mully-pdf.R
In mully: Create, Modify and Visualize Multi-Layered Networks

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup,eval=FALSE---------------------------------------------------------
#  require(devtools)
#  install_github("frankkramer-lab/mully")

## -----------------------------------------------------------------------------
library("mully")

## ----eval=FALSE---------------------------------------------------------------
#  g=mully("MyFirstMully",direct = F)

## ----eval=FALSE---------------------------------------------------------------
#  g=addLayer(g, c("Gene", "Drug", "Disease"))

## ----eval=FALSE---------------------------------------------------------------
#  g=addNode(g,"d1","disease",attributes=list(type="t1"))
#  
#  g=addNode(g,"d2","disease",attributes=list(type="t1"))
#  
#  g=addNode(g,"d3","disease",attributes=list(type="t1"))
#  
#  g=addNode(g,"dr1","drug",attributes=list(effect="strong"))
#  
#  g=addNode(g,"dr2","drug",attributes=list(effect="strong"))
#  
#  g=addNode(g,"dr3","drug",attributes=list(effect="moderate"))
#  
#  g=addNode(g,"g1","gene",attributes=list(desc="AF"))
#  
#  g=addNode(g,"g2","gene",attributes=list(desc="BE"))
#  
#  #See vertices attributes
#  print(getNodeAttributes(g))

## ----eval=FALSE---------------------------------------------------------------
#  g=addEdge(g,"dr1","d2",list(name="treats"))
#  g=addEdge(g,"dr1","d2",list(name="extraEdge"))
#  g=addEdge(g,"d2","g1",list(name="targets"))
#  g=addEdge(g,"g2","dr3",list(name="mutates and causes"))
#  g=addEdge(g,"dr3","d3",list(name="treats"))
#  
#  print(getEdgeAttributes(g))
#  
#  removeEdge(g,"d2","dr1",multi=T)

## ----eval=FALSE---------------------------------------------------------------
#  #Create a Second graph
#  g1=mully()
#  
#  g1=addLayer(g1,c("protein","drug","gene"))
#  
#  g1=addNode(g1,"dr4","drug",attributes=list(effect="strong"))
#  g1=addNode(g1,"dr5","drug",attributes=list(effect="strong"))
#  g1=addNode(g1,"dr6","drug",attributes=list(effect="moderate"))
#  
#  g1=addNode(g1,"p1","protein")
#  g1=addNode(g1,"p2","protein")
#  g1=addNode(g1,"p3","protein")
#  
#  g1=addNode(g1,"g3","gene")
#  g1=addNode(g1,"g4","gene")
#  
#  g1=addEdge(g1,nodeStart = "p2",nodeDest = "p3",attributes = list(name="interacts"))
#  g1=addEdge(g1,nodeStart = "dr6",nodeDest = "g4",attributes = list(name="targets"))
#  
#  #Merge both graphs
#  g12=merge(g,g1)
#  
#  #Print the graph
#  print(g12)

## ----eval=FALSE---------------------------------------------------------------
#  plot(g12,layout = "scaled")

## ----eval=FALSE---------------------------------------------------------------
#  plot3d(g12)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  addEdge(g,"dr3","g2",attributes=list(name="newEdge"))

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  addLayer(g,"Complex")

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  attributes=list("specie"="Homo Sapiens")
#  addNode(g = g,nodeName = "g3",layerName = "Gene",attributes = attributes)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  exportCSV(g)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  ##Print all Edges
#  getEdgeAttributes(g)
#  ##Get a Single Edge
#  getEdgeAttributes(g,"d2","g1")

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  getIDEdge(g,"d2","dr1")

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  getLayer(g,"gene")

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  getLayersCount(g)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  getNodeAttributes(g,layerByName = TRUE)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  isLayer(g,"Gene")
#  isLayer(g,"Complex")

## ----eval=FALSE---------------------------------------------------------------
#  
#  #Create First Graph
#  g=mully::demo()
#  
#  #Create Second Graph
#  g1 <- mully("MySecondMully",direct = F)
#  
#  g1 <- addLayer(g1, c("gene", "Protein", "Drug"))
#  
#  g1=addNode(g1,"p1","Protein",attributes=list(type="t1"))
#  
#  g1=addNode(g1,"p2","Protein",attributes=list(type="t1"))
#  
#  g1=addNode(g1,"p3","Protein",attributes=list(type="t1"))
#  
#  g1=addNode(g1,"dr6","drug",attributes=list(effect="strong"))
#  
#  g1=addNode(g1,"dr7","drug",attributes=list(effect="strong"))
#  
#  g1=addNode(g1,"dr8","drug",attributes=list(effect="moderate"))
#  
#  g1=addNode(g1,"g3","gene",attributes=list(desc="AF"))
#  
#  g1=addNode(g1,"g9","gene",attributes=list(desc="BE"))
#  
#  g1=addEdge(g1,"dr8","g9",list(name="targets"))
#  
#  g1=addEdge(g1,"p3","p2",list(name="interactWith"))
#  
#  #Merge Graphs
#  merge(g,g1)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  print(g)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  removeEdge(g,"dr1","d2",multi=TRUE)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  removeLayer(g,"gene",trans=TRUE)

## ----eval=FALSE---------------------------------------------------------------
#  g=mully::demo()
#  removeNode(g,"dr1",trans=TRUE)