## ----setup, include = FALSE------------------------------------------------------------------------------------------- options(width=120) knitr::opts_chunk$set( collapse = TRUE, eval=interactive(), echo=TRUE, comment = "#>" ) ## ----loadLibrary, results='hide', echo=FALSE-------------------------------------------------------------------------- # library(RCyjs) ## ----createGraph, results='hide'-------------------------------------------------------------------------------------- # nodes <- c("A", "T") # g <- graphNEL(nodes, edgemode="directed") # g <- graph::addEdge("A", "T", g) ## ----defaultAttributes, results='hide'-------------------------------------------------------------------------------- # nodeDataDefaults(g, attr="label") <- "undefined" # nodeDataDefaults(g, attr="type") <- "undefined" # nodeDataDefaults(g, attr="flux") <- 0 # edgeDataDefaults(g, attr="edgeType") <- "undefined" ## ----assignAttributes, results='hide'--------------------------------------------------------------------------------- # nodeData(g, nodes, attr="label") <- c("Activator", "Target") # nodeData(g, nodes, attr="type") <- c("ligand", "receptor") # edgeData(g, "A", "T", attr="edgeType") <- "binds" ## ----displayGraph, results='hide'------------------------------------------------------------------------------------- # rcy <- RCyjs(title="RCyjs vignette") # setGraph(rcy, g) # layout(rcy, "grid") # fit(rcy, padding=200) # setDefaultStyle(rcy) ## ----builtinShapes---------------------------------------------------------------------------------------------------- # getSupportedNodeShapes(rcy) # getSupportedEdgeDecoratorShapes(rcy) ## ----changeSomeDefaults, results='hide'------------------------------------------------------------------------------- # setDefaultNodeShape(rcy, "roundrectangle") # setDefaultNodeSize(rcy, 50) # setDefaultNodeColor(rcy, "lightgreen") # setDefaultNodeFontSize(rcy, 8) # setDefaultNodeFontColor(rcy, "darkgreen") # setDefaultEdgeLineStyle(rcy, "dotted") # setDefaultEdgeWidth(rcy, 1) # setDefaultEdgeLineColor(rcy, "black") # setDefaultNodeBorderWidth(rcy, 2) # setDefaultNodeBorderColor(rcy, "white") # setBackgroundColor(rcy, "#F0F0F0") # setDefaultEdgeTargetArrowShape(rcy, "arrow") # redraw(rcy) ## ----specificNodeVisualAssignements, results='hide'------------------------------------------------------------------- # setNodeColor(rcy, "A", "lightblue") # setNodeSize(rcy, "T", 80) # setNodeShape(rcy, "A", "hexagon") # setNodeBorderWidth(rcy, "A", 3) # redraw(rcy) ## ----resetStyle, results='hide'--------------------------------------------------------------------------------------- # setDefaultStyle(rcy) ## ----layouts, results='hide'------------------------------------------------------------------------------------------ # for(layout.name in getLayoutStrategies(rcy)){ # layout(rcy, layout.name) # Sys.sleep(1) # } # layout(rcy, "grid") # fit(rcy, padding=150) ## ----simpleExample, results='hide'------------------------------------------------------------------------------------ # library(RCyjs) # gDemo <- simpleDemoGraph() # noaNames(gDemo) # edaNames(gDemo) # noa(gDemo, "type") # noa(gDemo, "lfc") # eda(gDemo, "edgeType") # eda(gDemo, "score") ## ----twoNodeExample, results="hide", echo=FALSE----------------------------------------------------------------------- # loadStyleFile(rcy, system.file(package="RCyjs", "extdata", "vignetteStyle.js")) # redraw(rcy) # layout(rcy, "grid") # tbl.pos <- getPosition(rcy) # for(i in 1:10){ # new.activator.flux <- i * 100 # if(new.activator.flux > 1000) # new.activator.flux <- 1000 # new.target.flux <- (i-3) * 100 # setNodeAttributes(rcy, "flux", c("A", "T"), c(new.activator.flux, new.target.flux)) # tbl.pos$x[1] <- tbl.pos$x[1] + 5 # tbl.pos$x[2] <- tbl.pos$x[2] - 5 # tbl.pos$y <- jitter(tbl.pos$y, amount=2) # setPosition(rcy, tbl.pos) # redraw(rcy) # Sys.sleep(0.3) # } # # ## ----sessionInfo------------------------------------------------------------------------------------------------------ # sessionInfo()