## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"RCy3" %in% installed.packages()){ # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) ## ---- eval=FALSE-------------------------------------------------------------- # g <- new ('graphNEL', edgemode='directed') # g <- graph::addNode ('A', g) # g <- graph::addNode ('B', g) # g <- graph::addNode ('C', g) # g <- graph::addEdge ('A', 'B', g) # g <- graph::addEdge ('B', 'C', g) # cw <- CytoscapeWindow ('vignette', graph=g, overwrite=TRUE) # displayGraph (cw) # layoutNetwork (cw, layout.name='grid') ## ----------------------------------------------------------------------------- # g <- new ('graphNEL', edgemode='directed') # g <- graph::addNode ('A', g) # g <- graph::addNode ('B', g) # g <- graph::addNode ('C', g) # g <- graph::addEdge ('A', 'B', g) # g <- graph::addEdge ('B', 'C', g) # net.suid <- createNetworkFromGraph (g, 'vignette') ## ----------------------------------------------------------------------------- # node.df <- data.frame(id=c("A","B","C","D"), # stringsAsFactors=FALSE) # edge.df <- data.frame(source=c("A","A","A","C"), # target=c("B","C","D","D"), # interaction=c("inhibits","interacts","activates","interacts"), # optional # stringsAsFactors=FALSE) # g <- cyPlot(node.df, edge.df) # cw <- CytoscapeWindow("vignette2", g) # displayGraph(cw) # layoutNetwork(cw, "force-directed") ## ----------------------------------------------------------------------------- # node.df <- data.frame(id=c("A","B","C","D"), # stringsAsFactors=FALSE) # edge.df <- data.frame(source=c("A","A","A","C"), # target=c("B","C","D","D"), # interaction=c("inhibits","interacts","activates","interacts"), # optional # stringsAsFactors=FALSE) # net.suid <- createNetworkFromDataFrames (node.df, edge.df, "vignette2") ## ---- eval=FALSE-------------------------------------------------------------- # g <- initNodeAttribute (graph=g, attribute.name='moleculeType', # attribute.type='char', # default.value='undefined') # g <- initNodeAttribute (graph=g, 'lfc', 'numeric', 0.0) # nodeData (g, 'A', 'moleculeType') <- 'kinase' # nodeData (g, 'B', 'moleculeType') <- 'TF' # nodeData (g, 'C', 'moleculeType') <- 'cytokine' # nodeData (g, 'D', 'moleculeType') <- 'cytokine' # nodeData (g, 'A', 'lfc') <- -1.2 # nodeData (g, 'B', 'lfc') <- 1.8 # nodeData (g, 'C', 'lfc') <- 3.2 # nodeData (g, 'D', 'lfc') <- 2.2 # cw = setGraph (cw, g) # displayGraph (cw) ## ----------------------------------------------------------------------------- # node.data <- data.frame(id=c('A','B','C','D'), # moleculeType=c('kinase','TF','cytokine','cytokine'), # lfc=c(-1.2, 1.8, 3.2, 2.2), # stringsAsFactors = FALSE) # loadTableData(node.data, 'id') ## ---- eval=FALSE-------------------------------------------------------------- # setDefaultNodeShape (cw, 'OCTAGON') # setDefaultNodeColor (cw, '#AAFF88') # setDefaultNodeSize (cw, 80) # setDefaultNodeFontSize (cw, 40) ## ----------------------------------------------------------------------------- # setNodeShapeDefault ('OCTAGON') # setNodeColorDefault ('#AAFF88') # setNodeSizeDefault (80) # setNodeFontSizeDefault (40) ## ---- eval=FALSE-------------------------------------------------------------- # attribute.values <- c ('kinase', 'TF', 'cytokine') # node.shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE') # setNodeShapeRule (cw, 'moleculeType', attribute.values, node.shapes) # setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0), # c ('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000'), # mode='interpolate') # control.points = c (-1.2, 2.0, 4.0) # node.sizes = c (30, 40, 60, 80, 90) # setNodeSizeRule (cw, 'lfc', control.points, node.sizes, mode='interpolate') ## ----------------------------------------------------------------------------- # attribute.values <- c ('kinase', 'TF', 'cytokine') # node.shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE') # setNodeShapeMapping('moleculeType', attribute.values, node.shapes) # setNodeColorMapping('lfc', c(-3.0, 0.0, 3.0), # c('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000')) # control.points = c (-1.2, 2.0, 4.0) # node.sizes = c (30, 40, 60, 80, 90) # setNodeSizeMapping('lfc',control.points, node.sizes) ## ---- eval=FALSE-------------------------------------------------------------- # selectNodes(cw, 'B') # nodes <- getSelectedNodes (cw) # selectFirstNeighborsOfSelectedNodes (cw) ## ----------------------------------------------------------------------------- # selectNodes('B', 'name') #or 'id' # nodes <- getSelectedNodes() # selectFirstNeighbors() ## ----------------------------------------------------------------------------- # nodes <- selectNodes('B', 'name')$nodes ## ---- eval=FALSE-------------------------------------------------------------- # saveImage(cw, "sample_image", "png", h = 800) # saveNetwork(cw, "sample_session", format = "cys") ## ----------------------------------------------------------------------------- # exportImage("sample_image", "png", h= 800) # saveSession("sample_session") ## ----------------------------------------------------------------------------- # browseVignettes('RCy3')