fst_matrix
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fst_matrix [2007/12/21 13:49] – heidi | fst_matrix [2008/07/22 13:31] (current) – external edit 127.0.0.1 | ||
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ylab=" | ylab=" | ||
</ | </ | ||
+ | |||
===== rad data from a HTML file ===== | ===== rad data from a HTML file ===== | ||
Line 113: | Line 114: | ||
box() | box() | ||
</ | </ | ||
+ | |||
+ | |||
+ | ===== read data from a XML file ===== | ||
+ | * file: Node auslesen_matrix_PairwiseFst.r | ||
+ | * document page: 20 | ||
+ | |||
+ | \\ | ||
+ | **code:** | ||
+ | < | ||
+ | #----open XML package------------------------------------------------- | ||
+ | library(XML) | ||
+ | |||
+ | #----read data between an XML tag------------------------------------- | ||
+ | filename = " | ||
+ | tag = "// | ||
+ | doc = xmlTreeParse(filename, | ||
+ | ch = getNodeSet(doc, | ||
+ | |||
+ | subDoc = xmlDoc(ch[[1]]) | ||
+ | tagData <- xpathApply(subDoc, | ||
+ | free(subDoc) | ||
+ | # | ||
+ | |||
+ | # | ||
+ | #----split string---- | ||
+ | tagData2 <- as.character(tagData) | ||
+ | |||
+ | tagData3 <- strsplit(tagData2, | ||
+ | tagMatrix <- as.matrix(as.data.frame(tagData3)) | ||
+ | tagMatrix <- tagMatrix[4: | ||
+ | Data <- strsplit(tagMatrix, | ||
+ | |||
+ | #----to string matrix---- | ||
+ | Row <- length(Data) | ||
+ | |||
+ | Matrix <- as.matrix(as.data.frame(Data[1])) | ||
+ | Matrix <- rbind(Matrix, | ||
+ | |||
+ | for(n in 2:(Row)){ | ||
+ | nextrow <- as.matrix(as.data.frame(Data[n])) | ||
+ | nextrow <- rbind(nextrow, | ||
+ | Matrix <- cbind(Matrix, | ||
+ | } | ||
+ | Matrix <- Matrix[5: | ||
+ | |||
+ | #----to numeric matrix---- | ||
+ | numericList <- as.numeric(Matrix[, | ||
+ | numericMatrix <- t(as.matrix(numericList)) | ||
+ | |||
+ | for(n in 2:(Row)){ | ||
+ | numericList <- as.numeric(Matrix[, | ||
+ | numericMatrix <- rbind(numericMatrix, | ||
+ | } | ||
+ | numericMatrix | ||
+ | |||
+ | # numericTable <- as.table(numericMatrix) | ||
+ | # numericTable | ||
+ | |||
+ | DistanceMatrix <- numericMatrix | ||
+ | |||
+ | #----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, | ||
+ | | ||
+ | | ||
+ | |||
+ | image.plot(x, | ||
+ | xlab=" | ||
+ | legend.mar=4.3, | ||
+ | contour(DistanceMatrix, | ||
+ | axis(1, at = c(1: | ||
+ | axis(2, at = c(1:b), labels=c(b: | ||
+ | box() | ||
+ | </ | ||
+ | |||
+ | ===== move legend ===== | ||
+ | * file: matrix_PairwiseFst.r | ||
+ | * document page: 22 | ||
+ | |||
+ | \\ | ||
+ | **code:** | ||
+ | < | ||
+ | #----read data-------------------------------------------------------------- | ||
+ | read.table(" | ||
+ | header=TRUE, | ||
+ | as.matrix.data.frame(Data) -> Matrix | ||
+ | |||
+ | a <- ncol(Matrix) | ||
+ | b <- nrow(Matrix) | ||
+ | |||
+ | x <- c(1:a) | ||
+ | y <- c(1:b) | ||
+ | |||
+ | #----draw plot-------------------------------------------------------------- | ||
+ | library(fields) | ||
+ | ColorRamp <- rgb( seq(1, | ||
+ | seq(1, | ||
+ | seq(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)) | ||
+ | } | ||
+ | |||
+ | Matrix <- rotate270.matrix(Matrix) | ||
+ | |||
+ | #----draw matrix plot---- | ||
+ | image.plot(x, | ||
+ | xlab=" | ||
+ | cex=1.0, side=4, line=2), axes = FALSE) | ||
+ | contour(Matrix, | ||
+ | axis(1, at = c(1:a)) | ||
+ | axis(2, at = c(1:b), labels=c(b: | ||
+ | box() | ||
+ | </ | ||
+ | |||
fst_matrix.1198241343.txt.gz · Last modified: 2008/07/22 13:30 (external edit)