Nothing
R/visualizeBiopax.R
In rBiopaxParser: Parses BioPax files and represents them in R
Defines functions
combineNodes
removeNodes
colorGraphNodes
uniteGraphs
diffGraphs
intersectGraphs
calcGraphOverlap
plotRegulatoryGraph
layoutRegulatoryGraph
transitiveReduction
transitiveClosure
pathway2RegulatoryGraph
pathway2AdjacancyMatrix
Documented in
calcGraphOverlap
colorGraphNodes
combineNodes
diffGraphs
intersectGraphs
layoutRegulatoryGraph
pathway2AdjacancyMatrix
pathway2RegulatoryGraph
plotRegulatoryGraph
removeNodes
transitiveClosure
transitiveReduction
uniteGraphs
###############################################################################
#
# visualizeBiopax.R: This file contains the all functions related to visualizing a parsed Biopax model.
# Generation of graphs, layout, adjacency matrices, modification of graphs.
# author: Frank Kramer <dev@frankkramer.de>
#
# This is released under GPL-2.
#
# Documentation was created using roxygen
#
###############################################################################
#' This function generates an adjacency matrix from the activations/inhibitions of a pathway in a biopax model.
#'
#' This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix.
#' See pathway2RegulatoryGraph for more details.
#'
#' @param biopax A biopax model
#' @param pwid string
#' @param expandSubpathways logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
#' @param splitComplexMolecules logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.
#' @param useIDasNodenames logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
#' @param verbose logical
#' @return Returns the adjacency matrix representing the regulatory graph of the supplied pathway.
#' @author Frank Kramer
#' @export
#' @import data.table
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' pathway2AdjacancyMatrix(biopax, pwid1)
pathway2AdjacancyMatrix <- function(biopax, pwid, expandSubpathways=TRUE, splitComplexMolecules=TRUE, useIDasNodenames=FALSE, verbose=TRUE) {
if(!("biopax" %in% class(biopax))) stop("Error: pathway2AdjacancyMatrix: parameter biopax has to be of class biopax.")
if(!("character" %in% class(pwid))) stop("Error: pathway2AdjacancyMatrix: parameter pwid has to be of class character.")
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
mygraph = pathway2RegulatoryGraph(biopax, pwid, expandSubpathways=expandSubpathways, splitComplexMolecules=splitComplexMolecules, useIDasNodenames=useIDasNodenames, verbose=verbose)
ttt = as(mygraph,"graphAM")
as(ttt,"matrix")
}
#test: pwid = "pid_p_200067_wnt_signaling_pathway"
# i = "pid_i_203122_inhibitor_1"
# pwid = "pid_p_200020_wnt_noncanonical_pathway"
# i = "pid_i_203122_inhibitor_1"
#
#' This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model.
#'
#' This functions builds a graph from the pathway components of the supplied pathway.
#' Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc.
#' If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph.
#' There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.
#'
#' @param biopax A biopax model
#' @param pwid string
#' @param expandSubpathways logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
#' @param splitComplexMolecules logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.
#' @param useIDasNodenames logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
#' @param verbose logical
#' @return Returns the representing the regulatory graph of the supplied pathway in a node-edge-list graph.
#' @author Frank Kramer
#' @export
#' @import data.table
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' plotRegulatoryGraph(mygraph)
pathway2RegulatoryGraph <- function(biopax, pwid, expandSubpathways=TRUE, splitComplexMolecules=TRUE, useIDasNodenames=FALSE, verbose=TRUE) {
if(is.null(biopax) || !("biopax" %in% class(biopax))) stop("Error: pathway2RegulatoryGraph: parameter biopax has to be of class biopax.")
biopaxlevel = biopax$biopaxlevel
if(is.null(pwid) ||!("character" %in% class(pwid))) stop("Error: pathway2RegulatoryGraph: parameter pwid has to be of class character.")
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
pwid = unique(striphash(pwid))
#first make an node edge list, because its easier
mygraph = new(getClassDef("graphNEL", package="graph"))
graph::edgemode(mygraph) = "directed"
#get pathway component list
pw_component_list = listPathwayComponents(biopax,pwid, returnIDonly=T)
if(length(pw_component_list)==0) {warning("Pathway seems to have no pathway components"); return(NULL)}
pw_component_list = selectInstances(biopax,id=pw_component_list, includeReferencedInstances=TRUE, returnCopy=TRUE)
pw_component_list$property = tolower(pw_component_list$property)
setkeyv(pw_component_list, cols=c("id","class","property"))
pw_controls = pw_component_list[tolower(pw_component_list$class) %chin% c("control","catalysis","modulation","templatereactionregulation"),]
#verbose
if(length(pw_controls$id)==0) {
warning("warning: pathway2RegulatoryGraph: supplied graph has no regulatory pathway components. Returning NULL.")
return(NULL)
} else {
if(verbose) {
message(paste("Found",length(unique(pw_controls$id)), "pathway components. Putting them together..."))
}
}
#currently considers only controls //TODO: Consider subpathways!
for(i in unique(pw_controls$id)) {
instance = pw_controls[id==i,]
#if type neither inhibition nor activation i dont know what to do anyways.
#Cancer Cell Map doesnt set control-type of catalysises to ACTIVATION although it is required by biopax level 2 standards. quick fix here:
if(biopax$biopaxlevel == 2) {
type = as.character(instance[property=="control-type"]$property_value)
}
if(biopax$biopaxlevel == 3) {
type = as.character(instance[property=="controltype"]$property_value)
}
if(length(type)==0) {
if(tolower(as.character(instance[1,class])) == "catalysis") {
type="ACTIVATION"
} else {
next
}
}
if ( !grepl("activation",type,ignore.case=TRUE) & !grepl("inhibition",type,ignore.case=TRUE)) {
next
}
#controllers are physicalentityparticipants, get those
controller_ids = striphash(as.character(unique(instance[property=="controller"]$property_attr_value)))
controllers = NA
for(i2 in controller_ids) {
c_instance = pw_component_list[id==i2,]
#each physicalentityparticipant has exactly 1 physicalentity, get that and get the name!
if(biopax$biopaxlevel == 2) {
c_instance = pw_component_list[id==striphash(c_instance[property=="physical-entity"]$property_attr_value),]
}
if(splitComplexMolecules & any(isOfClass(c_instance,"complex"))) {
if(useIDasNodenames) {
controllers = c(controllers, as.character( splitComplex(pw_component_list, i2, returnIDonly=T, biopaxlevel=biopaxlevel) ))
} else {
controllers = c(controllers, as.character( splitComplex(pw_component_list, i2, biopaxlevel=biopaxlevel)$name ))
}
} else {
if(useIDasNodenames) {
controllers = c(controllers, c_instance$id[1])
} else {
controllers = c(controllers, getInstanceProperty(pw_component_list,c_instance$id[1], biopaxlevel=biopaxlevel))
}
}
}
#controlleds are interactions or pathways. ignoring pathways for now
controlled_ids = striphash(as.character(unique(instance[property=="controlled"]$property_attr_value)))
controlleds = NA
for(i2 in controlled_ids) {
c_instance = pw_component_list[id==i2,]
#depending on type of c_instance we must differentiate here.
#pathway=ignore,interaction=ignore(this is only a nice field with a name in PID anyways),
#complexAssembly=we deal with a complex. split up or dont and return names
#biochemicalReaction=...
