rossman.r

### Following up on
### http://codeandculture.wordpress.com/2010/02/28/more-r-headaches

library(igraph)
library(plyr) # Hadley Wickham FTW, as usual

## ----------------------------------------------------------------------
## NB for file reading and writing below, we're assuming figures/ and
## data/ subdirs exist in the working directory. Change paths as
## appropriate. 
## ----------------------------------------------------------------------

## Generate some fake data. Not the right format (no attributes) but
## that's not relevant here ...
g <- erdos.renyi.game(100, 0.05)
la <- layout.fruchterman.reingold(g)
summary(g)

plot(g, layout=la, vertex.size=4, vertex.label=NA,
     edge.color="gray60", edge.arrow.size=0.3, margin=0)

## Make 53 random graphs, as a list.
g.list <- rlply(53, erdos.renyi.game(100, 0.05))

## Look at one of the graphs
summary(g.list[[23]])

## Write them to separate files in the data/ subdirectory, to
## approximate where GR starts from.
for(i in 1:53) write.graph(g.list[[i]], file=paste("data/",i,"-g.net",sep=""), format="pajek")

### ----------------------------------------------------------------------
### Now we are kind of where GR begins: data in separate files, need
### to read them in, and get them into a list.
### ----------------------------------------------------------------------

## Get the filenames (just find .net files.)
all.the.filenames <- list.files("data/", pattern="\\.net$")
all.the.filenames <- paste("data/", all.the.filenames, sep="")

## Watch out for unix sort/numbering conventions! Numbers inside file
## names are not numerically sortable. ls (and so the vector here)
## will count them 1, 10, 11, 12 ... 2, 20, 21, 22, ... etc. Reorder
## them to get the numbers right. 

## Extract the numbers and reorder the names properly.
ind <- order(as.numeric(gsub("[^[:digit:]]", "", all.the.filenames)))
all.the.filenames <- all.the.filenames[ind]

## Now read in the data files to a list, without looping. llply() is
## from the plyr library; you could use lapply(), too.
g.list.new <- llply(all.the.filenames, read.graph, format="pajek")

### ----------------------------------------------------------------------
### Generate a sequence of PNGs graphplots in the figures/ subdir,
### without looping.
### ----------------------------------------------------------------------

png(file="figures/chrnet_hc%d.png") # see ?png for the %d trick here
l_ply(g.list.new, plot, layout=la, vertex.size=4, vertex.label=NA,
      edge.color="gray60", edge.arrow.size=0.3, margin=0)
dev.off()

### Finally, generate the gif without having to renumber the files
### individually.
png.filenames <- list.files("figures/", pattern="\\.png$")

## Resort properly again
ind <- order(as.numeric(gsub("[^[:digit:]]", "", png.filenames)))
png.filenames <- png.filenames[ind]
png.filenames <- paste("figures/", png.filenames, sep="") # add the path back
png.string <- capture.output(cat(png.filenames))

## Open a pipe to the shell to execute the convert command
## directly.
gifpipe <- pipe(paste("convert", png.string,
                 "figures/out.gif", sep=" "), "w")
close(gifpipe)