Multiple plots in R with different settings for ea

In the graph below,

Is it possible to create same graph with less lines of codes? I mean, since each Figs. A-D has different label settings, I have to write settings for each Fig. which makes it longer.

The graph below is produced with the data in pdf device.
Any help with these issues is highly appreciated.(Newbie to R!). Since all the code is too long to post here, I have posted a part relevant to the problem here for Fig.C

#FigC
label1=c(0,100,200,300)
plot(data$TimeVariable2C,data$Variable2C,axes=FALSE,ylab="",xlab="",xlim=c(0,24),
     ylim=c(0,2.4),xaxs="i",yaxs="i",pch=19)
lines(data$TimeVariable3C,data$Variable3C)
axis(2,tick=T,at=seq(0.0,2.4,by=0.6),label= seq(0.0,2.4,by=0.6))
axis(1,tick=T,at=seq(0,24,by=6),label=seq(0,24,by=6))
mtext("(C)",side=1,outer=F,line=-10,adj=0.8)
minor.tick(nx=5,ny=5)

par(new=TRUE)
plot(data$TimeVariable1C,data$Variable1C,axes=FALSE,xlab="",ylab="",type="l",
     ylim=c(800,0),xaxs="i",yaxs="i")
axis(3,xlim=c(0,24),tick=TRUE,at= seq(0,24,by=6),label=seq(0,24,by=6),col.axis="violetred4",col="violetred4")
axis(4,tick=TRUE,at= label1,label=label1,col.axis="violetred4",col="violetred4")
polygon(data$TimeVariable1C,data$Variable1C,col='violetred4',border=NA)

You ask many questions in the same OP. I will try to answer to just one : How to simplify your code or rather how to call it once for each letter. I think it is better to put your data in the long format. For example, This will create a list of 4 elements

ll <- lapply(LETTERS[1:4],function(let){
  dat.let <- dat[,grepl(let,colnames(dat))]
  dd <- reshape(dat.let,direction ='long',
                v.names=c('TimeVariable','Variable'),
                varying=1:6)
  dd$time <- factor(dd$time)
  dd$Type <- let
  dd
}
)

ll is a list of 4 data.frame, where each one that looks like :

head(ll[[1]])
 time TimeVariable Variable id Type
1.1    1            0        0  1    A
2.1    1            0        5  2    A
3.1    1            8      110  3    A
4.1    1           16        0  4    A
5.1    1           NA       NA  5    A
6.1    1           NA       NA  6    A

Then you can use it like this for example :

library(Hmisc)

layout(matrix(1:4, 2, 2, byrow = TRUE))
lapply(ll,function(data){
  label1=c(0,100,200,300)
  Type <- unique(dat$Type)
  dat <- subset(data,time==2)
  x.mm <- max(dat$Variable,na.rm=TRUE)
  plot(dat$TimeVariable,dat$Variable,axes=FALSE,ylab="",xlab="",xlim=c(0,x.mm),
       ylim=c(0,2.4),xaxs="i",yaxs="i",pch=19)
  dat <- subset(data,time==2)
  lines(dat$TimeVariable,dat$Variable)
  axis(2,tick=T,at=seq(0.0,2.4,by=0.6),label= seq(0.0,2.4,by=0.6))
  axis(1,tick=T,at=seq(0,x.mm,by=6),label=seq(0,x.mm,by=6))
  mtext(Type,side=1,outer=F,line=-10,adj=0.8)
  minor.tick(nx=5,ny=5)
  par(new=TRUE)
  dat <- subset(data,time==1)
  plot(dat$TimeVariable,dat$Variable,axes=FALSE,xlab="",ylab="",type="l",
       ylim=c(800,0),xaxs="i",yaxs="i")
  axis(3,xlim=c(0,24),tick=TRUE,at= seq(0,24,by=6),label=seq(0,24,by=6),col.axis="violetred4",col="violetred4")
  axis(4,tick=TRUE,at= label1,label=label1,col.axis="violetred4",col="violetred4")
  polygon(dat$TimeVariable,dat$Variable,col='violetred4',border=NA)
})

Another advantage of using the long data format is to use ``ggplot2andfacet_wrap` for example .

 ## transform your data to a data.frame
 dat.l <- do.call(rbind,ll)
 library(ggplot2)
 ggplot(subset(dat.l,time !=1)) +
  geom_line(aes(x=TimeVariable,y=Variable,group=time,color=time))+
  geom_polygon(data=subset(dat.l,time ==1),
              aes(x=TimeVariable,y=60-Variable/10,fill=Type))+
  geom_line(data=subset(dat.l,time ==1),
               aes(x=TimeVariable,y=Variable,fill=Type))+
  facet_wrap(~Type,scales='free')