#any conversion: add up left & rights and get the names
if(any(isOfClass(c_instance,c("conversion"),considerInheritance = TRUE)) || any(isOfClass(c_instance,c("templatereaction")))) {
leftrights = striphash(c_instance[property=="left" | property=="right" | property=="product"]$property_attr_value)
for(i3 in leftrights) {
#every left/right is an physicalentityparticipants, get that as above
leftrights_instance = pw_component_list[id==i3,]
if(biopax$biopaxlevel == 2) {
leftrights_instance = pw_component_list[id==striphash(leftrights_instance[property=="physical-entity"]$property_attr_value),]
}
#split complexes?
if(splitComplexMolecules & any(isOfClass(leftrights_instance,"complex"))) {
if(useIDasNodenames) {
controlleds = c(controlleds, as.character( splitComplex(pw_component_list, i3, returnIDonly=T, biopaxlevel=biopaxlevel) ))
} else {
controlleds = c(controlleds, as.character( splitComplex(pw_component_list, i3, biopaxlevel=biopaxlevel)$name ))
}
} else {
if(useIDasNodenames) {
controlleds = c(controlleds, as.character(leftrights_instance[1]$id))
} else {
controlleds = c(controlleds, getInstanceProperty(pw_component_list,leftrights_instance[1]$id, biopaxlevel=biopaxlevel))
}
}
}
}
}
controllers = striphash(unique(controllers))
controlleds = striphash(unique(controlleds))
controllers = controllers[!is.na(controllers) & !is.null(controllers) & nchar(controllers) > 0 ]
controlleds = controlleds[!is.na(controlleds) & !is.null(controlleds) & nchar(controlleds) > 0 ]
#only add viable directed edges:
if(length(controllers)==0 | length(controlleds)==0) {
next
}
#verbose
if(verbose) {
message(paste("Adding to graph: ",unique(as.character(instance[,"class"])), "-", type,
"Controllers: ", paste(controllers, collapse=" "), "Controlleds: ", paste(controlleds, collapse=" ")))
}
#now we have the controllers and controlleds lists, add edge
# leave out duplicates
newnodes = unique(c(controllers,controlleds))
# only add new nodes that are not null, na or empty strings
newnodes = newnodes[!(newnodes %in% graph::nodes(mygraph))]
if(length(newnodes)>0) mygraph = graph::addNode(newnodes,mygraph)
#set weight: activation 1, inhibition = -1
if ( tolower(type)=="activation" ) {
weights = 1
} else {
weights = -1
}
# add all edges from controllers to controlleds.
for(i_controllers in controllers) {
for(i_controlleds in controlleds) {
#skip edges to self
if(i_controllers != i_controlleds) {
#if edge already exists throw a warning and skip
if(!(i_controlleds %in% unlist(graph::edges(mygraph, which=i_controllers)))) {
mygraph = graph::addEdge(i_controllers, i_controlleds,mygraph,weights=weights)
} else {
warning( paste("Problem while adding edge (weight=",weights,") to graph: Edge already exists between ",i_controllers," and ",i_controlleds," (weight=",unlist(graph::edgeWeights(mygraph))[paste(i_controllers,i_controlleds,sep=".")],"). Skipping this edge.",sep="" ) )
}
}
}
}
}
mygraph
}
#' This function generates the transitive closure of the supplied graph.
#'
#' This function generates the transitive closure of the supplied graph. In short: if A->B->C then an edge A->C is added.
#' Edge weights are conserved if possible (in a hopefully smart way). This is a simple convenience wrapper for the RBGL function transitive.closure.
#'
#' @param mygraph graphNEL
#' @return Returns the transitive closure of the supplied graph.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' tc = transitiveClosure(mygraph)
transitiveClosure <- function(mygraph) {
if(!require(graph)) {
message(paste("This functions needs the graph package installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(!require(RBGL)) {
message(paste("This functions needs the RBGL package installed, albeit it cannot be found.","\n"))
return(NULL)
}
RBGL::transitive.closure(mygraph)
# accessibles = acc(mygraph,graph::nodes(mygraph))
# for(n in names(accessibles)) {
# for(c in names(accessibles[[n]])) {
# if(accessibles[[n]][[c]]>1) {
# #cat(paste("adding",n,c,"\n"))
# mygraph = graph::addEdge(from=n,to=c, graph=mygraph, weights=1) ###FIX! XXX
# }
# }
# }
# mygraph
}
#' This function generates the transitive reduction of the supplied graph.
#'
#' This function is deprecated due to nem dropping out of Bioconductor in BioC 4.0.
#' This function generates the transitive reduction of the supplied graph. In short: if A->B->C AND A->C then edge A->C is removed.
#' This is a simple convenience wrapper for the NEM function transitive.reduction. Be aware of implications on the edge weights!
#'
#' @param mygraph graphNEL
#' @return Returns the transitive reduction of the supplied graph.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' tr = transitiveReduction(mygraph)
transitiveReduction <- function(mygraph) {
warning("This function is deprecated due to nem dropping out of Bioconductor. Returning NULL.")
return(NULL)
}
#' This function generates a (more or less) beautiful layout for a regulatory graph.
#'
#' This function generates a (more or less) beautiful layout for a regulatory graph.
#' Call this after you generated a graph with pathway2RegulatoryGraph. Since beauty is always in the eye of the beholder consider this a starting point for making your graphs even nicer.
#' Rgraphviz with dot layout is used.
#' Edges are green/red with normal/tee arrowheads for activations/inhibitions.
#' If you want to specifically paint subgraphs in different colors use lists of vectors with node names for parameter subgraphs and vector of color names for subgraphs.color for your choice of color.
#' The output can be further tweaked by setting layout options using nodeRenderInfo(mygraph) <- list() ...
#' See the Rgraphviz and Graphviz documentations.
#'
#' @param mygraph graphNEL
#' @param label Label of the graph
#' @param node.fixedsize logical. If font size is fixed or variable in regards to the nodes.
#' @param edge.weights vector. which colors to use for weighted edges
#' @param edge.arrowheads vector. which arrowheads to use for weighted edges
#' @param subgraphs A list of character vectors with node names defining the sub graphs.
#' @param subgraphs.colors vector. which colors to use for subgraphs
#' @return Returns the supplied graph in a layouted form with several parameters set for regulatory graph plotting.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph = layoutRegulatoryGraph(mygraph)
#' plotRegulatoryGraph(mygraph)
layoutRegulatoryGraph <- function(mygraph, label="", node.fixedsize=FALSE, edge.weights=c("green","black","red"), edge.arrowheads=c("normal","tee"),
subgraphs=list(), subgraphs.colors=c("#B3E2CD","#FDCDAC","#F4CAE4","#E6F5C9","#FFF2AE")) {
if(is.null(mygraph)) stop("Error: layoutRegulatoryGraph: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(mygraph))) stop("Error: layoutRegulatoryGraph: supplied graph has to be of class graphNEL.")
if(length(nodes(mygraph))==0) {
warning("warning: layoutRegulatoryGraph: supplied graph has no nodes. No layout was done.")
