Nothing
R/getNonMetabolicGraph.R
In TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach
getNonMetabolicGraph <-
function(pathwayList,ambiguousEdgeDirection="bi-directed",ambiguousEdgeList=c("unknow","compound","hidden compound","state change","binding/association","dissociation"),simpleGraph=TRUE,splitCompoundSubType=TRUE,verbose=FALSE){
if(!is.list(pathwayList)) stop("users must input a list type of data which include pathways")
if(!ambiguousEdgeDirection %in% c("bi-directed","single","delete")) stop("ambiguousEdgeDirection should be one of bi-directed, single, or delete")
pathwayListLength<-length(pathwayList)
graphList<-list()
Na<-c()#
if(pathwayListLength>0){
for(t in 1:pathwayListLength){
if(verbose==TRUE)
print(paste("deal with the pathway ",t," in ",pathwayListLength, " pathways",sep=""))
Na[t]<-pathwayList[[t]]$pathwayAttrs$number
entrylength<-0
entrylength<-length(pathwayList[[t]]$entry)
name<-c();ID<-c();id<-c();names<-c();type<-c();reaction<-c();link<-c()
graphics_name<-c();graphics_fgcolor<-c();graphics_bgcolor<-c()
graphics_type<-c();graphics_x<-c();graphics_y<-c()
graphics_width<-c();graphics_height<-c();graphics_coords<-c()
group<-list()
#component_id<-as.character(component_id)
j<-0
k<-0
for(i in 1:entrylength){
if(pathwayList[[t]]$entry[[i]]$type!="group"){
j<-j+1
id[j]<-pathwayList[[t]]$entry[[i]]$id
names[j]<-pathwayList[[t]]$entry[[i]]$name
type[j]<-pathwayList[[t]]$entry[[i]]$type
reaction[j]<-pathwayList[[t]]$entry[[i]]$reaction
link[j]<-pathwayList[[t]]$entry[[i]]$link
graphics_name[j]<-pathwayList[[t]]$entry[[i]]$graphics$name
graphics_fgcolor[j]<-pathwayList[[t]]$entry[[i]]$graphics$fgcolor
graphics_bgcolor[j]<-pathwayList[[t]]$entry[[i]]$graphics$bgcolor
graphics_type[j]<-pathwayList[[t]]$entry[[i]]$graphics$type
graphics_x[j]<-pathwayList[[t]]$entry[[i]]$graphics$x
graphics_y[j]<-pathwayList[[t]]$entry[[i]]$graphics$y
graphics_width[j]<-pathwayList[[t]]$entry[[i]]$graphics$width
graphics_height[j]<-pathwayList[[t]]$entry[[i]]$graphics$height
graphics_coords[j]<-pathwayList[[t]]$entry[[i]]$graphics$coords
}else if(pathwayList[[t]]$entry[[i]]$type=="group"){
k<-k+1
group[[k]]<-pathwayList[[t]]$entry[[i]]$component
names(group)[k]<-pathwayList[[t]]$entry[[i]]$id
}
}
entrylength<-j
########################################################################################################
#####################################
relationlength<-0
relaionlength<-length(pathwayList[[t]]$relation)
entry1<-c();entry2<-c();type1<-c();subtype_name<-c();subtype_value<-c();ii<-0;
if(!(pathwayList[[t]]$relation[[1]]$entry1=="unknow")){
for(i in 1:relaionlength){
group_hit<-FALSE
if(length(group)>0){
group_left<-group[names(group) %in% pathwayList[[t]]$relation[[i]]$entry1]
group_right<-group[names(group) %in% pathwayList[[t]]$relation[[i]]$entry2]
if(length(group_left)>0&&length(group_right)>0){#
group_hit<-TRUE
for(uu in seq(group_left[[1]])){
for(uuu in seq(group_right[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}##for
}
}else if(length(group_left)>0&&length(group_right)<1){#
group_hit<-TRUE
for(uu in seq(group_left[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}## for
}else if(length(group_left)<1&&length(group_right)>0){#
group_hit<-TRUE
for(uuu in seq(group_right[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}## for
}
}#end length(group)
if(group_hit==FALSE){#
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if((!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList))||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}#end group_hit==FALSE
}#end for(i in 1:relaionlength)
}#end if(!(pathwayList[[t]]$relation[[1]]$entry1=="unknow"))
########################################################################################################
###############################################################
if(length(entry1)==0||(pathwayList[[t]]$relation[[1]]$entry1=="unknow")){
graphList[[t]]<-graph.empty(n=0,directed=TRUE)
graphList[[t]]<-add.vertices(graphList[[t]],entrylength,name=id,id=id,names=names,
type=type,reaction=reaction,link=link,graphics_name=graphics_name,
graphics_fgcolor=graphics_fgcolor,graphics_bgcolor=graphics_bgcolor,graphics_type=graphics_type,
