haplotype_distance
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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 | ||
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image.plot(x, | image.plot(x, | ||
distance matrix", | distance matrix", | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== rotated and more labels ===== | ||
+ | * file: matrix_HapDistanceMatrix.r | ||
+ | * document page: 8 | ||
+ | |||
+ | \\ | ||
+ | **code:** | ||
+ | < | ||
+ | Data <- read.table(" | ||
+ | |||
+ | Columns <- ncol(Data ) + 1 | ||
+ | Row <- nrow(Data) | ||
+ | |||
+ | x <- 3 | ||
+ | n <- 1 | ||
+ | |||
+ | DistanceMatrix <- as.matrix(scan(" | ||
+ | what=double(0), | ||
+ | DistanceMatrix <- cbind(DistanceMatrix, | ||
+ | DistanceMatrix <- DistanceMatrix[, | ||
+ | |||
+ | n <- n + 1 | ||
+ | x <- x + 1 | ||
+ | |||
+ | while(n< | ||
+ | nextrow <- as.matrix(scan(" | ||
+ | | ||
+ | nextrow <- cbind(t(nextrow), | ||
+ | nextrow <- nextrow[, | ||
+ | |||
+ | DistanceMatrix <- rbind(DistanceMatrix, | ||
+ | |||
+ | 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) | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | xlab=" | ||
+ | contour(DistanceMatrix, | ||
+ | axis(1, at = c(1: | ||
+ | axis(2, at = c(1:b), labels=c(b: | ||
+ | box() | ||
</ | </ | ||
haplotype_distance.1198235627.txt.gz · Last modified: 2008/07/22 13:30 (external edit)