Network theory has been used for many years in the modeling and analysis of complex systems, as epidemiology, biology and biomedicine . As the data evolves and becomes more heterogeneous and complex, monoplex networks become an oversimplification of the corresponding systems. This imposes a need to go beyond traditional networks into a richer framework capable of hosting objects and relations of different scales, called Multilayered Network Mully, multilayer networks, is an R package that provides a multilayer network framework. Using this package, the user can create, modify and visualize graphs with multiple layers. This package is an extension to the igraph package that provides a monolayer graph framework. The package is implemented as a part of the Multipath Project directed by Dr. Frank Kramer . ## Publication More information and references can be found in the mully paper:
require(devtools)
install_github("frankkramer-lab/mully")library("mully")In this section, we provide a demo to test the package by calling some of the function. After running this script, you will have a graph g with 3 layers and 8 nodes. the graph can also be modified by calling other functions. Please refer to help to see the available functions. ### Create new mully graph
g=mully("MyFirstMully",direct = F)g=addLayer(g, c("Gene", "Drug", "Disease"))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))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)#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)plot(g12,layout = "scaled")plot3d(g12)mully functions are divided into different files depending on their functionnality range: Constructor , Layers Functions , Node Functions , Edge Functions , Merge Function , Visualization Functions , Import Functions , Export Functions , Demo.
| 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 the edges 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 |
Add an edge
The function is used to add an edge to a given mully graph. mully supports multi-edges, i.e. two nodes can be connected with multiple edges. The uniqueness of the edges is based on the connection with the attributes. When adding a new connection between two nodes that are already cnnected, the new edge should have different attributes. The function needs the following arguments:
The function returns the graph, with the added edge.
Example
g=mully::demo()
addEdge(g,"dr3","g2",attributes=list(name="newEdge"))Add a layer or a set of layers to a graph
The function is used to add a new layer to a given mully graph. The layer name should be unique and should not already exist in the graph. The names are not case-sensitive. the function has an internal count, and assigns new IDs to new layers. The internal counr number only increases, i.e. it does not change after deleting a lyer. Therefore the ID of the last added layer is not necessarily the number of layers in the mully graph. The function needs the following arguments:
The function returns the graph, with the layers added.
Example
g=mully::demo()
addLayer(g,"Complex")Add a node with assigned layer and attributes to a graph
The function is used to add a node to a given mully graph. The layer to which this node should be added is required. Nodes on single layers should be unique, but can not be on different layers. Layer Names are not case-sensitive. The function needs the following arguments:
The function returns the graph, with the new node.
Example
g=mully::demo()
attributes=list("specie"="Homo Sapiens")
addNode(g = g,nodeName = "g3",layerName = "Gene",attributes = attributes)Export mully into CSV files
The function is used to export a given mully graph in the CSV Format. Three files will be generated, respectively containing the layers’, nodes’ and edges’ information. The function needs the following arguments:
Example
g=mully::demo()
exportCSV(g)Get the attributes of the edges connecting two nodes
The function is used to obtain information on the edges in a given mully graph. The information can be on a single edge or all the edges in the graph. The function needs the following arguments:
The function returns a dataframe containing the edges with their attributes. If both nodes’ arguments are missing, it returns the complete information on edges and their attributes.
Example
g=mully::demo()
##Print all Edges
getEdgeAttributes(g)
##Get a Single Edge
getEdgeAttributes(g,"d2","g1")Get the ids of the edges connecting two nodes
The function is used to get the internal ID of an edge in a given mully graph. The function needs the following arguments:
The nodes passed to this function as arguments should be the unique names assigned to the nodes upon addition. mully supports multi-edges, therefore this function may return a list of edges connecting two nodes. The function returns a list containing the ids of the edges connecting the nodes.
Example
g=mully::demo()
getIDEdge(g,"d2","dr1")Get the id of a node
The function is used to get the internal ID of a given node in a given mully graph. The function needs the following arguments:
The function returns the id of the specified node.
Get the nodes on a layer in a graph
The function is used to get the nodes on a given layer in a given mully graph. The layer name is not case-sensitive. The function needs the following arguments:
The function returns a List of the nodes on the given layer.
Example
g=mully::demo()
getLayer(g,"gene")Get the number of layers in a graph
The function is used to get the number of layers in a given mully graph. The function needs the following arguments:
The function returns the count of the layers.
Example
g=mully::demo()
getLayersCount(g)Get a node from a graph
The function is used to get a node from a given mully graph as an igraph.vs object. The function needs the following arguments:
The function returns the node as igraph.vs.