graphics_x=graphics_x,graphics_y=graphics_y,graphics_width=graphics_width,
graphics_height=graphics_height,graphics_coords=graphics_coords)
}else{
Vertices<-data.frame(ID=id,id=id,names=names,type=type,reaction=reaction,link=link,
graphics_name=graphics_name,graphics_fgcolor=graphics_fgcolor,graphics_bgcolor=graphics_bgcolor,
graphics_type=graphics_type,graphics_x=graphics_x,graphics_y=graphics_y,
graphics_width=graphics_width,graphics_height=graphics_height,graphics_coords=graphics_coords)
Edges<-data.frame(entry1=entry1,entry2=entry2,type=type1,subtype_name=subtype_name,
subtype_value=subtype_value)
graphList[[t]]<-graph.data.frame(Edges,directed=TRUE,Vertices)
}
graphList[[t]]<-set.graph.attribute(graphList[[t]],"name",pathwayList[[t]]$pathwayAttrs$name)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"number",pathwayList[[t]]$pathwayAttrs$number)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"org",pathwayList[[t]]$pathwayAttrs$org)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"title",pathwayList[[t]]$pathwayAttrs$title)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"image",pathwayList[[t]]$pathwayAttrs$image)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"link",pathwayList[[t]]$pathwayAttrs$link)
} #end for(t in 1:pathwayListLength)
}#end if(pathwayListLength>0)
names(graphList)<-Na
if(simpleGraph==TRUE)
graphList<-getSimpleGraph(graphList)
return(graphList)
}
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getNonMetabolicGraph <-
function(pathwayList,ambiguousEdgeDirection="bi-directed",ambiguousEdgeList=c("unknow","compound","hidden compound","state change","binding/association","dissociation"),simpleGraph=TRUE,splitCompoundSubType=TRUE,verbose=FALSE){
if(!is.list(pathwayList)) stop("users must input a list type of data which include pathways")
if(!ambiguousEdgeDirection %in% c("bi-directed","single","delete")) stop("ambiguousEdgeDirection should be one of bi-directed, single, or delete")
pathwayListLength<-length(pathwayList)
graphList<-list()
Na<-c()#
if(pathwayListLength>0){
for(t in 1:pathwayListLength){
if(verbose==TRUE)
print(paste("deal with the pathway ",t," in ",pathwayListLength, " pathways",sep=""))
Na[t]<-pathwayList[[t]]$pathwayAttrs$number
entrylength<-0
entrylength<-length(pathwayList[[t]]$entry)
name<-c();ID<-c();id<-c();names<-c();type<-c();reaction<-c();link<-c()
graphics_name<-c();graphics_fgcolor<-c();graphics_bgcolor<-c()
graphics_type<-c();graphics_x<-c();graphics_y<-c()
graphics_width<-c();graphics_height<-c();graphics_coords<-c()
group<-list()
#component_id<-as.character(component_id)
j<-0
k<-0
for(i in 1:entrylength){
if(pathwayList[[t]]$entry[[i]]$type!="group"){
j<-j+1
id[j]<-pathwayList[[t]]$entry[[i]]$id
names[j]<-pathwayList[[t]]$entry[[i]]$name
type[j]<-pathwayList[[t]]$entry[[i]]$type
reaction[j]<-pathwayList[[t]]$entry[[i]]$reaction
link[j]<-pathwayList[[t]]$entry[[i]]$link
graphics_name[j]<-pathwayList[[t]]$entry[[i]]$graphics$name
graphics_fgcolor[j]<-pathwayList[[t]]$entry[[i]]$graphics$fgcolor
graphics_bgcolor[j]<-pathwayList[[t]]$entry[[i]]$graphics$bgcolor
graphics_type[j]<-pathwayList[[t]]$entry[[i]]$graphics$type
graphics_x[j]<-pathwayList[[t]]$entry[[i]]$graphics$x
graphics_y[j]<-pathwayList[[t]]$entry[[i]]$graphics$y
graphics_width[j]<-pathwayList[[t]]$entry[[i]]$graphics$width
graphics_height[j]<-pathwayList[[t]]$entry[[i]]$graphics$height
graphics_coords[j]<-pathwayList[[t]]$entry[[i]]$graphics$coords
}else if(pathwayList[[t]]$entry[[i]]$type=="group"){
k<-k+1
group[[k]]<-pathwayList[[t]]$entry[[i]]$component
names(group)[k]<-pathwayList[[t]]$entry[[i]]$id
}
}
entrylength<-j
########################################################################################################
#####################################
relationlength<-0
relaionlength<-length(pathwayList[[t]]$relation)
entry1<-c();entry2<-c();type1<-c();subtype_name<-c();subtype_value<-c();ii<-0;
if(!(pathwayList[[t]]$relation[[1]]$entry1=="unknow")){
for(i in 1:relaionlength){
group_hit<-FALSE
if(length(group)>0){
group_left<-group[names(group) %in% pathwayList[[t]]$relation[[i]]$entry1]
group_right<-group[names(group) %in% pathwayList[[t]]$relation[[i]]$entry2]
