####################################################################################
## RedeR, dynamic networks in R
## Copyright (C) 2012  CRI-CRUK
##
## Source code to reproduce benchmark for RedeR software.
##
## RedeR program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 2 of the License, or
## (at your option) any later version.
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
## You should have received a copy of the GNU General Public License
## along with this program. If not, see <http://www.gnu.org/licenses/>.
##
## Mauro Castro - mauro.castro@cancer.org.uk
###################################################################################

#------------------------------------------------------------------------------------
# simple function to generate series of scale-free netwoks
#..returns either igraph or graphNEL formats
graph.scale.free<-function(n=100, tp=c("igraph","graphNEL")){
	#get a ramdom graph with n nodes and p probability for drawing an edge
	g1 <- barabasi.game(n=n, directed=FALSE)
	if(tp[1]=="igraph")return(g1)
	#get nodes and edges to build a graphNEL object
	name <- as.character(seq(vcount(g1)) - 1)
	al <- get.adjlist(g1, "out")
	al <- lapply(al, function(x) as.character(x))
    names(al) <- name
    g2 <- new("graphNEL", nodes=name, edgeL=al, edgemode="undirected")	
	return(g2)
}
# returns a vector with geometric progression (used to set graph size)!
gp <- function(init, mult, n){ 
	if(n==1){ init } else { gp(c(init, init[length(init)] * mult), mult, n-1) }
}

#------------------------------------------------------------------------------------
# function to plot results from performance tests
plotbenchmark<-function(res){
	library(gplots)
	
	# re-order available tests
	tests<-c("baseline","igraph","Rgraphviz","tkplot","RCytoscape","RedeR")
	idx<-tests%in%names(res)
	res<-res[tests[idx]]
	
	# function to plot benchmark results
	plotbm<-function(x, y, ylim, col, lab, pch, cex=0.6, lwd=1.2){
		sem <- apply(y,1,sd, na.rm=TRUE)
		y   <- apply(y,1,mean, na.rm=TRUE)
		dy  <- ylim[2]-ylim[1]
		checklen <- sem/dy
		sem[checklen<0.01]=dy*0.01
		plotCI(x=x, y=y, uiw=sem, add=TRUE, barcol=col, pch=pch, 
			   col=col,cex=0.8, pt.bg=col, type='l', gap=0.0, lwd=lwd)
		points(x=x, y=y, pch=pch, col=col, cex=cex, bg="white")
	}
	
	# set plot layout (quartz will work only in Mac!)
	quartz(width=8, height=4.5)
	graphics::layout(matrix(c(1,2), 1, 2, byrow=TRUE))

	# an empty plot
	xlab="Network size (n vertices)"
	ylab="Time (s)"
	ylim=c(0,2800)
	xlim=c(2,16384)
	plot(x=xlim, y=ylim, ylab=ylab, xlab=xlab, type="n", main="",sub=NULL, xlim=xlim, 
		ylim=ylim, mgp=c(2.0, 0.6, 0), bty='n', log="x", cex.axis=0.7, cex.lab=0.9)
	
	# set labels, colors and formats
	labs=c('baseline','igraph','Rgraphviz/Graphviz','igraph/tkplot','RCytoscape/CytoscapeRPD','RedeR')
	names(labs)=tests
	cols=c('black','grey30','grey60','green','blue','red')
	names(cols)=tests
	pchs<-c(18,22,24,21,21,21)
	names(pchs)=tests
	
	# legends
	legend("topleft", legend=labs[c(1,2,3)], title="image rendering", 
		col=cols[c(1,2,3)],pch=pchs[c(1,2,3)], cex=0.65,bty="n")
	legend("left", legend=labs[c(4,5,6)], title="data tranfer + image rendering", 
		col=cols[c(4,5,6)],pch=pchs[c(4,5,6)], cex=0.65,bty="n")				 
		
	# main plot 	
	for(i in 1:length(res)){
		plotbm(res[[i]]$nodecount,res[[i]]$timecount,ylim=ylim, 
			col=cols[names(res)[i]],lab=labs[names(res)[i]],pch=pchs[names(res)[i]])
	}

	# another empty plot
	ylim=c(0,10)
	plot(x=xlim, y=ylim, ylab=ylab, xlab=xlab, type="n", main="", sub=NULL, xlim=xlim, 
		ylim=ylim, mgp=c(2.0, 0.6, 0), bty='n', log="x",cex.axis=0.7, cex.lab=0.9)
	
	# zoom on the 1st 10 seconds!
	for(i in 1:length(res)){
		plotbm(res[[i]]$nodecount,res[[i]]$timecount, ylim=ylim, col=cols[names(res)[i]],
			lab=labs[names(res)[i]],pch=pchs[names(res)[i]], cex=0.8, lwd=1.5)
	}
	
}

#------------------------------------------------------------------------------------