RPath: A Web-App for Biologic Pathway Exploration

RPath is a web application for the end-to-end manipulation of biologic pathways. Its divided in three modules: built-in search engine via the Pathway Commons' API, analysis techniques using SPARQL queries and graph visualization.

Download

To download RPath just clone the Git repository hosted in GitHub:

$ git clone https://github.com/benhid/rpath.git

Prerequisites

• R 3.4

Launching RPath will install any missing packages.

Usage

To start up the app download the source code, then go to the R folder and run the app.R file.

Or by just running one command:

# install.packages("shiny")
shiny::runGitHub("RPath", "benhid", subdir = "R/")

Using Docker

It's possible to run the web-app inside a Docker container. First, build the image from the Dockerfile:

sudo docker build -t khaosresearch/rpath .

e.g.

sudo docker run -it -p 3838:3838 khaosresearch/rpath

Custom modules

Every module in RPath is listed on the modules folder. Each of them contains at least two files: <module_name>.R and <module_name>Panel.R. The first one will be used on the server-side of the app. The other one defines the user interface.

In order to RPath to load a new module, edit the file modules.R to insert the name of the module:

# Modules to be loaded.
# Each module must consists of one directory with two files: 
#     ./R/modules/<module_name>
#       |-- <module_name>.R
#       '-- <module_name>Panel.R.
modules.tabs <- c("search", "data_summary", "visualization", "user_manual")

# Modules to be disabled until search is perform.
# This list consists of the values of the tab panels.
#     e.g. tabPanel("Visualization", value = "visTab", ...)
modules.hidden.tabs <- c("analysisTab", "visTab")

After that, to get the URL from the selected pathway of the search process, use:

URL <- getRowFromDf()