## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"RCy3" %in% installed.packages()){ # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) ## ----------------------------------------------------------------------------- # cytoscapePing () # cytoscapeVersionInfo () ## ----------------------------------------------------------------------------- # nodes <- data.frame(id=c("node 0","node 1","node 2","node 3"), # group=c("A","A","B","B"), # categorical strings # score=as.integer(c(20,10,15,5)), # integers # stringsAsFactors=FALSE) # edges <- data.frame(source=c("node 0","node 0","node 0","node 2"), # target=c("node 1","node 2","node 3","node 3"), # interaction=c("inhibits","interacts","activates","interacts"), # optional # weight=c(5.1,3.0,5.2,9.9), # numeric # stringsAsFactors=FALSE) # # createNetworkFromDataFrames(nodes,edges, title="my first network", collection="DataFrame Example") ## ----------------------------------------------------------------------------- # setVisualStyle('Marquee') ## ----------------------------------------------------------------------------- # style.name = "myStyle" # defaults <- list(NODE_SHAPE="diamond", # NODE_SIZE=30, # EDGE_TRANSPARENCY=120, # NODE_LABEL_POSITION="W,E,c,0.00,0.00") # nodeLabels <- mapVisualProperty('node label','id','p') # nodeFills <- mapVisualProperty('node fill color','group','d',c("A","B"), c("#FF9900","#66AAAA")) # arrowShapes <- mapVisualProperty('Edge Target Arrow Shape','interaction','d',c("activates","inhibits","interacts"),c("Arrow","T","None")) # edgeWidth <- mapVisualProperty('edge width','weight','p') # # createVisualStyle(style.name, defaults, list(nodeLabels,nodeFills,arrowShapes,edgeWidth)) # setVisualStyle(style.name) ## ----------------------------------------------------------------------------- # g = new ('graphNEL', edgemode='directed') # g = graph::addNode ('A', g) # g = graph::addNode ('D', g) # g = graph::addNode ('C', g, edges = list('D')) # g = graph::addNode ('B', g, edges = list(c('A','D','C'))) # createNetworkFromGraph (g, title='simple network', collection='GraphNEL Example') ## ----------------------------------------------------------------------------- # df <- data.frame (moleculeType=c('kinase','TF','cytokine','cytokine'), # log2fc=c(1.8,3.0,-1.2,-2.5), # row.names = c('A','B','C','D'), # row.names = node names # stringsAsFactors = FALSE) # important when loading strings! # loadTableData (df) ## ----------------------------------------------------------------------------- # setNodeShapeDefault ('OCTAGON') # setNodeColorDefault ('#AAFF88') # setNodeSizeDefault (60) # setNodeFontSizeDefault (30) ## ----------------------------------------------------------------------------- # getNodeShapes () # diamond, ellipse, trapezoid, triangle, etc. # column <- 'moleculeType' # values <- c ('kinase', 'TF','cytokine') # shapes <- c ('DIAMOND', 'TRIANGLE', 'RECTANGLE') # setNodeShapeMapping (column, values, shapes) ## ----------------------------------------------------------------------------- # column <- 'log2fc' # control.points <- c (-3.0, 0.0, 3.0) # colors <- c ('#5588DD', '#FFFFFF', '#DD8855') # setNodeColorMapping (column, control.points, colors) ## ----------------------------------------------------------------------------- # control.points <- c (-2.0, 0.0, 2.0) # colors <- c ('#2255CC', '#5588DD', '#FFFFFF', '#DD8855','#CC5522') # setNodeColorMapping (column, control.points, colors) ## ----------------------------------------------------------------------------- # control.points = c (-3.0, 2.0, 3.0) # sizes = c (20, 80, 90) # setNodeSizeMapping (column, control.points, sizes) # ## ----------------------------------------------------------------------------- # selectNodes ('C','name') ## ----------------------------------------------------------------------------- # getSelectedNodes () ## ----------------------------------------------------------------------------- # selectFirstNeighbors () ## ----------------------------------------------------------------------------- # node.names <- getSelectedNodes () ## ----------------------------------------------------------------------------- # clearSelection() # ?clearSelection ## ----------------------------------------------------------------------------- # saveSession('vignette_session') #.cys ## ----------------------------------------------------------------------------- # full.path=paste(getwd(),'vignette_image',sep='/') # exportImage(full.path, 'PNG', zoom=200) #.png scaled by 200% # exportImage(full.path, 'PDF') #.pdf # ?exportImage ## ----------------------------------------------------------------------------- # help(package=RCy3) ## ----------------------------------------------------------------------------- # cyrestAPI() # CyREST API # commandsAPI() # Commands API ## ----------------------------------------------------------------------------- # commandsHelp("help") ## ----------------------------------------------------------------------------- # commandsHelp("help network") ## ----------------------------------------------------------------------------- # commandsHelp("help network select") ## ----------------------------------------------------------------------------- # browseVignettes("RCy3")