return(mygraph)
}
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(label != "") graph::graphRenderInfo(mygraph) <- list(label=label, labelJust="l", labelLoc="t")
graph::nodeRenderInfo(mygraph) <- list(shape="ellipse", fill="#e0e0e0", fixedsize=node.fixedsize)
#graph::nodeRenderInfo(mygraph) <- list(iwidth="2", iheight="2")
mygraph = Rgraphviz::layoutGraph(mygraph)
#GRAPH
# graph rendering info
if(label != "") graph::graphRenderInfo(mygraph) <- list(label=label, labelJust="l", labelLoc="t")
#EDGES
# generate a list of all edges, preinitialized with the weights
x = unlist(graph::edgeData(mygraph))
names(x) = gsub(".weight","",names(x))
names(x) = gsub("|","~",names(x), fixed=TRUE)
#set edge arrowheads
arrowhead = x
arrowhead[TRUE] = rep(edge.arrowheads[1],length(x))
arrowhead[x==1] = edge.arrowheads[1]
arrowhead[x==-1] = edge.arrowheads[2]
graph::edgeRenderInfo(mygraph) <- list(arrowhead=arrowhead)
#set edge colors
color = x
color[TRUE] = rep(edge.weights[2],length(x))
color[x==1] = edge.weights[1]
color[x==-1] = edge.weights[3]
graph::edgeRenderInfo(mygraph) <- list(col=color)
#NODES
#shape size and fill of nodes
graph::nodeRenderInfo(mygraph) <- list(shape="ellipse", fill="#e0e0e0", fixedsize=node.fixedsize)
#SUBGRAPHS
if(length(subgraphs) > 0) {
for(i in 1:length(subgraphs)) {
for(n in subgraphs[[i]]) {
graph::nodeRenderInfo(mygraph)$fill[n] <- subgraphs.colors[i]
}
}
}
return(mygraph)
}
#' This function layouts a regulatory graph and plots it using Rgraphviz.
#'
#' This function takes a regulatory graph as generated by pathway2regulatoryGraph and plots it using standard layout options of layoutRegulatoryGraph.
#' This function is a wrapper for layoutRegulatoryGraph with standard parameters.
#' Subgraphs can be painted with different colors. This can be done by passing parameter subgraph a list of character vectors with node names.
#'
#' @param mygraph graphNEL, regulatory graph
#' @param subgraphs list of character vectors with node names
#' @param layoutGraph logical. If FALSE the graph is not laid out again but send directly to Rgraphviz::renderGraph.
#' @return none
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' plotRegulatoryGraph(mygraph)
plotRegulatoryGraph <- function(mygraph, subgraphs=list(), layoutGraph=TRUE) {
if(is.null(mygraph)) stop("Error: plotRegulatoryGraph: supplied graph parameter was NULL.")
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!("graphNEL" %in% class(mygraph))) stop("Error: plotRegulatoryGraph: supplied graph has to be of class graphNEL.")
if(length(nodes(mygraph))==0) {
warning("warning: plotRegulatoryGraph: supplied graph has no nodes. No plotting was done.")
return(mygraph)
}
temp = mygraph
if(layoutGraph) {
temp = layoutRegulatoryGraph(temp, subgraphs=subgraphs)
}
Rgraphviz::renderGraph(temp)
}
#' This function calculates the overlap of 2 graphs
#'
#' This function calculates the overlap of supplied graph1 with graph2.
#' Layout and weights of graph1 are kept.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @return Returns a list containing the compared graphs and edge- and node-wise overlap between them.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' calcGraphOverlap(mygraph1,mygraph2)
calcGraphOverlap <- function(graph1, graph2) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
edges_overlap = (length(graph::edgeNames(graph1)) - length(setdiff(graph::edgeNames(graph1), graph::edgeNames(graph2)))) / length(graph::edgeNames(graph1))
nodes_overlap = (length(graph::nodes(graph1)) - length(setdiff(graph::nodes(graph1), graph::nodes(graph2)))) / length(graph::nodes(graph1))
list(graph1=graph1, graph2=graph2, edges_overlap = edges_overlap , nodes_overlap = nodes_overlap)
}
#' This function returns a graph computed by the insection of supplied graph1 and graph2.
#'
#' This function returns a graph computed by the insection of supplied graph1 and graph2.
#' Layout and weights of graph1 are kept.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @return Returns the intersection of graph1 and graph2.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(intersectGraphs(mygraph1,mygraph2))
intersectGraphs <- function(graph1, graph2) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = setdiff(e1,e2)
for(x in 1:length(i)) {
temp = graph::removeEdge(i[[x]][1],i[[x]][2], temp)
}
for(x in setdiff(graph::nodes(graph1), graph::nodes(graph2))) {
temp = graph::removeNode(x, temp)
}
temp
}
#' This function returns the different nodes and edges between graph1 and graph2.
#'
#' This function returns the different nodes and edges between graph1 and graph2.
#' Layout options of graph1 are kept.
#' Coloring currently not implemented.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @param colorNodes logical
#' @param colors character vector of colors. If colorNodes==TRUE these colors are used for graph1 and graph2 respectivley.
#' @return Return the diff between the graphs.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(diffGraphs(mygraph1,mygraph2))
diffGraphs <- function(graph1, graph2, colorNodes=TRUE, colors=c("#B3E2CD","#FDCDAC") ) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = intersect(e1,e2)
for(x in 1:length(i)) {
temp = graph::removeEdge(i[[x]][1],i[[x]][2], temp)
}
temp
}
#' This function unites two graphs.
#'
#' This function unites the two supplied graphs. Layout parameters from graph1 are used.
#' If colorNodes==TRUE the returned graph has different colors for overlapping nodes and nodes individual for each graph.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @param colorNodes logical
#' @param colors colors character vector of colors. If colorNodes==TRUE these colors are used for graph1 and graph2 respectivley.
#' @return Return a graph generated by uniting the two supplied graphs
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(uniteGraphs(mygraph1,mygraph2))
uniteGraphs <- function(graph1, graph2, colorNodes=TRUE, colors=c("#B3E2CD","#FDCDAC","#F4CAE4")) { #color: yellow, lightblue, lightgreen
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
graph::graphRenderInfo(temp)$laidout <- FALSE
#ADD NODES
for(i in setdiff(graph::nodes(graph2), graph::nodes(graph1))) {
temp = graph::addNode(i, temp)
}
#ADD EDGES
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = setdiff(e2,e1)
for(x in 1:length(i)) {
temp = graph::addEdge(i[[x]][1],i[[x]][2], temp, as.numeric(graph::edgeData(graph2,i[[x]][1],i[[x]][2], "weight")))
}
#shape size and fill of nodes
nodevector = as.vector(rep(1,length(graph::nodes(temp))))
names(nodevector) = graph::nodes(temp)
node.shape = nodevector
node.shape[TRUE] = "ellipse"
graph::nodeRenderInfo(temp)$shape <- node.shape
#LAYOUT GRAPH
temp = Rgraphviz::layoutGraph(temp)
#set shape again. strange rgraphviz behavior
graph::nodeRenderInfo(temp)$shape <- node.shape
node.fill = nodevector
node.fill[TRUE] = colors[1]
graph::nodeRenderInfo(temp)$fill <- node.fill
### reuse previous layout of graph1
if(!is.null(graph::nodeRenderInfo(graph1)$height[1])) {
node.height = nodevector
node.height[TRUE] = graph::nodeRenderInfo(graph1)$height[1]
graph::nodeRenderInfo(temp)$height <- node.height
}
if(!is.null(graph::nodeRenderInfo(graph1)$width[1])) {
node.width = nodevector
node.width[TRUE] = graph::nodeRenderInfo(graph1)$width[1]
graph::nodeRenderInfo(temp)$width <- node.width
}
if(!is.null(graph::nodeRenderInfo(graph1)$fontsize[1])) {
node.fontsize = nodevector
node.fontsize[TRUE] = graph::nodeRenderInfo(graph1)$fontsize[1]
graph::nodeRenderInfo(temp)$fontsize <- node.fontsize
}
if(!is.null(graph::nodeRenderInfo(graph1)$labelfontsize[1])) {
node.labelfontsize = nodevector
node.labelfontsize[TRUE] = graph::nodeRenderInfo(graph1)$labelfontsize[1]
graph::nodeRenderInfo(temp)$labelfontsize <- node.labelfontsize
}
if(!is.null(graph::nodeRenderInfo(graph1)$labelfontsize[1])) {
node.fixedsize = nodevector
node.fixedsize[TRUE] = graph::nodeRenderInfo(graph1)$fixedsize[1]
graph::nodeRenderInfo(temp)$fixedsize <- node.fixedsize
}
#COLOR SUBGRAPHS
#only graph1
for(n in setdiff(graph::nodes(graph1), graph::nodes(graph2))) {
graph::nodeRenderInfo(temp)$fill[n] <- colors[2]
}
#only graph2
for(n in setdiff(graph::nodes(graph2), graph::nodes(graph1))) {
graph::nodeRenderInfo(temp)$fill[n] <- colors[3]
}
#COLOR EDGES
# generate a list of all edges, preinitialized with the weights
edge.weights=c("green","black","red")
x = unlist(graph::edgeData(temp))
names(x) = gsub(".weight","",names(x))
names(x) = gsub("|","~",names(x), fixed=TRUE)
#set edge arrowheads
edge.arrowheads=c("normal","tee")
arrowhead = x
arrowhead[TRUE] = rep(edge.arrowheads[1],length(x))
arrowhead[x==1] = edge.arrowheads[1]
arrowhead[x==-1] = edge.arrowheads[2]
graph::edgeRenderInfo(temp) <- list(arrowhead=arrowhead)
#set edge colors
color = x
color[TRUE] = rep(edge.weights[2],length(x))
color[x==1] = edge.weights[1]
color[x==-1] = edge.weights[3]
graph::edgeRenderInfo(temp) <- list(col=color)
return(temp)
}
#' This function colors the nodes of a graph.
