====== expected/observed haplotype ======
===== barplot =====
  * file: bar2_HaplotypeFreq.r
  * document page: 6

\\
**code:**
<code>
read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ObsHaplotypeFreq_mt.txt”,
            skip=5, row.names=1, fill=TRUE )-> Observed

  nrow(Observed) -> rObs
  ncol(Observed) -> cObs

  newObserved <- Observed[1:(rObs-1),1:(cObs-1)]

read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ExpHaplotypeFreq_mt.txt",
            skip=6, row.names=1, fill=TRUE) -> Expected

  nrow(Expected) -> rExp
  ncol(Expected) -> cExp
  
  newExpected <- Expected[,1:(cExp-3)]

HaplotypeFreq <- as.matrix(newExpected)
HaplotypeFreq <- cbind(HaplotypeFreq, as.matrix(newObserved))
tHaplotypeFreq <- t(HaplotypeFreq)

null <- matrix(0, ncol=1, nrow=rExp)
ExpSd <- cbind((Expected[,2]), as.matrix(null))
sdpos <- tHaplotypeFreq + t(ExpSd)
sdneg <- tHaplotypeFreq - t(ExpSd) 

library(gplots)

 mp <- barplot2(tHaplotypeFreq ,beside=TRUE, main="Haplotype Frequency",
                legend = c("Expected", "Observed"), xlab="Allel",
 		ylab="relative Frequenci", ylim=c(0,(max(tHaplotypeFreq)+(max(HaplotypeFreq)/4))),
    plot.ci = TRUE, ci.l =sdneg, ci.u =sdpos,
    plot.grid = TRUE , col=c( gray(0.8), gray(0.2)))            
    mtext(side = 1, at = colMeans(mp), line = 0.5, text = c(1:rExp), cex=0.7)
    box()
</code>


===== lines =====
  * file: lines_HaplotypeFreq.r
  * document page: 7

\\
**code:**
<code>
read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ObsHaplotypeFreq_mt.txt",
            skip=5 ,row.names=1, fill=TRUE )-> Observed

  nrow(Observed) -> rObs
  ncol(Observed) -> cObs

  newObserved <- Observed[1:(rObs-1),1:(cObs-1)]

read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ExpHaplotypeFreq_mt.txt",
            skip=6, row.names=1, fill=TRUE) -> Expected

  nrow(Expected) -> rExp
  ncol(Expected) -> cExp
  
  newExpected <- Expected[,1:(cExp-3)]
    
sdExp <- Expected[,2]
sdExpUp <- newExpected + sdExp
sdExpLo <- newExpected - sdExp
    
plot(newObserved, type="l", xlab="Allel", ylab="relative Frequency", main="Haplotype Frequency", xaxt="n")
    axis(1, 1:rExp, cex.axis=0.6)
    lines(newExpected, col="red")
    lines(sdExpUp, lty=2, col="red") 
    lines(sdExpLo, lty=2, col="red")
    legend("topright", c("Observed", "Expected", "Expected +/- sd"),
  	     lty=c(1,1,2), bty="n", col=c("black", "red", "red"))
</code>

==== save graphic as a .png file =====
  * file: lines_HaplotypeFreq.r
  * document page: 15

\\
**code:**
<code>
read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ObsHaplotypeFreq_mt.txt",
            skip=5 ,row.names=1, fill=TRUE )-> Observed

  nrow(Observed) -> rObs
  ncol(Observed) -> cObs

  newObserved <- Observed[1:(rObs-1),1:(cObs-1)]

read.table("D:/Heidi/Master/R_Daten/HaplotypeFrequency/ExpHaplotypeFreq_mt.txt",
            skip=6, row.names=1, fill=TRUE) -> Expected

  nrow(Expected) -> rExp
  ncol(Expected) -> cExp
  
  newExpected <- Expected[,1:(cExp-3)]
    
sdExp <- Expected[,2]
sdExpUp <- newExpected + sdExp
sdExpLo <- newExpected - sdExp

png("D:/Heidi/Master/R_Graphiken/lines_HaplotypeFreq.png", width=550,height=550)
    
  plot(newObserved, type="l", xlab="Allel", ylab="relative Frequency", main="Haplotype Frequency", xaxt="n")
    axis(1, 1:rExp, cex.axis=0.6)
    lines(newExpected, col="red")
    lines(sdExpUp, lty=2, col="red") 
    lines(sdExpLo, lty=2, col="red")
    legend("topright", c("Observed", "Expected", "Expected +/- sd"), lty=c(1,1,2),
            bty="n", col=c("black", "red", "red")) 

dev.off()
</code>