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Linked_subdirectories
generate_data
html
www
ReadMe.Rmd
ReadMe.html
ReadMe.md
ReadMedata.Rmd
ReadMedata.html
model_data_read.R
server.R
ui.R

ReadMe.md

Cyto Shiny Pilot tool

October 20, 2015

ui.R and server.R are the two required files for shiny to run. (alternately they can be combined into one file named app.R) In our current implementation, all R functions, java script and data needed needed for the app are sourced in the top of the ui.R file.

Shiny needs everything in the same directory or a sub directory of the directory in which ui.R and server.R are found. Here is the sub directory structure (as of July 20, 2015).

Sub Directory Structure

Linked_subdirectories

This directory contains three subdirectories:

data

This is all of the OMICS data as well as the script model_data_read.r which is sourced in via ui.r and reads in the data. Reference data (for edge or attribute creation etc) is also stored here.

R_functions

As the name implies these are all R functions which are used to assemble the networks from the raw data etc. Some of these functions are called from server.r to subset the network and create the attributes etc.

R_to_Cyjs_wrapper_functions

CCN2_pie.R

This R function takes a dataframe of nodes and a dataframe of edges and returns a long list of character strings with the node and edge data formatted for cytoscape.js. (JSON format data?) Currently there is some hard coding for it to work with the H1N1, H3N2, and H5N1 viruses, and some tweaking of formats from the original version.

cytoscapeJsSimpleNetwork3_strain.R

This R function uses the output from CCN2_pie.R to generate the cytocscape.JS graph displayed by shiny.

www

Any Javascript that is sourced in via javascript is found here. Currently it is all cytoscape.js however any java script sourced in the same way is placed here since the subdirectory name "www" is where shiny looks for javascript.

html

graphics for help section placed here.

shinyapps

This is created by shiny, so does not need to be copied.