#'
#' This function colors nodes of a graph, usually this is used to color subgraphs
#' or add a color hue correlating with the expression level or fold change to the molecules.
#'
#' @param graph1 graphNEL
#' @param nodes vector of node names specifiying which nodes to color. must be same length as parameter foldChanges
#' @param values vector of values indicating fold changes, gene expression values or similar. colors are mapped linearly over the range of these values
#' @param colors string. either "greenred" or "yellowred", specifying which color gradient to use.
#' @return Returns a graph with specified nodes colored according to the foldChanges
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph1 = layoutRegulatoryGraph(mygraph1)
#' # retrieve all nodes
#' nodes = nodes(mygraph1)
#' # random expression data for your nodes
#' values = rnorm(length(nodes), mean=6, sd=2)
#' # color nodes of the graph
#' mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred")
#' # plot the now colored graph
#' plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
colorGraphNodes <- function(graph1, nodes, values, colors=c("greenred","yellowred")) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph1)) stop("Error: colorGraphNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph1))) stop("Error: colorGraphNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph1))==0) {
warning("warning: colorGraphNodes: supplied graph has no nodes. No coloring was done.")
return(graph1)
}
ncol = length(nodes)
r=seq(0,1,length=ncol)
r2=seq(-1,1,length=ncol)
if(colors=="greenred") {
col = hcl(h=ifelse(r2>0, 90-90*abs(r2), 90+90*abs(r2)), c=30+50*abs(r2)^0.2, l=92-72*abs(r2)^1.5)
}
if(colors=="yellowred") {
col = hcl(h=90-90*r, c=30+50*r^0.2, l=90-60*r^1.5)
}
lim = range(values)
x=findInterval(values, seq(lim[1],lim[2],diff(lim)/ncol)[-c(1,ncol+1)])+1
res=col[x]
for(n in 1:length(nodes)) {
graph::nodeRenderInfo(graph1)$fill[nodes[n]] = res[n]
}
return(graph1)
}
#' This function gracefully removes nodes from a regulatory graph.
#'
#' This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly.
#' The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.
#'
#' @param graph graphNEL
#' @param nodes vector of node names specifiying which nodes to remove.
#' @return Returns a graph with specified nodes removed.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph1 = layoutRegulatoryGraph(mygraph1)
#' # retrieve all nodes
#' nodes = nodes(mygraph1)
#' # random expression data for your nodes
#' values = rnorm(length(nodes), mean=6, sd=2)
#' # color nodes of the graph
#' mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred")
#' # plot the now colored graph
#' plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
removeNodes <- function(graph, nodes) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph)) stop("Error: removeNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph))) stop("Error: removeNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph))==0) {
warning("warning: removeNodes: supplied graph has no nodes. No removing was done.")
return(graph)
}
for (j in 1:length(nodes)) {
##get outgoing edges of nodes
outw = edgeWeights(graph,nodes[j])[[1]]
oute=names(outw)
##get incoming edges
inw=c()
for(w in nodes(graph))
{inw[w] = edgeWeights(graph)[[w]][nodes[j]]}
inw=na.omit(inw)
ine=names(inw)
###create new edges if necessary and delete nodes
if(length(inw)==0 | length(outw)==0) {
message(paste("Removing node", nodes[j],"which has either no incomming or no outgoing edges."))
graph = removeNode(nodes[j], graph)
}
else {
for(p in ine) {
for(ch in oute) {
if(p == ch) next;
if(is.na(edgeWeights(graph)[[p]][ch])) {
if(!is.na(edgeWeights(graph)[[ch]][p])) {
warning(paste("Not adding edge from", p,"to",ch,"with weight",inw[p]*outw[ch],"because we already have an edge the other way round.") )
next;
}
message(paste("Adding edge from", p,"to",ch,"with weight",inw[p]*outw[ch]))
graph = addEdge(p, ch, graph, as.integer(inw[[p]])*as.integer(outw[[ch]]))
}
}
}
message(paste("Removing node", nodes[j],"."))
graph = removeNode(nodes[j], graph)
}
}
return(graph)
}
#' This function gracefully combines nodes of a regulatory graph.
#'
#' This gracefully combines nodes from a regulatory graph. This is basically a wrapper for graph::combineNodes(nodes, graph, newName, collapseFunction=max).
#' If there are duplicated edges for the nodes, the maximum edgeweight will be used for the new connection.
#'
#' @param nodes vector of node names specifiying which nodes to combine.
#' @param graph graphNEL
#' @param newName string. Name of the newly created node that will combine the specified nodes.
#' @return Returns a graph with specified nodes removed.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
combineNodes <- function(nodes, graph, newName) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph)) stop("Error: combineNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph))) stop("Error: combineNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph))==0) {
warning("warning: combineNodes: supplied graph has no nodes. No removing was done.")
return(graph)
}
return(graph::combineNodes(nodes, graph, newName, collapseFunction=max))
}
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Defines functions combineNodes removeNodes colorGraphNodes uniteGraphs diffGraphs intersectGraphs calcGraphOverlap plotRegulatoryGraph layoutRegulatoryGraph transitiveReduction transitiveClosure pathway2RegulatoryGraph pathway2AdjacancyMatrix
Documented in calcGraphOverlap colorGraphNodes combineNodes diffGraphs intersectGraphs layoutRegulatoryGraph pathway2AdjacancyMatrix pathway2RegulatoryGraph plotRegulatoryGraph removeNodes transitiveClosure transitiveReduction uniteGraphs
###############################################################################
#
# visualizeBiopax.R: This file contains the all functions related to visualizing a parsed Biopax model.
# Generation of graphs, layout, adjacency matrices, modification of graphs.
# author: Frank Kramer <dev@frankkramer.de>
#
# This is released under GPL-2.
#
# Documentation was created using roxygen
#
###############################################################################
#' This function generates an adjacency matrix from the activations/inhibitions of a pathway in a biopax model.
