In vdumeaux/mixtR: Matched Interaction across Tissues (MIxT) data analysis

The MIxT web application is designed for exploring the results from the MIxT analysis comparing transcriptional profiles from two matched tissues across individuals.

For a more detailed description of the ideas and design of the MIxT web application please refer to "Building Applications For Interactive Data Exploration In Systems Biology" by Fjukstad et al. and the source code here.

The mixtApp package

To build the MIxT web application, your will need the mixtApp, a wrapper package calling the mixtR functions and storing pre-computed data objects.

If you want to modify the data, you can easily rebuild the web application as follow.

First clone down the mixtApp repository:

$ git clone https://github.com/vdumeaux/mixtApp.git

Then cd into the mixtApp directory and add the pre-computed data outputs you obtained from the mixtR package in the data/ folder. To save the data objects, you can modify the data url in data-raw/datasets.R and run the script:

$ R -f data-raw/datasets.R

You can also replace the data objects manually. Please make sure that the objects name and format match the description detailed in the mixtR vignette.

You then need to rebuild the mixtApp package containing the new data using

$ R CMD INSTALL .

Next up is building the docker container with your new mixtApp package.

Still in the mixtApp/ directory, run:

docker build -t compute-service .
docker run --name=compute-service -t compute-service

which build and run the container. It should appear with the docker ps command:

 docker ps
CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS               NAMES
08c9889b705e        compute-service     "/bin/sh -c 'go ru..."   4 seconds ago       Up 4 seconds        80/tcp              compute-service

The compute service is now running, so next up is starting the web application container. This is luckily a one liner:

docker run -p 8000:80 --link compute-service -e COMPUTE_SERVICE=compute-service:80 --name=mixt -t fjukstad/mixt-stroma

That's it! You can now visit the application that displays you own data running on localhost:8000.

If you need more details on the docker commands you can have a look atdocs.docker.com.

vdumeaux/mixtR documentation built on May 3, 2019, 4:58 p.m.