Shiny: Difference between revisions
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= Tips = | = Tips = | ||
[http://deanattali.com/blog/advanced-shiny-tips/ Shiny tips & tricks for improving your apps and solving common problems] by Dean Attali. | [http://deanattali.com/blog/advanced-shiny-tips/ Shiny tips & tricks for improving your apps and solving common problems] by Dean Attali. | ||
= Modularize your shiny apps = | |||
https://www.r-exercises.com/2018/10/15/modularize-your-shiny-apps-exercises/ | |||
= [http://withr.me/a-shiny-app-serves-as-shiny-server-load-balancer/ A Shiny-app Serves as Shiny-server Load Balancer] = | = [http://withr.me/a-shiny-app-serves-as-shiny-server-load-balancer/ A Shiny-app Serves as Shiny-server Load Balancer] = |
Revision as of 16:45, 15 October 2018
Preliminary
The following is what we see on a browser after we run an example from shiny package. See http://rstudio.github.com/shiny/tutorial/#hello-shiny. Note that the R session needs to be on; i.e. R command prompt will not be returned unless we press Ctrl+C or ESC.
More shiny examples can be found on https://github.com/rstudio/shiny-examples shiny-examples.
shiny depends on websockets, caTools, bitops, digest packages.
Q & A:
- Tutorial: http://wch.github.io/shiny/tutorial/
- Layout: http://shiny.rstudio.com/articles/layout-guide.html
Q: If we run runExample('01_hello') in Rserve from an R client, we can continue our work in R client without losing the functionality of the GUI from shiny. Question: how do we kill the job?- If I run the example "01_hello", the browser only shows the control but not graph on Firefox? A: Use Chrome or Opera as the default browser.
- Q: How difficult to put the code in Gist:github? A: Just create an account. Do not even need to create a repository. Just go to http://gist.github.com and create a new gist. The new gist can be secret or public. A secret gist can not be edited again after it is created although it works fine when it was used in runGist() function.
Deploy to run locally
Follow the instruction here, we can do as following (Tested on Windows OS)
- Create a desktop shortcut with target "C:\Program Files\R\R-3.0.2\bin\R.exe" -e "shiny::runExample('01_hello')" . We can name the shortcut as we like, e.g. R+shiny
- Double click the shortcut. The Windows Firewall will be popped up and say it block some features of the program. It does not matter if we choose Allow access or Cancel.
- Look at the command prompt window (black background console window), it will say something like
Listening on port 7510
at the last line of the console. - Open your browser (Chrome or Firefox works), and type the address http://localhost:7510. You will see something magic happen.
- If we don't want to play with it, we can close the browser and close the command console (hit 'x')too.
Deploy on cloud
https://www.r-bloggers.com/deploying-r-rstudio-and-shiny-applications-on-unbuntu-server/
Shiny server series part 1: setting up. It includes setting up A- and CNAME records on DigitalOcean.
Deploy on shinyapps.io
See Getting started with shinyapps.io page.
Limitations of the free account (5 applications, 25 active hours) on shinyapps.io.
Shinyapps.io can accept google account to sign up. I create an account and a test application/instance on
- https://taichimd.shinyapps.io/stock/ (quantmod, ggplot2, reshape2, magrittr, rvest packages were used)
- https://taichimd.shinyapps.io/tspgov (ggplot2, reshape2, magrittr, rvest, plotly)
The R packages our shiny app uses will be automatically downloaded by shinyapps.io service. See the package dependencies section on http://shiny.rstudio.com/articles/shinyapps.html.
After we run rsconnect() command to deploy our apps, a new subfolder rsconnect will be created under our app folder. I add this folder to .gitignore file.
For the shiny apps we uploaded to shinyapps.io, we can download them back. The download bundle will also include packrat subfolder (packrat.lock file and desc subfolder). See here for more about packrat.
Shiny server installation
Each app directory needs to be copied to /srv/shiny-server/ (which links to /opt/shiny-server/) directory using sudo.
The default port is 3838. That is, the remote computer can access the website using http://xxx.xxx.x.xx:3838/AppName.