#'
#' This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix.
#' See pathway2RegulatoryGraph for more details.
#'
#' @param biopax A biopax model
#' @param pwid string
#' @param expandSubpathways logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
#' @param splitComplexMolecules logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.
#' @param useIDasNodenames logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
#' @param verbose logical
#' @return Returns the adjacency matrix representing the regulatory graph of the supplied pathway.
#' @author Frank Kramer
#' @export
#' @import data.table
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' pathway2AdjacancyMatrix(biopax, pwid1)
pathway2AdjacancyMatrix <- function(biopax, pwid, expandSubpathways=TRUE, splitComplexMolecules=TRUE, useIDasNodenames=FALSE, verbose=TRUE) {
if(!("biopax" %in% class(biopax))) stop("Error: pathway2AdjacancyMatrix: parameter biopax has to be of class biopax.")
if(!("character" %in% class(pwid))) stop("Error: pathway2AdjacancyMatrix: parameter pwid has to be of class character.")
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
mygraph = pathway2RegulatoryGraph(biopax, pwid, expandSubpathways=expandSubpathways, splitComplexMolecules=splitComplexMolecules, useIDasNodenames=useIDasNodenames, verbose=verbose)
ttt = as(mygraph,"graphAM")
as(ttt,"matrix")
}
#test: pwid = "pid_p_200067_wnt_signaling_pathway"
# i = "pid_i_203122_inhibitor_1"
# pwid = "pid_p_200020_wnt_noncanonical_pathway"
# i = "pid_i_203122_inhibitor_1"
#
#' This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model.
#'
#' This functions builds a graph from the pathway components of the supplied pathway.
#' Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc.
#' If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph.
#' There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.
#'
#' @param biopax A biopax model
#' @param pwid string
#' @param expandSubpathways logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
#' @param splitComplexMolecules logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.
#' @param useIDasNodenames logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
#' @param verbose logical
#' @return Returns the representing the regulatory graph of the supplied pathway in a node-edge-list graph.
#' @author Frank Kramer
#' @export
#' @import data.table
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' plotRegulatoryGraph(mygraph)
pathway2RegulatoryGraph <- function(biopax, pwid, expandSubpathways=TRUE, splitComplexMolecules=TRUE, useIDasNodenames=FALSE, verbose=TRUE) {
if(is.null(biopax) || !("biopax" %in% class(biopax))) stop("Error: pathway2RegulatoryGraph: parameter biopax has to be of class biopax.")
biopaxlevel = biopax$biopaxlevel
if(is.null(pwid) ||!("character" %in% class(pwid))) stop("Error: pathway2RegulatoryGraph: parameter pwid has to be of class character.")
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
pwid = unique(striphash(pwid))
#first make an node edge list, because its easier
mygraph = new(getClassDef("graphNEL", package="graph"))
graph::edgemode(mygraph) = "directed"
#get pathway component list
pw_component_list = listPathwayComponents(biopax,pwid, returnIDonly=T)
if(length(pw_component_list)==0) {warning("Pathway seems to have no pathway components"); return(NULL)}
pw_component_list = selectInstances(biopax,id=pw_component_list, includeReferencedInstances=TRUE, returnCopy=TRUE)
pw_component_list$property = tolower(pw_component_list$property)
setkeyv(pw_component_list, cols=c("id","class","property"))
pw_controls = pw_component_list[tolower(pw_component_list$class) %chin% c("control","catalysis","modulation","templatereactionregulation"),]
#verbose
if(length(pw_controls$id)==0) {
warning("warning: pathway2RegulatoryGraph: supplied graph has no regulatory pathway components. Returning NULL.")
return(NULL)
} else {
if(verbose) {
message(paste("Found",length(unique(pw_controls$id)), "pathway components. Putting them together..."))
}
}
#currently considers only controls //TODO: Consider subpathways!
for(i in unique(pw_controls$id)) {
instance = pw_controls[id==i,]
#if type neither inhibition nor activation i dont know what to do anyways.
#Cancer Cell Map doesnt set control-type of catalysises to ACTIVATION although it is required by biopax level 2 standards. quick fix here:
if(biopax$biopaxlevel == 2) {
type = as.character(instance[property=="control-type"]$property_value)
}
if(biopax$biopaxlevel == 3) {
type = as.character(instance[property=="controltype"]$property_value)
}
if(length(type)==0) {
if(tolower(as.character(instance[1,class])) == "catalysis") {
type="ACTIVATION"
} else {
next
}
}
if ( !grepl("activation",type,ignore.case=TRUE) & !grepl("inhibition",type,ignore.case=TRUE)) {
next
}
#controllers are physicalentityparticipants, get those
controller_ids = striphash(as.character(unique(instance[property=="controller"]$property_attr_value)))
controllers = NA
for(i2 in controller_ids) {
c_instance = pw_component_list[id==i2,]
#each physicalentityparticipant has exactly 1 physicalentity, get that and get the name!
if(biopax$biopaxlevel == 2) {
c_instance = pw_component_list[id==striphash(c_instance[property=="physical-entity"]$property_attr_value),]
}
if(splitComplexMolecules & any(isOfClass(c_instance,"complex"))) {
if(useIDasNodenames) {
controllers = c(controllers, as.character( splitComplex(pw_component_list, i2, returnIDonly=T, biopaxlevel=biopaxlevel) ))
} else {
controllers = c(controllers, as.character( splitComplex(pw_component_list, i2, biopaxlevel=biopaxlevel)$name ))
}
} else {
if(useIDasNodenames) {
controllers = c(controllers, c_instance$id[1])
} else {
controllers = c(controllers, getInstanceProperty(pw_component_list,c_instance$id[1], biopaxlevel=biopaxlevel))
}
}
}
#controlleds are interactions or pathways. ignoring pathways for now
controlled_ids = striphash(as.character(unique(instance[property=="controlled"]$property_attr_value)))
controlleds = NA
for(i2 in controlled_ids) {
c_instance = pw_component_list[id==i2,]
#depending on type of c_instance we must differentiate here.
#pathway=ignore,interaction=ignore(this is only a nice field with a name in PID anyways),
#complexAssembly=we deal with a complex. split up or dont and return names
#biochemicalReaction=...
