====== haplotype distance ======
* 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" )
===== rotated and more labels =====
* file: matrix_HapDistanceMatrix.r
* document page: 8
\\
**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))
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)
# 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)
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", axes = FALSE)
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()