• file: matrix_FstMatrix.r
• document page: 2

code:

read.table("D:/Heidi/Master/R_Daten/FstMatrix/DistanceMatrix_mic.txt",
            header=TRUE, skip=1 ,row.names=1, fill=TRUE ) -> Data

as.matrix.data.frame(Data) -> Matrix
  Matrix
a <- ncol(Matrix)
b <- nrow(Matrix)
x <- c(1:a)
y <- c(1:b)

library(fields)
  ColorRamp <- rgb( seq(1,0,length=256),  # Red
                    seq(1,0,length=256),  # Green
                    seq(1,1,length=256))  # Blue

  image.plot(x,y,Matrix, col=ColorRamp, main="Distance matrix: No. of
              different alleles (FST)", xlab="Populations",
              ylab="Populations", legend.lab="Number of different Allels (FST)")

• file: matrix_PairwiseFst_HTML.r
• document page: 16

code:

#----read HTML/XML file----
whole <- readLines("D:/Heidi/Master/R_Daten/XML/PairwiseFst_HTML_geändert.html")
  whole

x <- 1
while(x <= length(whole)){
  if(whole[x] == "<FstDistanceMatrix>"){
     Begin <<- x
  }
  if(whole[x] == "</FstDistanceMatrix>"){
     End <<- x
  }
  x <- x + 1
}

#----how much rows to read----
Data <- scan("D:/Heidi/Master/R_Daten/XML/PairwiseFst_HTML_geändert.html", skip=End-2, nlines=1)

Columns <- (length(Data))
Row <- Columns

#----read data row by row:----
x <- (Begin+2)
n <- 1

DistanceMatrix <- as.matrix(scan("D:/Heidi/Master/R_Daten/XML/PairwiseFst_HTML_geändert.html",
                                  what=double(0), skip=x, nlines=1, nmax=n))
DistanceMatrix <- cbind(DistanceMatrix, matrix(NA, ncol=(Columns), nrow=1))
DistanceMatrix <- DistanceMatrix[,2:Columns]

n <- n + 1
x <- x + 1

while(n<(Row)){
  nextrow <- as.matrix(scan("D:/Heidi/Master/R_Daten/XML/PairwiseFst_HTML_geändert.html",
                             what=double(0), skip=x, nlines=1, nmax=n))
  nextrow <- cbind(t(nextrow), matrix(NA, ncol=(Columns), nrow=1))
  nextrow <- nextrow[,2:Columns]

  DistanceMatrix <- rbind(DistanceMatrix, nextrow)

  n <- n + 1
  x <- x + 1
}

#----Mirror matrix (left-right)----
mirror.matrix <- function(x) {
  xx <- as.data.frame(x);
  xx <- rev(xx);
  xx <- as.matrix(xx);
  xx;
}

#----Rotate matrix 270 clockworks----
rotate270.matrix <- function(x) {
  mirror.matrix(t(x))
}

DistanceMatrix <- rotate270.matrix(DistanceMatrix)

#----draw matrix plot----
library(fields)

  a <- ncol(DistanceMatrix)
  b <- nrow(DistanceMatrix) 
  x <- c(1:a)
  y <- c(1:b)

  ColorRamp <- rgb( seq(1,0,length=256),  # Red
                    seq(1,0,length=256),  # Green
                    seq(1,1,length=256))  # Blue

    image.plot(x,y,DistanceMatrix, col=ColorRamp, main="Distance matrix: No. of different allels (FST)",
                xlab="Population", ylab="Population", axes = FALSE, legend.mar=4.3, legend.width=0.8,
                legend.lab="Number of different allels (Fst)")
        contour(DistanceMatrix, add = TRUE)
        axis(1, at = c(1:a),cex.axis=0.7)
        axis(2, at = c(1:b), labels=c(b:1),cex.axis=0.7)
        box()