In this package, we use opencpu server to do the data analysis and generate report. These functions are all in R/rmdtext.R. They are top wrappers of doing one-step analysis.
The rmarkdown template files are all in \inst\rmd by default. The rmarkdown template needs very often update (this pacakge is still under active development), therefore we let the r wrapper function read the rmarkdown files directly from github/gitlab. By doing this, the opencpu server do not need to update the package each time when there is a update of the rmarkdown template. Once the pacakge is relative stabilized, the wrapper function will turn to using rmardown files locally.
How to setup? 1--In order to use this function, users need to have an opencpu server setup first (check the opencpu website for the installation). You need to write down the api url, like http://ipv4-address/ocpu/library/rmdocpu/R/sub-function-name It would be better to have one or even more opencpu servers as backup.
2--Install this rmdocpu package from the github
devtools::install_github("ningzhibin/rmdocpu")
How to use?
First choice is using it in R, as demoed in the R_curl_ocpu_test_debug.R in the rmd folder Once you know the principle how to upload (post) your data table, and download the report file (curl), you will be able to adapt this in to java, python, javascripit in html.
Requires Ubuntu 20.04 (Focal) or 18.04 (Bionic)
On a fresh system, like AWS EC2.
sudo add-apt-repository -y ppa:opencpu/opencpu-2.2
sudo apt-get update
sudo apt-get upgrade
Installs OpenCPU server
sudo apt-get install -y opencpu-server
Done! Open http://yourhost/ocpu in your browser
In order to instal RCurl pacakge in R, you need to install curl on Linux system first
sudo apt -y install libcurl4-openssl-dev
In order to do rmarkdown by opencpu, an pandoc on system level needs to be installed.
sudo apt-get install -y pandoc pandoc-citeproc
Then start R as root
sudo R
Then install R oackages from either CRAN or Github (requries devtools)
install.packages(c("RCurl","devtools","ggplot2"，"rmarkdown","pheatmap","dbplyr"，"Data.table","dbplyr"，"dplyr","DT"，"ggforce","ggfortify"，"ggrepel","gplots","Hmisc","plotly","reshape2"，"rrcov","rrcovNA","rrcovNA","shinyjs","shinyWidgets","vegan","scatterplot3d"))
devtools::install_github("talgalili/d3heatmap")
devtools::install_github("ningzhibin/rmdocpu")