• file: matrix_HapDistanceMatrix.r
• document page: 5

code:

Data <- read.table("D:/Heidi/Master/R_Daten/HaplotypeDistance/HapDistanceMatrix_mt.txt" , skip=1)

Columns <- ncol(Data ) + 1
Row <- nrow(Data)

x <- 3
n <- 1

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

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

  DistanceMatrix <- rbind(DistanceMatrix, nextrow)

  n <- n + 1
  x <- x + 1   
}
 
a <- ncol(DistanceMatrix)
b <- nrow(DistanceMatrix)

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,DistanceMatrix, col=ColorRamp, main="Inter-haplotypic
              distance matrix", xlab="Haplotype", ylab="Haplotype" )