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06graphTemposManual.R
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06graphTemposManual.R
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rm(list = ls())
#Did you change it to your base location?
baseDir="~/LeadNPC/"
setwd(baseDir)
source(file = "bin/00base.R")
load("./Data/allTranscriptogramers80")
load("./Data/tfs.RData")
load("./Data/colors.RData")
library(igraph)
library(RedeR)
library(transcriptogramer)
library(ggplot2)
library(purrr)
myTheme<-list()
zoom=30
myTheme$nestShape='ROUNDED_RECTANGLE'
myTheme$nestColor='#ffffff'
myTheme$nestLineWidth=4*(100/zoom)
myTheme$nestFontSize=24*(100/zoom)
myTheme$nestFontX=5
myTheme$nestFontY=10.8
myTheme$isAssign=TRUE
p<-matrix(0,ncol = 2, nrow = nrow(transc[[1]]@ordering))
i=1
for(i in 1:2){
object<-transc[[i]]
j=1
for(j in 1:length(object@clusters)){
pontos<-object@clusters[[j]]
#colnames(pontos)<-c("x","y")
p[pontos[[1]]:pontos[[2]],i]<-2^(i)
}
}
genesIndex<-p[,1]+p[,2]
#se 1 G3, se 2 G4, se 4 G5, se 3 G3 e G4, 6 G4 e G5, se 7 G3 G4 e G5 se 0 ninguem
g0<-object@ordering$Protein[genesIndex==0]
g1<-object@ordering$Protein[genesIndex==2]
g12<-object@ordering$Protein[genesIndex==6]
g2<-object@ordering$Protein[genesIndex==4]
#check
length(g1)+length(g12)+length(g2)+length(g0)-
nrow(object@ordering)
#limites dos clusteres
clusters<-list()
object<-transc[[1]]
for(i in 1:2){
c1<-(unlist(map(transc[[i]]@clusters, 1)))
c2<-(unlist(map(transc[[i]]@clusters, 2)))
clusters[[i]]<-data.frame(ini=c1,fim=c2)
}
i=1
#intersecção dos clusteres
load(file = "./Data/clusteres.RData")
#load(file = "./Data/clusteresSB.RData")
c1<-clusteres$T1
c2<-clusteres$T2
clusters12<-data.frame(Protein = transc[[2]]@ordering$Protein,
Position = transc[[2]]@ordering$Position,
Clust1 = NA,
Clust2 = NA)
for(i in 1:12){
clusters12$Clust1[clusters12$Position%in%c(clusters[[1]]$ini[i]:clusters[[1]]$fim[i])]<-i
}
for(i in 1:12){
clusters12$Clust2[clusters12$Position%in%c(clusters[[2]]$ini[i]:clusters[[2]]$fim[i])]<-i
}
clusters12$Clust1[clusters12$Clust1==12]<-1
clusters12$Clust2[clusters12$Clust2==12]<-1
# save(clusters12,file='./Data/clusters12.RData')
load(file='./Data/clusters12.RData')
protSymbol<-transc[[1]]@Protein2Symbol
colnames(protSymbol)<-c("Protein", "Symbol")
clusters12<-merge(clusters12,protSymbol, by="Protein", all.x = T)
clusters12$tFactor<-"ELLIPSE"
#clusters12$tFactor[clusters12$Symbol%in%tfs]<-"DIAMOND"
clusters12$Cor1<-color[[1]][clusters12$Clust1]
clusters12$Cor2<-color[[2]][clusters12$Clust2]
cl12<-(clusters12[!(is.na(clusters12$Clust1) & is.na(clusters12$Clust2)),])
load(file = "./Data/cl12.RData")
load(file='./Data/clusters12.RData')
#Grapho master ----
#cria grafo base para os outros
gMaster <- graph_from_data_frame(transc[[1]]@association, directed = F)
gMaster<-att.mapv(g = gMaster, dat = cl12, refcol = 1)
V(gMaster)$nodeShape <- "CIRCLE"
E(gMaster)$edgeColor<-"#c9c9c9ff"
#cria dtf com intersecção
cltRef<-data.frame(c1=c1,c2=c2)
#inicia o port
rdp <- RedPort()
RedeR::calld(rdp)
#extrai genes para grupos 3 4 5 com base no 3 ref3
#inicioLoop ----
ref2=4
myTheme$nestLineType="DOTTED"
# Cluster 1 int 2 ----
#rede pai
nodesP<-subset(clusters12,Clust2==1,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
nodesF2<-subset(clusters12,Clust1==2,select = c("Protein") )
nodesF2$Protein<-as.character(nodesF2$Protein)
nodesF3<-subset(clusters12,Clust1==3,select = c("Protein") )
nodesF3$Protein<-as.character(nodesF3$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][1]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][1]
V(pai)$nodeColor[V(pai)$name %in% nodesF2$Protein]<-color[[1]][2]
V(pai)$nodeColor[V(pai)$name %in% nodesF3$Protein]<-color[[1]][3]
V(pai)$size <- 10
#name1<-paste0("Cluster",ref2,"Intervalo 1")
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=30)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*200*2,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
escala<-round(sum(nodesP$Protein%in%nodesF2$Protein)/nrow(nodesP)*200*2,0)
nestNodes(rdp, nodes = nodesF2$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
escala<-round(sum(nodesP$Protein%in%nodesF3$Protein)/nrow(nodesP)*200*2,0)
