inst/usecases/droso_ppi.R
In kasperdanielhansen/Rgraphviz: Provides plotting capabilities for R graph objects
## 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("<html><head><title>Klick mich!</title></head><body>\n", con)
imageMap(ag, con, fpng, tags=list(HREF=url, TITLE=title), width=width, height=height)
writeLines(c('<h3>Legend</h3><font color="#377EB8">blue: Suppression</font><br>',
'<font color="#E41A1C">red: Enhancement</font><br>',
'<font color="black">black: both!</font><br>',
'<font color="#8DA0CB">grey: Y2H (solid for "high confidence")<br>'), con=con)
writeLines("</body></html>", con)
dev.off()
close(con)
cat("Now open the file droso_ppi.html with your browser.\n")
},
x11 = {}
)
kasperdanielhansen/Rgraphviz documentation built on Nov. 4, 2022, 4:14 a.m.
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## 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("<html><head><title>Klick mich!</title></head><body>\n", con)
imageMap(ag, con, fpng, tags=list(HREF=url, TITLE=title), width=width, height=height)
writeLines(c('<h3>Legend</h3><font color="#377EB8">blue: Suppression</font><br>',
'<font color="#E41A1C">red: Enhancement</font><br>',
'<font color="black">black: both!</font><br>',
'<font color="#8DA0CB">grey: Y2H (solid for "high confidence")<br>'), con=con)
writeLines("</body></html>", con)
dev.off()
close(con)
cat("Now open the file droso_ppi.html with your browser.\n")
},
x11 = {}
)
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