Chapter 5 Shiny

5.1 Tencent log

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# Step1 Install R
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sudo apt-get install r-base-core

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# Step2 Install packages
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## Use R to install packages
install.packages("BiocManager")
BiocManager::install("shiny")

## Install shiny-sever
sudo apt-get install gdebi-core
wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.14.948-amd64.deb
sudo gdebi shiny-server-1.5.14.948-amd64.deb

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# Step3 Set shiny sever
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# check the condition of shiny sever
sudo systemctl status shiny-server.service

# After the end, the shiny user will appear, set the shiny user password
## Firstly, switch to root mode
sudo -i
## Then, set the password
sudo passwd shiny

## Third, add groups
sudo groupadd shiny-apps
sudo usermod -aG shiny-apps shiny
sudo usermod -aG shiny-apps ubuntu

## Fourth, change the owner of the specified file to the specified user or group
sudo chown -R shiny:shiny-apps /srv/shiny-server
sudo chmod g+w /srv/shiny-server
sudo chmod g+s /srv/shiny-server

## Fifth, go to shiny user
su - shiny

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# Step4 Configure .Rprofile
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vi .Rrofile

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# Step5 Configure .Renviron
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vi .Renviron
R_LIBS=/home/shiny/R_Library

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# Step6 Install R packages
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install.packages("BiocManager")
BiocManager::install("remotes")
BiocManager::install("shiny")
BiocManager::install("ggplot2")
BiocManager::install("dplyr")

library(shiny)
library(ggplot2)
library(dplyr)

remotes::install_github("Github-Yilei/ggcor")
remotes::install_github("hfang-bristol/XGR")
remotes::install_github("tuantuangui/MNet")

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# Step7 Shiny sets port 3838
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# Step8 cp the shiny project folders to /srv/shiny-server/
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cp -r MNet/ /srv/shiny-server/
sudo chown R shiny:shiny MNet/
  
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# Step9 Restart shiny server
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sudo systemctl restart shiny-server.service

## If an error occurs, check the log file
/var/log/shiny-server/

##If successful it displays the following contents
http:/124.221.255.21:3838/MNet

www.mnet.vip

5.2 Shiny app log

您可以将开发好的Shiny APP部署在自己的服务器上，或是将其部署在公共的平台（即shinyapps.io）上。这里仅分享后者。对于如何将Shiny APP部署到自己的服务器中，将在未来进行补充。 部署至shinyapps.io平台操作步骤:

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# Step1 在shinyapps.io官网上注册账号。您会被要求填写用户名
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# Step2 重新打开shinyapps.io官网，单击右上角Dashboard按钮（图1）。进入Dashboard界面（图2）后，单击左侧边栏Acccount > Tokens。您将在右侧主面板中看到Token和Secret信息。单击“Show”按钮，弹出对话框。
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# Step3 不要关闭该网页。现假设您的APP名称是"myapp"。在本地的文件浏览器中新建一个文件夹，名为"myapp"。确保该文件夹中有“app.R”文件，并且"app.R"文件的末尾要有shinyApp函数（或能返回与shinyApp函数相同类型的对象的函数）。
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# Step4 用RStudio打开文件"app.R"。在命令行窗口中输入runApp()。这一步称为本地测试。若您的Shiny APP成功运行，方可进行下一步。
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# Step5 运行以下代码。若报错提示您未安装某些包，则采用install.package安装相应的包即可。代码运行完成后，会自动弹出一个网页，网页内容即是您的Shiny APP，表明部署完成。
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if(!require(rsconnect)) install.packages("rsconnect")
rsconnect::setAccountInfo(name='Your Account',
                          token='Your Token',
                          secret='Your Secret')
#name, token, secret信息来源于Step2网页中的对话框
deployApp()

如果出bug：
library(BiocManager)
r=BiocManager::repositories()
#getOption("repos")[["CRAN"]] = "http://cran.r-project.org"
r[6] <- "http://cran.r-project.org"
options(repos =r)