The mixtApp R package provides the data and statistical analyses used in the compute service for the MIxT web application (Matched Interactions Across Tissues - blood:tumor example).
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.
If you want to modify the data being used in the web application you'll have to rebuild the mixtApp package yourself, and start the different services manually.
First clone down the mixtApp repository:
$ git clone https://github.com/vdumeaux/mixtApp.git
Install dependencies in R
install.packages("devtools")
install.packages("ggplot2")
install.packages("BiocManager")
BiocManager::install("Biobase")
install.packages("DBI")
install.packages("RSQLite")
BiocManager::install("AnnotationDbi")
BiocManager::install("GO.db")
install.packages(c("latticeExtra","Hmisc", "reshape"))
BiocManager::install(c("illuminaHumanv3.db", "illuminaHumanv4.db"))
BiocManager::install(c("limma"))
install.packages(c("WGCNA","animation", "plyr", "dplyr", "igraph", "GGally", "network", "sna"))
BiocManager::install(c("breastCancerVDX", "hgu133a.db"))
BiocManager::install(c("genefu", "iC10"))
BiocManager::install("preprocessCore")
$ cd mixtApp
# modify the data-raw/datasets.R file to load your data.
$ R -f data-raw/datasets.R
$ R CMD INSTALL .
Data must be formatted as described in the mixtR package.
Next up is building the compute service container with your new mixtApp package.
Still in the mixtApp/ directory, run:
docker build -t compute-service .
which build the container for you. Now you can start it up to accept requests on
port 8787 by running
docker run --name=compute-service -t compute-service
and 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 lucily one liner:
docker run -p 8000:80 --link compute-service -e COMPUTE_SERVICE=compute-service:80 --name=mixt -t fjukstad/mixt
That's it! You can now visit the application running on localhost:8000.
If you need more details on the docker commands you can have a look atdocs.docker.com.