Movatterモバイル変換

## Introduction Network theory has beenused for many years in the modeling and analysis of complex systems, asepidemiology, biology and biomedicine . As the data evolves and becomesmore heterogeneous and complex, monoplex networks become anoversimplification of the corresponding systems. This imposes a need togo beyond traditional networks into a richer framework capable ofhosting objects and relations of different scales, called MultilayeredNetworkMully,multilayer networks,is an R package that provides a multilayer network framework. Using thispackage, the user can create, modify and visualize graphs with multiplelayers. This package is an extension to theigraph package thatprovides a monolayer graph framework. The package is implemented as apart oftheMultipath Project directed byDr. FrankKramer . ## Publication More information and references can be foundin the mully paper:

Installation

Installation from CRAN

Installation via Github

Test the package

In this section, we provide a demo to test the package by callingsome of the function. After running this script, you will have a graph gwith 3 layers and 8 nodes. the graph can also be modified by callingother functions. Please refer to help to see the available functions.### Create new mully graph

Add Layers

Add/print Nodes

  g=addNode(g,"d1","disease",attributes=list(type="t1"))print("Node d1 added as disease")  g=addNode(g,"d2","disease",attributes=list(type="t1"))print("Node d2 added as disease")  g=addNode(g,"d3","disease",attributes=list(type="t1"))print("Node d3 added as disease")  g=addNode(g,"dr1","drug",attributes=list(effect="strong"))print("Node dr1 added as drug")  g=addNode(g,"dr2","drug",attributes=list(effect="strong"))print("Node dr2 added as drug")  g=addNode(g,"dr3","drug",attributes=list(effect="moderate"))print("Node dr3 added as drug")  g=addNode(g,"g1","gene",attributes=list(desc="AF"))print("Node g1 added as gene")  g=addNode(g,"g2","gene",attributes=list(desc="BE"))print("Node g2 added as gene")#See vertices attributesprint(getNodeAttributes(g))#The Result:# name n type   effect desc#   1   d1 3   t1     <NA> <NA>#   2   d2 3   t1     <NA> <NA>#   3   d3 3   t1     <NA> <NA>#   4  dr1 2 <NA>   strong <NA>#   5  dr2 2 <NA>   strong <NA>#   6  dr3 2 <NA> moderate <NA>#   7   g1 1 <NA>     <NA>   AF#   8   g2 1 <NA>     <NA>   BE

Add/print/remove Edges

  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)#The Result:#      V1  V2               name#   1  d2 dr1             treats#   2  d2 dr1          extraEdge#   3  d2  g1            targets#   4 dr3  g2 mutates and causes#   5  d3 dr3             treatsremoveEdge(g,"d2","dr1",multi=T)

Merge two graphs

#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 graphprint(g12)# Printing this graph gives this result:#   mully --  MyFirstMully# 4 Layers:#     ID    Name NameLower#   1  1    Gene      gene#   2  2    Drug      drug#   3  3 Disease   disease#   4  4 protein   protein## 16 Nodes:#     name n type   effect desc#   1    d1 3   t1     <NA> <NA>#   2    d2 3   t1     <NA> <NA>#   3    d3 3   t1     <NA> <NA>#   4   dr1 2 <NA>   strong <NA>#   5   dr2 2 <NA>   strong <NA>#   6   dr3 2 <NA> moderate <NA>#   7    g1 1 <NA>     <NA>   AF#   8    g2 1 <NA>     <NA>   BE#   9   dr4 2 <NA>   strong <NA>#   10  dr5 2 <NA>   strong <NA>#   11  dr6 2 <NA> moderate <NA>#   12   p1 4 <NA>     <NA> <NA>#   13   p2 4 <NA>     <NA> <NA>#   14   p3 4 <NA>     <NA> <NA>#   15   g3 1 <NA>     <NA> <NA>#   16   g4 1 <NA>     <NA> <NA>## 7 Edges:#      V1  V2               name#   1  d2 dr1             treats#   2  d2 dr1          extraEdge#   3  d2  g1            targets#   4 dr3  g2 mutates and causes#   5  d3 dr3             treats#   6  p2  p3          interacts#   7 dr6  g4            targets

Function	Description
`mully(name,direct)`	Constructor Function, Create an empty multilayered graph
`print(g)`	Print function
`addLayer(g, nameLayer)`	Add a layer or a set of layers to a graph
`removeLayer(g, name,trans)`	Delete a layer or a set of layers from a graph
`isLayer(g, name)`	Verify if the layer exists in a graph
`getLayersCount(g)`	Get the number of layers in a graph
`getLayer(g, nameLayer)`	Get the nodes on a layer in a graph
`getNode(g,nameNode)`	Get a node from a graph
`getIDNode(g,nameNode)`	Get the id of a node
`addNode(g, nodeName, layerName, attributes)`	Add a node with assigned layer and attributes to a graph
`removeNode(g, name,trans)`	Delete a node or a set of nodes from a graph
`getNodeAttributes(g,nameNode)`	Get the attributes of one or all nodes
`addEdge(g, nodeStart, nodeDest, attributes)`	Add an edge
`removeEdge(g, nodeStart, nodeDest,attributes, multi)`	Delete an edge
`getEdgeAttributes(g,nodeStart,nodeDest)`	Get the attributes of the edges connecting two nodes or all theedges in the graph
`getIDEdge(g,nodeStart,nodeDest)`	Get the ids of the edges connecting two nodes
`merge(g1,g2)`	Merge or unite two graphs
`plot(g,layout)`	Plot the graph in 2D
`plot3d(g)`	Plot the graph in 3D using rgl
`importGraphCSV(name,direct,layers,nodes,edges)`	Import a mully graph from csv files
`importLayersCSV(g,file)`	Import layers to a mully graph from a CSV file
`importNodesCSV(g,file)`	Import nodes to a mully graph from a CSV file
`importEdgesCSV(g,file)`	Import edges to a mully graph from a CSV file