timings<-read.table("~/Desktop/Timing.txt",header=T,sep="\t")
timings[,3:17]<-timings[,3:17]*-1
timings[,7]<-timings[,7]*-1
timings[,9]<-timings[,9]*-1


plottimings<-function(startoffset=0,endoffset=0,coltoplot=0) {
library(RColorBrewer)
system('echo "">>~/Desktop/Timing.txt')
timings<-read.table("~/Desktop/Timing.txt",header=T,sep="\t")
timings[,3:17]<-timings[,3:17]*-1
timings[,7]<-timings[,7]*-1
timings[,9]<-timings[,9]*-1
starttimes<-c(-20000000000,-4600000000, -542000000, -488000000, -444000000, -416000000, -359000000, -299000000, -251000000, -200000000, -146000000, -65500000, -55800000, -33900000, -23030000, -5330000, -2590000, -12000,0)
endtimes<-c(-4600000000,-542000000, -488000000, -444000000, -416000000, -360000000, -299000000, -251000000, -200000000, -146000000, -65500000, -55800000, -33900000, -23030000, -5330000, -2590000, -12000, 0, 7590000000)
periodnames<-c("", "Precambrian", "Cambrian", "Ordovician", "Silurian", "Devonian", "Carboniferous", "Permian", "Triassic", "Jurassic", "Cretaceous", "Paleocene", "Eocene", "Oligocene", "Miocene", "Pliocene", "Pleistocene", "Holocene", "Future")
shortperiodnames<-c("","Precambrian", "Cambrian", "Ordovician", "Silurian", "Devonian", "Carboniferous", "Permian", "Triassic", "Jurassic", "Cretaceous", "Paleocene", "Eocene", "Oligocene", "Miocene", "Pliocene", "", "", "Future")
namestouse<-shortperiodnames




startperiod=1+startoffset
endperiod=length(periodnames)-endoffset
if (startperiod>1 && endperiod<length(periodnames)) {
	namestouse<-periodnames
}


plot(x=c(min(starttimes[startperiod:endperiod]),max(10000000,max(endtimes[startperiod:endperiod]))),y=c(-1,1),type="n",yaxt="n",bty="n",xlab="Time",ylab="")
colors<-c("white",brewer.pal(12,"Paired"),brewer.pal(12,"Paired"))
for (i in startperiod:endperiod) {
	heightpoint=max(0.2,0.8-0.04*i)
	text(labels= namestouse[i],x=mean(c(starttimes[i],endtimes[i])),y=heightpoint,srt=45,adj=c(0,0.5))
	if (i>1) {
	lines(x=rep(mean(c(starttimes[i],endtimes[i])),2),y=c(heightpoint,0),lwd=1,col="black")
	}
	lines(x=c(starttimes[i],endtimes[i]),y=c(0,0),lwd=50, lend=1,col=colors[i])
}
nrows=dim(timings)[1]
if (coltoplot>2) {
	lines(x=rep(timings[1,coltoplot],2),y=c(0,-0.5),col="purple",lwd=5)
	text(x=timings[1,coltoplot],y=-0.6,label=names(timings)[coltoplot],cex=1.1,adj=c(0,0),srt=-45)
	for (i in 2:nrows) {
		lines(x=rep(timings[i,coltoplot],2),y=c(0,-0.3),col="black",lwd=3)
		}
	}
}

addcolumn<-function(coltoplot,timings=timings) {
	nrows=dim(timings)[1]
	if (coltoplot>2) {
	lines(x=rep(timings[1,coltoplot],2),y=c(0,-0.5),col="purple",lwd=5)
	text(x=timings[1,coltoplot],y=-0.6,label=names(timings)[coltoplot],cex=1.1,adj=c(0,0),srt=-45)
	for (i in 2:nrows) {
		lines(x=rep(timings[i,coltoplot],2),y=c(0,-0.3),col="black",lwd=3)
		}
	}	
}