cytoscape-automation

Cytoscape Automation for Script Writers in R

Collection of sample scripts and notebooks that provide support for automation.

Visit the collection of Rmd notebooks to browse and download content interactively.

Also see RCy3 for a set of R functions to facilitate Cytoscape automation.

Developer Notes

1. Collect Rmds in the notebooks directory to be included in the Cytoscape Rmd Notebook menu system.
2. In RStudio, open a project with a working directory at cytoscape-automation/for-scripters/R/.
3. Update _site.yml to include any new or updated entries. Each item in the table of contents is described by two lines, for text label and href:

   - text: "RCy3 use cases"
     href: RCy3-use-cases.nb.html
   

4. Build the .nb.html files and update index.html and site_libs with this command:

lapply(list.files("notebooks","*.Rmd"), function(x) rmarkdown::render(paste("notebooks",x,sep="/")))
rmarkdown::render("notebooks/index.Rmd","html_document")

1. Commit and push updated files to make updated notebooks avalable.

2. Update Colab notebooks in colab folder.

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