nestNodes(rdp, nodes = nodesF3$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 2 int 2 ----
#rede pai
nPai=2
nF1=4
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][nF1]
V(pai)$size <- 10
#name1<-paste0("Cluster",ref2,"Intervalo 1")
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*200,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 3 int 2 ----
#rede pai
nPai=3
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 4 int 2 ----
#rede pai
nPai=4
nF1=5
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][nF1]
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*200,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 6 int 2 ----
#rede pai
nPai=6
nF1=7
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][nF1]
V(pai)$size <- 10
#name1<-paste0("Cluster",ref2,"Intervalo 1")
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*100,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 7 int 2 ----
#está invertido. cluster 8 é maior que o 7
#rede pai
nPai=8
nF1=7
nodesP<-subset(clusters12,Clust1==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust2==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][7]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[2]][7]
V(pai)$size <- 10
#name1<-paste0("Cluster",ref2,"Intervalo 1")
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
escala<-85#round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*100,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 8 int 2 ----
#rede pai
nPai=8
nF1=9
nF2=10
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
nodesF2<-subset(clusters12,Clust1==nF2,select = c("Protein") )
nodesF2$Protein<-as.character(nodesF2$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][nF1]
V(pai)$nodeColor[V(pai)$name %in% nodesF2$Protein]<-color[[1]][nF2]
V(pai)$size <- 10
#name1<-paste0("Cluster",ref2,"Intervalo 1")
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*100,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
escala<-round(sum(nodesP$Protein%in%nodesF2$Protein)/nrow(nodesP)*100,0)
nestNodes(rdp, nodes = nodesF2$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
RedeR::selectNodes(rdp,nodesF1$Protein)
# Cluster 9 int 2 ----
#rede pai
nPai=9
nF1=11
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust1==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[1]][nF1]
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*200,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 10 int 2 ----
#rede pai
nPai=10
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 11 int 2 ----
#rede pai
nPai=11
nodesP<-subset(clusters12,Clust2==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[2]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
# Cluster 5 int 2 ----
#está invertido. cluster 6 é maior que o 5
#rede pai
nPai=6
nF1=5
nodesP<-subset(clusters12,Clust1==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
nodesF1<-subset(clusters12,Clust2==nF1,select = c("Protein") )
nodesF1$Protein<-as.character(nodesF1$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[1]][nPai]
V(pai)$nodeLineColor<-"#999999"
V(pai)$nodeColor[V(pai)$name %in% nodesF1$Protein]<-color[[2]][nF1]
V(pai)$size <- 10
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#bfbfefFF"
escala<-round(sum(nodesP$Protein%in%nodesF1$Protein)/nrow(nodesP)*100,0)
nestNodes(rdp, nodes = nodesF1$Protein,
#gcoord=c(25,25),
parent="N0",
gscale=escala,
theme=myTheme)
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
RedeR::selectNodes(rdp,nodesF1$Protein)
# Todos Intervalo 1 ----
nPai=7
for(nPai in 1:11){
nodesP<-subset(clusters12,Clust1==nPai,select = c("Protein") )
nodesP$Protein<-as.character(nodesP$Protein)
pai<-subgraph(graph=gMaster, v=V(gMaster)[V(gMaster)$name %in% nodesP$Protein])
#cores
V(pai)$nodeColor<-color[[1]][nPai]
V(pai)$nodeLineColor<-"#555555"
V(pai)$size <- 30
myTheme$nestAlias<-""
myTheme$nestLineColor<-"#444444FF"
resetd(rdp)
RedeR::addGraph(rdp, pai,
isNest=T,
gcoord=c(50,50), gscale=200, theme=myTheme,zoom=40)
myTheme$nestAlias<-""
deSelectNodes(rdp)
#relax(rdp,70,10,150,150,150,75,150,50,ps=T)
#aguarda
readline(prompt=paste0("i1c",nPai, ". Enter continua... "))
}