#any conversion: add up left & rights and get the names
if(any(isOfClass(c_instance,c("conversion"),considerInheritance = TRUE)) || any(isOfClass(c_instance,c("templatereaction")))) {
leftrights = striphash(c_instance[property=="left" | property=="right" | property=="product"]$property_attr_value)
for(i3 in leftrights) {
#every left/right is an physicalentityparticipants, get that as above
leftrights_instance = pw_component_list[id==i3,]
if(biopax$biopaxlevel == 2) {
leftrights_instance = pw_component_list[id==striphash(leftrights_instance[property=="physical-entity"]$property_attr_value),]
}
#split complexes?
if(splitComplexMolecules & any(isOfClass(leftrights_instance,"complex"))) {
if(useIDasNodenames) {
controlleds = c(controlleds, as.character( splitComplex(pw_component_list, i3, returnIDonly=T, biopaxlevel=biopaxlevel) ))
} else {
controlleds = c(controlleds, as.character( splitComplex(pw_component_list, i3, biopaxlevel=biopaxlevel)$name ))
}
} else {
if(useIDasNodenames) {
controlleds = c(controlleds, as.character(leftrights_instance[1]$id))
} else {
controlleds = c(controlleds, getInstanceProperty(pw_component_list,leftrights_instance[1]$id, biopaxlevel=biopaxlevel))
}
}
}
}
}
controllers = striphash(unique(controllers))
controlleds = striphash(unique(controlleds))
controllers = controllers[!is.na(controllers) & !is.null(controllers) & nchar(controllers) > 0 ]
controlleds = controlleds[!is.na(controlleds) & !is.null(controlleds) & nchar(controlleds) > 0 ]
#only add viable directed edges:
if(length(controllers)==0 | length(controlleds)==0) {
next
}
#verbose
if(verbose) {
message(paste("Adding to graph: ",unique(as.character(instance[,"class"])), "-", type,
"Controllers: ", paste(controllers, collapse=" "), "Controlleds: ", paste(controlleds, collapse=" ")))
}
#now we have the controllers and controlleds lists, add edge
# leave out duplicates
newnodes = unique(c(controllers,controlleds))
# only add new nodes that are not null, na or empty strings
newnodes = newnodes[!(newnodes %in% graph::nodes(mygraph))]
if(length(newnodes)>0) mygraph = graph::addNode(newnodes,mygraph)
#set weight: activation 1, inhibition = -1
if ( tolower(type)=="activation" ) {
weights = 1
} else {
weights = -1
}
# add all edges from controllers to controlleds.
for(i_controllers in controllers) {
for(i_controlleds in controlleds) {
#skip edges to self
if(i_controllers != i_controlleds) {
#if edge already exists throw a warning and skip
if(!(i_controlleds %in% unlist(graph::edges(mygraph, which=i_controllers)))) {
mygraph = graph::addEdge(i_controllers, i_controlleds,mygraph,weights=weights)
} else {
warning( paste("Problem while adding edge (weight=",weights,") to graph: Edge already exists between ",i_controllers," and ",i_controlleds," (weight=",unlist(graph::edgeWeights(mygraph))[paste(i_controllers,i_controlleds,sep=".")],"). Skipping this edge.",sep="" ) )
}
}
}
}
}
mygraph
}
#' This function generates the transitive closure of the supplied graph.
#'
#' This function generates the transitive closure of the supplied graph. In short: if A->B->C then an edge A->C is added.
#' Edge weights are conserved if possible (in a hopefully smart way). This is a simple convenience wrapper for the RBGL function transitive.closure.
#'
#' @param mygraph graphNEL
#' @return Returns the transitive closure of the supplied graph.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' tc = transitiveClosure(mygraph)
transitiveClosure <- function(mygraph) {
if(!require(graph)) {
message(paste("This functions needs the graph package installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(!require(RBGL)) {
message(paste("This functions needs the RBGL package installed, albeit it cannot be found.","\n"))
return(NULL)
}
RBGL::transitive.closure(mygraph)
# accessibles = acc(mygraph,graph::nodes(mygraph))
# for(n in names(accessibles)) {
# for(c in names(accessibles[[n]])) {
# if(accessibles[[n]][[c]]>1) {
# #cat(paste("adding",n,c,"\n"))
# mygraph = graph::addEdge(from=n,to=c, graph=mygraph, weights=1) ###FIX! XXX
# }
# }
# }
# mygraph
}
#' This function generates the transitive reduction of the supplied graph.
#'
#' This function is deprecated due to nem dropping out of Bioconductor in BioC 4.0.
#' This function generates the transitive reduction of the supplied graph. In short: if A->B->C AND A->C then edge A->C is removed.
#' This is a simple convenience wrapper for the NEM function transitive.reduction. Be aware of implications on the edge weights!
#'
#' @param mygraph graphNEL
#' @return Returns the transitive reduction of the supplied graph.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' tr = transitiveReduction(mygraph)
transitiveReduction <- function(mygraph) {
warning("This function is deprecated due to nem dropping out of Bioconductor. Returning NULL.")
return(NULL)
}
#' This function generates a (more or less) beautiful layout for a regulatory graph.
#'
#' This function generates a (more or less) beautiful layout for a regulatory graph.
#' Call this after you generated a graph with pathway2RegulatoryGraph. Since beauty is always in the eye of the beholder consider this a starting point for making your graphs even nicer.
#' Rgraphviz with dot layout is used.
#' Edges are green/red with normal/tee arrowheads for activations/inhibitions.
#' If you want to specifically paint subgraphs in different colors use lists of vectors with node names for parameter subgraphs and vector of color names for subgraphs.color for your choice of color.
#' The output can be further tweaked by setting layout options using nodeRenderInfo(mygraph) <- list() ...
#' See the Rgraphviz and Graphviz documentations.
#'
#' @param mygraph graphNEL
#' @param label Label of the graph
#' @param node.fixedsize logical. If font size is fixed or variable in regards to the nodes.
#' @param edge.weights vector. which colors to use for weighted edges
#' @param edge.arrowheads vector. which arrowheads to use for weighted edges
#' @param subgraphs A list of character vectors with node names defining the sub graphs.
#' @param subgraphs.colors vector. which colors to use for subgraphs
#' @return Returns the supplied graph in a layouted form with several parameters set for regulatory graph plotting.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph = layoutRegulatoryGraph(mygraph)
#' plotRegulatoryGraph(mygraph)
layoutRegulatoryGraph <- function(mygraph, label="", node.fixedsize=FALSE, edge.weights=c("green","black","red"), edge.arrowheads=c("normal","tee"),
subgraphs=list(), subgraphs.colors=c("#B3E2CD","#FDCDAC","#F4CAE4","#E6F5C9","#FFF2AE")) {
if(is.null(mygraph)) stop("Error: layoutRegulatoryGraph: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(mygraph))) stop("Error: layoutRegulatoryGraph: supplied graph has to be of class graphNEL.")
if(length(nodes(mygraph))==0) {
warning("warning: layoutRegulatoryGraph: supplied graph has no nodes. No layout was done.")
return(mygraph)
}
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(label != "") graph::graphRenderInfo(mygraph) <- list(label=label, labelJust="l", labelLoc="t")
graph::nodeRenderInfo(mygraph) <- list(shape="ellipse", fill="#e0e0e0", fixedsize=node.fixedsize)
#graph::nodeRenderInfo(mygraph) <- list(iwidth="2", iheight="2")
mygraph = Rgraphviz::layoutGraph(mygraph)
#GRAPH
# graph rendering info
if(label != "") graph::graphRenderInfo(mygraph) <- list(label=label, labelJust="l", labelLoc="t")
#EDGES
# generate a list of all edges, preinitialized with the weights
x = unlist(graph::edgeData(mygraph))
names(x) = gsub(".weight","",names(x))
names(x) = gsub("|","~",names(x), fixed=TRUE)
#set edge arrowheads
arrowhead = x
arrowhead[TRUE] = rep(edge.arrowheads[1],length(x))
arrowhead[x==1] = edge.arrowheads[1]
arrowhead[x==-1] = edge.arrowheads[2]
graph::edgeRenderInfo(mygraph) <- list(arrowhead=arrowhead)
#set edge colors
color = x
color[TRUE] = rep(edge.weights[2],length(x))
color[x==1] = edge.weights[1]
color[x==-1] = edge.weights[3]
graph::edgeRenderInfo(mygraph) <- list(col=color)
#NODES
#shape size and fill of nodes
graph::nodeRenderInfo(mygraph) <- list(shape="ellipse", fill="#e0e0e0", fixedsize=node.fixedsize)
#SUBGRAPHS
if(length(subgraphs) > 0) {
for(i in 1:length(subgraphs)) {
for(n in subgraphs[[i]]) {
graph::nodeRenderInfo(mygraph)$fill[n] <- subgraphs.colors[i]
}
}
}
return(mygraph)
}
#' This function layouts a regulatory graph and plots it using Rgraphviz.
