Differences

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--- haplotype_distance [2007/12/21 12:13] – created heidi
+++ haplotype_distance [2008/07/22 13:31] (current) – external edit 127.0.0.1
@@ Line 47: / Line 47: @@
   image.plot(x,y,DistanceMatrix, col=ColorRamp, main="Inter-haplotypic
               distance matrix", xlab="Haplotype", ylab="Haplotype" )
+</code>
+===== rotated and more labels =====
+  * file: matrix_HapDistanceMatrix.r
+  * document page: 8
+\\
+**code:**
+<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()
 </code>