CellChat Shiny App

This is CellChat's Shiny app docker container or standalone shiny app for our Cell-Cell Communication Atlas Explorer, which allows interactive exploration of the cell-cell communication that are analyzed by our CellChat R-package.

Running CellChat Shiny docker container:

• Step I: Please install docker if not on your system, and save your CellChat object from R/Rstudio as cellchat.rds using saveRDS().

• Step II: Download the prebuilt container to your system by running the command below in the terminal

docker pull ucigenomics/cellchatshiny:beta

• Step III: Run the cellchatshiny docker container by running the example command below in the terminal

docker run --name cellchatshiny -p 2020:3838 -d --restart unless-stopped -v /PATH_to_File/cellchat.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

• Step IV: Access the CellChat app by simply clicking the url or pasting the url into your browser: http://localhost:2020/Cellchat

NB: In Step III, you MUST specify the absolute path to the cellchat.rds file you saved by modifying the part /PATH_to_File/cellchat.rds in the above command.

Running multiple CellChat Shiny apps

To open two apps for simultaneously exploring cell-cell communication from two datasets, you would need to open a new instance of docker run, and assign a different container name (--name) and also host port (-p XXXX:3838). For example, here we create two apps for two CellChat objects cellchat_humanSkin_NL.rds and cellchat_humanSkin_LS.rds by running the command below in the terminal

docker pull ucigenomics/cellchatshiny:beta

docker run --name cellchatshiny_NL -p 2020:3838 -d --restart unless-stopped -v /Users/suoqinjin/Documents/CellChat/tutorial/cellchat_humanSkin_NL.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

docker run --name cellchatshiny_LS -p 2021:3838 -d --restart unless-stopped -v /Users/suoqinjin/Documents/CellChat/tutorial/cellchat_humanSkin_LS.rds:/srv/shiny-server/Cellchat/cellchat.rds ucigenomics/cellchatshiny:beta

We then can access the two CellChat apps using the two urls: http://localhost:2020/Cellchat and http://localhost:2021/Cellchat

Running CellChat standalone shiny app:

Currently this standalone shiny app can be only used in Linux system.

• Setup your shiny server and create a Cellchat subdirectory under '.../shiny-server/' and then copy global.R, server.R, and ui.R from this repository to the '.../shiny-server/Cellchat' directory.
• Generate your Cellchat object from R/Rstudio and save the object as 'cellchat.rds' file and copy this rds file to the same '.../shiny-server/Cellchat' directory
• Run the shiny server and open the Cellchat app from the Cellchat sublocation of the server url. e.g. 'http://localhost:3838/Cellchat'

Help or Suggestion

If you have any question, comment or suggestion, please post it in the 'Issues' section or contact cellchat.package@gmail.com.

Docker command

The full docker commands are list here. Below are several common used.

• docker run: Run a command in a new container
• docker ps: List all containers
• docker stop: Stop one or more running containers
• docker rm: Remove one or more containers