#'
#' This function takes a regulatory graph as generated by pathway2regulatoryGraph and plots it using standard layout options of layoutRegulatoryGraph.
#' This function is a wrapper for layoutRegulatoryGraph with standard parameters.
#' Subgraphs can be painted with different colors. This can be done by passing parameter subgraph a list of character vectors with node names.
#'
#' @param mygraph graphNEL, regulatory graph
#' @param subgraphs list of character vectors with node names
#' @param layoutGraph logical. If FALSE the graph is not laid out again but send directly to Rgraphviz::renderGraph.
#' @return none
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph = pathway2RegulatoryGraph(biopax, pwid1)
#' plotRegulatoryGraph(mygraph)
plotRegulatoryGraph <- function(mygraph, subgraphs=list(), layoutGraph=TRUE) {
if(is.null(mygraph)) stop("Error: plotRegulatoryGraph: supplied graph parameter was NULL.")
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!("graphNEL" %in% class(mygraph))) stop("Error: plotRegulatoryGraph: supplied graph has to be of class graphNEL.")
if(length(nodes(mygraph))==0) {
warning("warning: plotRegulatoryGraph: supplied graph has no nodes. No plotting was done.")
return(mygraph)
}
temp = mygraph
if(layoutGraph) {
temp = layoutRegulatoryGraph(temp, subgraphs=subgraphs)
}
Rgraphviz::renderGraph(temp)
}
#' This function calculates the overlap of 2 graphs
#'
#' This function calculates the overlap of supplied graph1 with graph2.
#' Layout and weights of graph1 are kept.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @return Returns a list containing the compared graphs and edge- and node-wise overlap between them.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' calcGraphOverlap(mygraph1,mygraph2)
calcGraphOverlap <- function(graph1, graph2) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
edges_overlap = (length(graph::edgeNames(graph1)) - length(setdiff(graph::edgeNames(graph1), graph::edgeNames(graph2)))) / length(graph::edgeNames(graph1))
nodes_overlap = (length(graph::nodes(graph1)) - length(setdiff(graph::nodes(graph1), graph::nodes(graph2)))) / length(graph::nodes(graph1))
list(graph1=graph1, graph2=graph2, edges_overlap = edges_overlap , nodes_overlap = nodes_overlap)
}
#' This function returns a graph computed by the insection of supplied graph1 and graph2.
#'
#' This function returns a graph computed by the insection of supplied graph1 and graph2.
#' Layout and weights of graph1 are kept.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @return Returns the intersection of graph1 and graph2.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(intersectGraphs(mygraph1,mygraph2))
intersectGraphs <- function(graph1, graph2) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = setdiff(e1,e2)
for(x in 1:length(i)) {
temp = graph::removeEdge(i[[x]][1],i[[x]][2], temp)
}
for(x in setdiff(graph::nodes(graph1), graph::nodes(graph2))) {
temp = graph::removeNode(x, temp)
}
temp
}
#' This function returns the different nodes and edges between graph1 and graph2.
#'
#' This function returns the different nodes and edges between graph1 and graph2.
#' Layout options of graph1 are kept.
#' Coloring currently not implemented.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @param colorNodes logical
#' @param colors character vector of colors. If colorNodes==TRUE these colors are used for graph1 and graph2 respectivley.
#' @return Return the diff between the graphs.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(diffGraphs(mygraph1,mygraph2))
diffGraphs <- function(graph1, graph2, colorNodes=TRUE, colors=c("#B3E2CD","#FDCDAC") ) {
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = intersect(e1,e2)
for(x in 1:length(i)) {
temp = graph::removeEdge(i[[x]][1],i[[x]][2], temp)
}
temp
}
#' This function unites two graphs.
#'
#' This function unites the two supplied graphs. Layout parameters from graph1 are used.
#' If colorNodes==TRUE the returned graph has different colors for overlapping nodes and nodes individual for each graph.
#'
#' @param graph1 graphNEL
#' @param graph2 graphNEL
#' @param colorNodes logical
#' @param colors colors character vector of colors. If colorNodes==TRUE these colors are used for graph1 and graph2 respectivley.
#' @return Return a graph generated by uniting the two supplied graphs
#' @author Frank Kramer
#' @export
#' @examples
#' # load data
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' pwid2 = "pid_p_100146_hespathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph2 = pathway2RegulatoryGraph(biopax, pwid2)
#' plotRegulatoryGraph(uniteGraphs(mygraph1,mygraph2))
uniteGraphs <- function(graph1, graph2, colorNodes=TRUE, colors=c("#B3E2CD","#FDCDAC","#F4CAE4")) { #color: yellow, lightblue, lightgreen
if(!require(graph)) {
message("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
if(!require(Rgraphviz)) {
message("This functions needs the Rgraphviz library installed, albeit it cannot be found. Check out the installation instructions!")