RHEL/CentOS 7
https://www.vultr.com/docs/how-to-install-shiny-server-on-centos-7
Raspberry Pi
http://atceiling.blogspot.com/2017/12/raspberry-pi-r-languager-shiny-server.html
R
sudo nano /etc/apt/sources.list # deb http://archive.raspbian.org/raspbian/ stretch main sudo apt-get update sudo apt-get install r-base r-base-core r-base-dev
Shiny-server
sudo apt-get install cmake sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\"" git clone https://github.com/rstudio/shiny-server.git cd shiny-server mkdir tmp cd tmp DIR=`pwd` PATH=$DIR/../bin:$PATH PYTHON=`which python` $PYTHON --version cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DPYTHON="$PYTHON" ../ make mkdir ../build (cd .. && ./bin/npm --python="$PYTHON" install) (cd .. && ./bin/node ./ext/node/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js --python="$PYTHON" rebuild) sudo make install sudo ln -s /usr/local/shiny-server/bin/shiny-server /usr/bin/shiny-server sudo useradd -r -m shiny sudo mkdir -p /var/log/shiny-server sudo mkdir -p /srv/shiny-server sudo mkdir -p /var/lib/shiny-server sudo chown shiny /var/log/shiny-server sudo mkdir -p /etc/shiny-server cd /etc/shiny-server/ sudo wget http://withr.me/misc/shiny-server.conf sudo shiny-server http://192.168.X.XXX:3838
建立 server.R 及 ui.R 程式
cd /srv/shiny-server mkdir hello_shiny cd hello_shiny # 分別建立 server.R 及 ui.R
Running shiny server as non-root: run_as
- https://stackoverflow.com/questions/36201019/run-shiny-server-as-non-root
- https://support.rstudio.com/hc/en-us/articles/219044787-Root-requirements-for-Shiny-Server
- http://docs.rstudio.com/shiny-server/#run_as
Reverse proxy: Deploy your own shiny server
- http://qualityandinnovation.com/2015/12/09/deploying-your-very-own-shiny-server/
- Setting up RStudio Server, Shiny Server and PostgreSQL
Shiny https: Securing Shiny Open Source with SSL
- http://ipub.com/shiny-https/
- ShinyProxy, SHINYPROXY 1.0.2
- https://www.jasperginn.nl/shiny-server-series-pt3/
Example of embedding shiny in your web page
http://michaeltoth.me/popularity-of-baby-names-since-1880.html
The R Shiny packages you need for your web apps
http://enhancedatascience.com/2017/07/10/the-packages-you-need-for-your-r-shiny-application/
Shiny + Docker
- See this post. It uses the gui of Docker called Kitematic.
- https://hub.docker.com/r/rocker/shiny/ Don't run R Shiny as a non-root user.
- Shiny Server on Docker: CentOS 7 Edition
- https://github.com/rocker-org/shiny
- https://www.r-bloggers.com/dockerizing-a-shiny-app/
- https://github.com/keberwein/docker_shiny-server_centos7 (Shiny + RStudio servers)
shinydashboard
- http://rstudio.github.io/shinydashboard/
- Dashboards made easy
- Using Shiny with Scheduled and Streaming Data
flexdashboard
- The output can be a static HTML file or a dynamic HTML (using shiny, highcharter, viridisLite, ...)
- https://rmarkdown.rstudio.com/flexdashboard/
- Introducing flexdashboards. The gauge component is cool.
- Real example containing gauges https://gallery.shinyapps.io/cran-gauge/
shinytheme
shiny + databases: pool package
https://blog.rstudio.com/2017/11/17/pool-0-1-3/
tags, hyperlinks
- https://stackoverflow.com/questions/42047422/create-url-hyperlink-in-r-shiny
- Customize your UI with HTML
dates
- https://stackoverflow.com/questions/22834778/r-shiny-daterangeinput-format
- http://www.noamross.net/blog/2014/2/10/using-times-and-dates-in-r---presentation-code.html
websocket
http://illposed.net/jsm2012.pdf
CentOS
- https://www.vultr.com/docs/how-to-install-shiny-server-on-centos-7
- https://github.com/rstudio/shiny-server/wiki/CentOS-step-by-step-Installation-Instructions
- http://blog.supstat.com/2014/05/install-rstudio-server-on-centos6-5/
Gallery
- Shiny User Showcase
- http://www.showmeshiny.com/
- Example of using googleVis: http://shinyeoda.cloudapp.net/
- Integrate with Javascript: https://github.com/wch/shiny-jsdemo and https://github.com/trestletech/ShinyDash-Sample
- interactiveDisplay (Bioconductor package, there is a STOP Application button too): http://www.bioconductor.org/packages/release/bioc/html/interactiveDisplay.html
- Party vote characteristics at the New Zealand General Election 2014, More things with the New Zealand Election Study
- genSurv : An interactive web-based tool for survival analysis in genomics research. The paper and the source code.
- gene2drug
- Stock
- http://shiny.rstudio.com/tutorial/written-tutorial/lesson6/
- Stock Closing Price History.
- Multiple stocks.
- google (flash is required, not accurate eg DOW). msn (Nice).
- yahoo (French only).
- S&P500 Dashboard, Github source code
Persistent data storage in Shiny apps
http://deanattali.com/blog/shiny-persistent-data-storage/
Password protection
- http://ipub.com/shiny-password-protect/
- https://auth0.com/blog/adding-authentication-to-shiny-server/
- https://www.r-bloggers.com/password-protect-shiny-apps/
- Authentication of Shiny-server Application Using a Simple Method
Install all required R packages
http://padamson.github.io/r/shiny/2016/03/13/install-required-r-packages.html
Three R Shiny tricks to make your Shiny app shines (2/3): Semi-collapsible sidebar
Simulations
Tips
Shiny tips & tricks for improving your apps and solving common problems by Dean Attali.
Modularize your shiny apps
https://www.r-exercises.com/2018/10/15/modularize-your-shiny-apps-exercises/
A Shiny-app Serves as Shiny-server Load Balancer
Shinyloadtest tools for load testing Shiny applications
Shiny-server System Performance Monitoring for Open Source Edition
Real Shiny Examples
- CellMinerDB from NCI/NIH.
- voomDDA: Discovery of Diagnostic Biomarkers and Classification of RNA-Seq Data. https://peerj.com/articles/3890/
- Interactive analysis of metagenomics data
- ExpressionDB, An open source platform for distributing genome-scale datasets
- GREIN : GEO RNA-seq Experiments Interactive Navigator and the paper