Get the attributes of a node
The function is used to get a node or a list of nodes with corresponding attributes from a given mully graph. If the node name is missing, the complete node information is extracted. The function needs the following arguments:
The function returns a dataframe containing the attributes of the specified node.
Example
g=mully::demo()
getNodeAttributes(g,layerByName = TRUE)Import Edges to a mully graph from a CSV file
The function is used to import edges to a mully graph. The function reads a CSV file and adds edges between existing nodes to the graph. The graph should already contain layers and nodes. The function needs the following arguments:
The function returns the mully graph with the added edges.
Import a mully graph from CSV files
The function is used to create a graph from CSV files. To create the
graph, three files are needed: the layers, nodes and edges. mully also
offers functions to import individual files containing nodes’, edges’
and layers information. See Functions importLayersCSV(),
importNodesCSV() and importEdgesCSV(). The
function needs the following arguments:
The function returns a new mully graph.
Import Layers to a mully graph from a CSV file
The function is used to add layers to a mully graph. The function reads a CSV file and adds the layers to the graph. The file should contain the layers’ names. Layer IDs are assigned automatically. The function needs the following arguments:
The function returns the mully graph with the added layers.
Import Nodes to a mully graph from a CSV file
The function is used to import nodes into an existing mully graph. The function reads a CSV file and adds the nodes with the attributes to the graph. The graph should already contain layers, and the nodes in the file should have an attribute n referring to the layer assignment. The function needs the following arguments:
The function returns the mully graph with the added nodes.
Is this a mully graph?
The function check if a given graph is a mully graph. The function needs the following arguments:
The function returns a boolean indicating whether the graph is or not a mully object. ### isLayer Verify if the layer exists in a graph
This function is used to check if a given mully graph contains a given layer. The layer name is not case-sensitive. The function needs the following arguments:
The function returns a boolean value.
Example
g=mully::demo()
isLayer(g,"Gene")
isLayer(g,"Complex")Merge or unite two graphs
The function is used to merge two mully graphs. The merge is layer based, i.e. nodes belonging to similar layers in both graphs will be combined in the returned graph. The node names are unique on single layers but can be redundant over different layers. The merge is based on the first arguments, therefore all elements of the second argument will be added to the first. The function needs the following arguments:
The function returns the merge of the two graphs. The merge is based on the first given graph.
Example
#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)Create an empty multilayered graph
The function create an empty mully graph. The function needs the following arguments:
The function returns the created multilayered graph. ### plot,mully Plot the graph in 2D
The function is used to plot the mully graph. It uses the plot function from igraph. We do not recommend using this function to plot big graphs, and use plot3d instead. The function needs the following arguments:
Plot the graph in 3D using rgl
The funstion is used to generate 3D interactive plots of a mully graph. The 3D plot is generated using the R Package rgl, and uses some of the arguments passed to the igraph function rgl.plot. Most of the arguments are set to default values, but can be changed. The layout is calculated internally based on the layers. The function needs the following arguments:
The function can take the following arguments supported and not ignored by rglplot}: vertex.label, vertex.label.color, edge.color, edge.width, edge.arrow.size,edge.arrow.width.
Print a mully graph
The function prints a mully graph. The function needs the following arguments:
Example
g=mully::demo()
print(g)Delete an edge
The function is used to remove an edge from a given mully graph. Since mully supports multi-edges, a boolean multi is needed to specify whether to delete multiple edges or a single edge. In case one edge should be deleted, the named list of attributes of the edge is required. The function needs the following arguments:
The function returns the graph with the deleted edges.
Example
g=mully::demo()
removeEdge(g,"dr1","d2",multi=TRUE)Delete a layer or a set of layers from a graph
The function is used to remove a layer from a given mully graph. Removing a layer results deleting all nodes assigned to the layer, and the edges connecting these nodes to other nodes in the graph. Transitive edges between nodes can be added by setting trans to TRUE. The function needs the following arguments:
The function returns the graph, with the given layer and its corresponding nodes and edges removed.
Example
g=mully::demo()
removeLayer(g,"gene",trans=TRUE)Delete a node or a set of nodes from a graph
The function is used to remove a node from a given mully graph. Removing a node results removing the edges connecting this node to other nodes in the graph. Transitive edges can also be added after deletion by setting trans to TRUE (a->b, b->c, removing b with trans=TRUE will add a->c). The function needs the following arguments:
The function returns the graph, with the nodes deleted.
Example
g=mully::demo()
removeNode(g,"dr1",trans=TRUE)