return(NULL)
}
temp = graph1
graph::graphRenderInfo(temp)$laidout <- FALSE
#ADD NODES
for(i in setdiff(graph::nodes(graph2), graph::nodes(graph1))) {
temp = graph::addNode(i, temp)
}
#ADD EDGES
e1 = strsplit(graph::edgeNames(graph1), split="~")
e2 = strsplit(graph::edgeNames(graph2), split="~")
i = setdiff(e2,e1)
for(x in 1:length(i)) {
temp = graph::addEdge(i[[x]][1],i[[x]][2], temp, as.numeric(graph::edgeData(graph2,i[[x]][1],i[[x]][2], "weight")))
}
#shape size and fill of nodes
nodevector = as.vector(rep(1,length(graph::nodes(temp))))
names(nodevector) = graph::nodes(temp)
node.shape = nodevector
node.shape[TRUE] = "ellipse"
graph::nodeRenderInfo(temp)$shape <- node.shape
#LAYOUT GRAPH
temp = Rgraphviz::layoutGraph(temp)
#set shape again. strange rgraphviz behavior
graph::nodeRenderInfo(temp)$shape <- node.shape
node.fill = nodevector
node.fill[TRUE] = colors[1]
graph::nodeRenderInfo(temp)$fill <- node.fill
### reuse previous layout of graph1
if(!is.null(graph::nodeRenderInfo(graph1)$height[1])) {
node.height = nodevector
node.height[TRUE] = graph::nodeRenderInfo(graph1)$height[1]
graph::nodeRenderInfo(temp)$height <- node.height
}
if(!is.null(graph::nodeRenderInfo(graph1)$width[1])) {
node.width = nodevector
node.width[TRUE] = graph::nodeRenderInfo(graph1)$width[1]
graph::nodeRenderInfo(temp)$width <- node.width
}
if(!is.null(graph::nodeRenderInfo(graph1)$fontsize[1])) {
node.fontsize = nodevector
node.fontsize[TRUE] = graph::nodeRenderInfo(graph1)$fontsize[1]
graph::nodeRenderInfo(temp)$fontsize <- node.fontsize
}
if(!is.null(graph::nodeRenderInfo(graph1)$labelfontsize[1])) {
node.labelfontsize = nodevector
node.labelfontsize[TRUE] = graph::nodeRenderInfo(graph1)$labelfontsize[1]
graph::nodeRenderInfo(temp)$labelfontsize <- node.labelfontsize
}
if(!is.null(graph::nodeRenderInfo(graph1)$labelfontsize[1])) {
node.fixedsize = nodevector
node.fixedsize[TRUE] = graph::nodeRenderInfo(graph1)$fixedsize[1]
graph::nodeRenderInfo(temp)$fixedsize <- node.fixedsize
}
#COLOR SUBGRAPHS
#only graph1
for(n in setdiff(graph::nodes(graph1), graph::nodes(graph2))) {
graph::nodeRenderInfo(temp)$fill[n] <- colors[2]
}
#only graph2
for(n in setdiff(graph::nodes(graph2), graph::nodes(graph1))) {
graph::nodeRenderInfo(temp)$fill[n] <- colors[3]
}
#COLOR EDGES
# generate a list of all edges, preinitialized with the weights
edge.weights=c("green","black","red")
x = unlist(graph::edgeData(temp))
names(x) = gsub(".weight","",names(x))
names(x) = gsub("|","~",names(x), fixed=TRUE)
#set edge arrowheads
edge.arrowheads=c("normal","tee")
arrowhead = x
arrowhead[TRUE] = rep(edge.arrowheads[1],length(x))
arrowhead[x==1] = edge.arrowheads[1]
arrowhead[x==-1] = edge.arrowheads[2]
graph::edgeRenderInfo(temp) <- list(arrowhead=arrowhead)
#set edge colors
color = x
color[TRUE] = rep(edge.weights[2],length(x))
color[x==1] = edge.weights[1]
color[x==-1] = edge.weights[3]
graph::edgeRenderInfo(temp) <- list(col=color)
return(temp)
}
#' This function colors the nodes of a graph.
#'
#' This function colors nodes of a graph, usually this is used to color subgraphs
#' or add a color hue correlating with the expression level or fold change to the molecules.
#'
#' @param graph1 graphNEL
#' @param nodes vector of node names specifiying which nodes to color. must be same length as parameter foldChanges
#' @param values vector of values indicating fold changes, gene expression values or similar. colors are mapped linearly over the range of these values
#' @param colors string. either "greenred" or "yellowred", specifying which color gradient to use.
#' @return Returns a graph with specified nodes colored according to the foldChanges
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph1 = layoutRegulatoryGraph(mygraph1)
#' # retrieve all nodes
#' nodes = nodes(mygraph1)
#' # random expression data for your nodes
#' values = rnorm(length(nodes), mean=6, sd=2)
#' # color nodes of the graph
#' mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred")
#' # plot the now colored graph
#' plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
colorGraphNodes <- function(graph1, nodes, values, colors=c("greenred","yellowred")) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph1)) stop("Error: colorGraphNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph1))) stop("Error: colorGraphNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph1))==0) {
warning("warning: colorGraphNodes: supplied graph has no nodes. No coloring was done.")
return(graph1)
}
ncol = length(nodes)
r=seq(0,1,length=ncol)
r2=seq(-1,1,length=ncol)
if(colors=="greenred") {
col = hcl(h=ifelse(r2>0, 90-90*abs(r2), 90+90*abs(r2)), c=30+50*abs(r2)^0.2, l=92-72*abs(r2)^1.5)
}
if(colors=="yellowred") {
col = hcl(h=90-90*r, c=30+50*r^0.2, l=90-60*r^1.5)
}
lim = range(values)
x=findInterval(values, seq(lim[1],lim[2],diff(lim)/ncol)[-c(1,ncol+1)])+1
res=col[x]
for(n in 1:length(nodes)) {
graph::nodeRenderInfo(graph1)$fill[nodes[n]] = res[n]
}
return(graph1)
}
#' This function gracefully removes nodes from a regulatory graph.
#'
#' This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly.
#' The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.
#'
#' @param graph graphNEL
#' @param nodes vector of node names specifiying which nodes to remove.
#' @return Returns a graph with specified nodes removed.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
#' pwid1 = "pid_p_100002_wntpathway"
#' mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
#' mygraph1 = layoutRegulatoryGraph(mygraph1)
#' # retrieve all nodes
#' nodes = nodes(mygraph1)
#' # random expression data for your nodes
#' values = rnorm(length(nodes), mean=6, sd=2)
#' # color nodes of the graph
#' mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred")
#' # plot the now colored graph
#' plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
removeNodes <- function(graph, nodes) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph)) stop("Error: removeNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph))) stop("Error: removeNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph))==0) {
warning("warning: removeNodes: supplied graph has no nodes. No removing was done.")
return(graph)
}
for (j in 1:length(nodes)) {
##get outgoing edges of nodes
outw = edgeWeights(graph,nodes[j])[[1]]
oute=names(outw)
##get incoming edges
inw=c()
for(w in nodes(graph))
{inw[w] = edgeWeights(graph)[[w]][nodes[j]]}
inw=na.omit(inw)
ine=names(inw)
###create new edges if necessary and delete nodes
if(length(inw)==0 | length(outw)==0) {
message(paste("Removing node", nodes[j],"which has either no incomming or no outgoing edges."))
graph = removeNode(nodes[j], graph)
}
else {
for(p in ine) {
for(ch in oute) {
if(p == ch) next;
if(is.na(edgeWeights(graph)[[p]][ch])) {
if(!is.na(edgeWeights(graph)[[ch]][p])) {
warning(paste("Not adding edge from", p,"to",ch,"with weight",inw[p]*outw[ch],"because we already have an edge the other way round.") )
next;
}
message(paste("Adding edge from", p,"to",ch,"with weight",inw[p]*outw[ch]))
graph = addEdge(p, ch, graph, as.integer(inw[[p]])*as.integer(outw[[ch]]))
}
}
}
message(paste("Removing node", nodes[j],"."))
graph = removeNode(nodes[j], graph)
}
}
return(graph)
}
#' This function gracefully combines nodes of a regulatory graph.
#'
#' This gracefully combines nodes from a regulatory graph. This is basically a wrapper for graph::combineNodes(nodes, graph, newName, collapseFunction=max).
#' If there are duplicated edges for the nodes, the maximum edgeweight will be used for the new connection.
#'
#' @param nodes vector of node names specifiying which nodes to combine.
#' @param graph graphNEL
#' @param newName string. Name of the newly created node that will combine the specified nodes.
#' @return Returns a graph with specified nodes removed.
#' @author Frank Kramer
#' @export
#' @examples
#' # load data and retrieve wnt pathway
#' data(biopaxexample)
combineNodes <- function(nodes, graph, newName) {
if(!require(graph)) {
message(paste("This functions needs the graph library installed, albeit it cannot be found. Check out the installation instructions!","\n"))
return(NULL)
}
if(is.null(graph)) stop("Error: combineNodes: supplied graph parameter was NULL.")
if(!("graphNEL" %in% class(graph))) stop("Error: combineNodes: supplied graph has to be of class graphNEL.")
if(length(nodes(graph))==0) {
warning("warning: combineNodes: supplied graph has no nodes. No removing was done.")
return(graph)
}
return(graph::combineNodes(nodes, graph, newName, collapseFunction=max))
}
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