## ----setup, include = FALSE-------------------------------------------------------------------------------------------
options(width=120)
knitr::opts_chunk$set(
   collapse = TRUE,
   eval=interactive(),
   echo=TRUE,
   comment = "#>"
)

## ---------------------------------------------------------------------------------------------------------------------
#  library(cyjShiny)
#  
#  # NETWORK DATA ----
#  tbl_nodes <- data.frame(id=c("A", "B", "C"),
#                          size=c(10, 20, 30),
#                          stringsAsFactors=FALSE)
#  
#  # Must have the interaction column
#  tbl_edges <- data.frame(source=c("A", "B", "C"),
#                          target=c("B", "C", "A"),
#                          interaction=c("inhibit", "stimulate", "inhibit"),
#                          stringsAsFactors=FALSE)
#  
#  graph_json <- toJSON(dataFramesToJSON(tbl_edges, tbl_nodes), auto_unbox=TRUE)
#  
#  # graph_json is a string with JSON content that is input to cytoscape.js
#  print(graph_json)
#  
#  cyjShiny(graph=graph_json, layoutName="cola")

## ---------------------------------------------------------------------------------------------------------------------
#  style_file <- system.file(file.path("demos", "rmarkdownDemo", "style.js"), package="cyjShiny")
#  cyjShiny(graph_json, layoutName="cola", styleFile=style_file)

## ---------------------------------------------------------------------------------------------------------------------
#  yeast_galactose_style_file <- system.file(file.path("demos", "rmarkdownDemo", "yeastGalactoseStyle.js"), package="cyjShiny")
#  yeast_galactose_graph <- readLines(system.file(file.path("demos", "rmarkdownDemo", "yeastGalactose.cyjs"), package="cyjShiny"))
#  
#  cyjShiny(yeast_galactose_graph, layoutName="fcose", styleFile=yeast_galactose_style_file)

## ---------------------------------------------------------------------------------------------------------------------
#  style_file <- system.file(file.path("demos", "rmarkdownDemo", "preset_style.js"), package="cyjShiny")
#  graph_json <- readLines(system.file(file.path("demos", "rmarkdownDemo", "preset_graph.js"), package="cyjShiny"))
#  cyjShiny(graph_json, layoutName="preset", styleFile=style_file)

## ---------------------------------------------------------------------------------------------------------------------
#  preset_graph_file <- system.file(file.path("demos", "fromCytoscapeDesktop", "small", "cyjshiny.cyjs"), package="cyjShiny")
#  graph_json <- readAndStandardizeJSONNetworkFile(preset_graph_file)
#  writeLines(graph_json, "cyjshiny_cytoscape_desktop.cyjs")
#  
#  cyjShiny(graph_json, layoutName="preset")

## ----app, prompt=TRUE, message=TRUE, results="hold", eval=FALSE-------------------------------------------------------
#  library(shiny)
#  library(cyjShiny)
#  library(graph)
#  library(jsonlite)
#  
#  # NETWORK DATA ----
#  tbl_nodes <- data.frame(id=c("A", "B", "C"),
#                          size=c(10, 20, 30),
#                          stringsAsFactors=FALSE)
#  
#  # Must have the interaction column
#  tbl_edges <- data.frame(source=c("A", "B", "C"),
#                          target=c("B", "C", "A"),
#                          interaction=c("inhibit", "stimulate", "inhibit"),
#                          stringsAsFactors=FALSE)
#  
#  graph_json <- toJSON(dataFramesToJSON(tbl_edges, tbl_nodes), auto_unbox=TRUE)
#  
#  # UI ----
#  ui <- fluidPage(cyjShinyOutput('cyjShiny'))
#  
#  # SERVER ----
#  server <- function(input, output, session) {
#    output$cyjShiny <- renderCyjShiny({
#      # Layouts (see js.cytoscape.org): cola, cose, circle, concentric, grid, breadthfirst, random, fcose, spread
#      cyjShiny(graph_json, layoutName="cola")
#    })
#  }
#  
#  # RUN ----
#  shinyApp(ui=ui, server=server)