.yml services:app:volumes for details)
  4. Log into the admin console (e.g. http://localhost:8080/admin), then click the 'Update annotation mapping' link.

Publications

  • Darzi Y, Yamate Y, Yamada T. FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. Bioinformatics, btz245. 20 April 2019; DOI: 10.1093/bioinformatics/btz245; PubMed PMID: 31004476.

License

FuncTree 2 is released under the MIT License.

functree-ng's People

Contributors

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Watchers

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Forkers

yutayamate karenfushimi khemlalnirmalkar standardgalactic scottdaniel

functree-ng's Issues

Use data from Ghost/KOfam-KOALA

I would like to display the KEGG annotations for strains on the functree KEGG dendrogram (I like it a lot). I get my KEGG annotations from KOfamKOALA (could be GhostKOALA). I can see how the data I get back from the KEGG mapper Pathway and Module (which show the KEGG annotations of my predicted proteins e.g for a genome) might be mapped to the input format for functree/functree-2 with a value based on the number of genes assigned to each KEGG category.
E.g.
KOALA data Functree input
Carbohydrate metabolism
00010 Glycolysis / Gluconeogenesis (18) --> n-map00010 tab v-0.0
K00134 HPA006_002788 n-K00134 tab v-1.0
K00138 HPA006_001058, HPA006_002801 n-K00138 tab v-2.0
K00163 HPA006_001900 n-K00163 tab v-1.0
K00174 HPA006_001700 n-K00174 tab v-1.0
K00175 HPA006_001701 etc.
But I can't see how to easily achieve that transformation - but neither do I understand, looking at the input data files for Streptomyces Mycobacteria and Ecoli how, or from what data, those values were calculated. My data input would look very different.
Is it possible to add more explanation on how to generate input data? And for me, how to input data for multiple strains as per your Streptomyces/Mycobacteri/Ecoli comparison.
Thanks

functree2 webpage is not available

Hi,
I find Functree2 very useful for my datasets but from last one-week webpage is not working,
whenever I upload something it says the page is not available or ajax error.
I am using this site https://bioviz.tokyo/functree2/
Please can you check what wrong with the page or something I need to try,
I will look forward to your response,
Thanks,
Khem

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