if(length(group_left)>0&&length(group_right)>0){#
group_hit<-TRUE
for(uu in seq(group_left[[1]])){
for(uuu in seq(group_right[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}##for
}
}else if(length(group_left)>0&&length(group_right)<1){#
group_hit<-TRUE
for(uu in seq(group_left[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-group_left[[1]][uu]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}## for
}else if(length(group_left)<1&&length(group_right)>0){#
group_hit<-TRUE
for(uuu in seq(group_right[[1]])){
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if(!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-group_right[[1]][uuu]
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}## for
}
}#end length(group)
if(group_hit==FALSE){#
for(j in seq(pathwayList[[t]]$relation[[i]]$subtype)){
if((!(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList))||(ambiguousEdgeDirection %in% c("single","bi-directed"))){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
type1[ii]<-"unknow"
subtype_name[ii]<-"unknow"
subtype_value[ii]<-"unknow"
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}else{
ii<-ii+1
entry1[ii]<-pathwayList[[t]]$relation[[i]]$entry1
entry2[ii]<-pathwayList[[t]]$relation[[i]]$entry2
type1[ii]<-pathwayList[[t]]$relation[[i]]$type
subtype_name[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$name
subtype_value[ii]<-pathwayList[[t]]$relation[[i]]$subtype[[j]]$value
}
}
if(ambiguousEdgeDirection=="bi-directed"&&(pathwayList[[t]]$relation[[i]]$subtype[[j]]$name %in% ambiguousEdgeList)){
if(splitCompoundSubType==TRUE&&pathwayList[[t]]$relation[[i]]$subtype[[j]]$name=="compound"){
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
ii<-ii+1
entry1[ii]<-entry2[ii-2]
entry2[ii]<-entry1[ii-2]
type1[ii]<-type1[ii-2]
subtype_name[ii]<-subtype_name[ii-2]
subtype_value[ii]<-subtype_value[ii-2]
}else{
ii<-ii+1
entry1[ii]<-entry2[ii-1]
entry2[ii]<-entry1[ii-1]
type1[ii]<-type1[ii-1]
subtype_name[ii]<-subtype_name[ii-1]
subtype_value[ii]<-subtype_value[ii-1]
}
}
}
}#end group_hit==FALSE
}#end for(i in 1:relaionlength)
}#end if(!(pathwayList[[t]]$relation[[1]]$entry1=="unknow"))
########################################################################################################
###############################################################
if(length(entry1)==0||(pathwayList[[t]]$relation[[1]]$entry1=="unknow")){
graphList[[t]]<-graph.empty(n=0,directed=TRUE)
graphList[[t]]<-add.vertices(graphList[[t]],entrylength,name=id,id=id,names=names,
type=type,reaction=reaction,link=link,graphics_name=graphics_name,
graphics_fgcolor=graphics_fgcolor,graphics_bgcolor=graphics_bgcolor,graphics_type=graphics_type,
graphics_x=graphics_x,graphics_y=graphics_y,graphics_width=graphics_width,
graphics_height=graphics_height,graphics_coords=graphics_coords)
}else{
Vertices<-data.frame(ID=id,id=id,names=names,type=type,reaction=reaction,link=link,
graphics_name=graphics_name,graphics_fgcolor=graphics_fgcolor,graphics_bgcolor=graphics_bgcolor,
graphics_type=graphics_type,graphics_x=graphics_x,graphics_y=graphics_y,
graphics_width=graphics_width,graphics_height=graphics_height,graphics_coords=graphics_coords)
Edges<-data.frame(entry1=entry1,entry2=entry2,type=type1,subtype_name=subtype_name,
subtype_value=subtype_value)
graphList[[t]]<-graph.data.frame(Edges,directed=TRUE,Vertices)
}
graphList[[t]]<-set.graph.attribute(graphList[[t]],"name",pathwayList[[t]]$pathwayAttrs$name)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"number",pathwayList[[t]]$pathwayAttrs$number)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"org",pathwayList[[t]]$pathwayAttrs$org)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"title",pathwayList[[t]]$pathwayAttrs$title)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"image",pathwayList[[t]]$pathwayAttrs$image)
graphList[[t]]<-set.graph.attribute(graphList[[t]],"link",pathwayList[[t]]$pathwayAttrs$link)
} #end for(t in 1:pathwayListLength)
}#end if(pathwayListLength>0)
names(graphList)<-Na
if(simpleGraph==TRUE)
graphList<-getSimpleGraph(graphList)
return(graphList)
}
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