## Plot a protein interaction graph with edge types
## (c) Wolfgang Huber 7 Mar 2005
library("Rgraphviz")
if(!exists("ft"))
load("droso_ppi.rda") ## see droso_ppi_prepare.R
output = c("png", "x11")[1]
## are there any multiple edges?
ftm = as.matrix(ft[,1:2])
ed = apply(ftm, 1, paste, collapse="---")
dup = duplicated(ed)
cat(sum(dup), "edges are duplicated.\n")
ftm = ftm[!dup,]
## make graphNEL
g = ftM2graphNEL(ftm)
## layout
colors = c("#FFFFB3", "#FDB462")
ag = agopen(g, name="", nodeAttrs=makeNodeAttrs(g,
fillcolor=colors[1+rnai[nodes(g), "Annotation..known.unknown."]]))
## now edit the edges
ed = AgEdge(ag)
for(i in seq(along=ed)) {
hd = ed[[i]]@head
tl = ed[[i]]@tail
wh = which(((ft[,1]==hd) & (ft[,2]==tl)) | (ft[,2]==hd) & (ft[,1]==tl))
cat(hd, tl, ":", wh, " --- ", ft$DIRECTION[wh], ft[wh, 7], "\n")
if("BOTH" %in% ft$DIRECTION[wh])
ed[[i]]@arrowtail = "open"
iatyp = unique(ft[wh, 7])
lwd = 2
switch(iatyp[1],
Enhancement = { col= "#E41A1C"; lty=1 },
Suppression = { col= "#377EB8"; lty=1 },
"Two Hybrid (High Confidence)" = { col= "#8DA0CB"; lty=1 },
"Two Hybrid" = { col= "#8DA0CB"; lwd=1; lty=2 },
stop(iatyp[1]))
if(all(c("Enhancement", "Suppression")%in% iatyp))
col="black"
ed[[i]]@lwd=lwd
ed[[i]]@lty=lty
ed[[i]]@color=col
}
AgEdge(ag)=ed
switch(output,
png = {
fhtml = "droso_ppi.html"
fpng = "droso_ppi.png"
width = height = 800
png(fpng, width=width, height=height)
},
x11 = {}
)
par(mai=rep(0,4))
plot(ag)
switch(output,
png = {
title = nodes(g)
url = paste("http://www.ensembl.org/Drosophila_melanogaster/textview?idx=All&q=",
nodes(g), "&x=0&y=0", sep="")
## Write an HTML file with the image map
con = file(fhtml, open="wt")
writeLines("Klick mich!\n", con)
imageMap(ag, con, fpng, tags=list(HREF=url, TITLE=title), width=width, height=height)
writeLines(c('Legend
blue: Suppression
',
'red: Enhancement
',
'black: both!
',
'grey: Y2H (solid for "high confidence")
'), con=con)
writeLines("", con)
dev.off()
close(con)
cat("Now open the file droso_ppi.html with your browser.\n")
},
x11 = {}
)