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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
@@ Line 25: / Line 25: @@
               ylab="Populations", legend.lab="Number of different Allels (FST)")
 </code>
 ===== rad data from a HTML file =====
@@ Line 113: / Line 114: @@
         box()
 </code>
+===== read data from a XML file =====
+  * file: Node auslesen_matrix_PairwiseFst.r
+  * document page: 20
+\\
+**code:**
+<code>
+#----open XML package-------------------------------------------------
+library(XML)
+#----read data between an XML tag-------------------------------------
+filename = "D:/Heidi/Master/R_Daten/XML/PairwiseFst_XML.xml"
+tag = "//Fst"
+doc = xmlTreeParse(filename, useInternal = TRUE)
+ch = getNodeSet(doc, tag)
+subDoc = xmlDoc(ch[[1]])
+tagData <- xpathApply(subDoc, tag, xmlValue)
+free(subDoc)
+#print(tagData, indent=FALSE)
+#----convert string data to a numeric matrix---------------------------
+#----split string----
+tagData2 <- as.character(tagData)
+tagData3 <- strsplit(tagData2, "\n")
+tagMatrix <- as.matrix(as.data.frame(tagData3))
+tagMatrix <- tagMatrix[4:nrow(tagMatrix)]
+Data <- strsplit(tagMatrix, "   ")
+#----to string matrix----
+Row <- length(Data)
+Matrix <- as.matrix(as.data.frame(Data[1]))
+Matrix <- rbind(Matrix, matrix(NA, ncol=1, nrow=(Row-1)))
+for(n in 2:(Row)){
+  nextrow <- as.matrix(as.data.frame(Data[n]))
+  nextrow <- rbind(nextrow, matrix(NA, ncol=1, nrow=(Row-n)))
+  Matrix <- cbind(Matrix, nextrow)
+}
+Matrix <- Matrix[5:nrow(Matrix),]
+#----to numeric matrix----
+numericList <- as.numeric(Matrix[,1])
+numericMatrix <- t(as.matrix(numericList))
+for(n in 2:(Row)){
+  numericList <- as.numeric(Matrix[,n])
+  numericMatrix <- rbind(numericMatrix, t(as.matrix(numericList)))
+}
+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(1,0,length=256),  # Red
+                   seq(1,0,length=256),  # Green
+                   seq(1,1,length=256))  # Blue
+    image.plot(x,y,DistanceMatrix, col=ColorRamp, main="Distance matrix: No. of different allels (FST)",
+                xlab="Population", ylab="Population", axes = FALSE, legend.lab="Number of different allels (Fst)",
+                legend.mar=4.3, legend.width=0.8)
+        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>
+===== move legend =====
+  * file: matrix_PairwiseFst.r
+  * document page: 22
+\\
+**code:**
+<code>
+#----read data--------------------------------------------------------------
+read.table("D:/Heidi/Master/R_Daten/FstMatrix/PairwiseFst_mic.txt",
+            header=TRUE, skip=5 ,row.names=1, fill=TRUE )-> Data
+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(1,0,length=256),  # Red
+                  seq(1,0,length=256),  # Green
+                  seq(1,1,length=256))  # Blue
+#----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,y,Matrix, col=ColorRamp, main="Distance matrix: No. of different alleles (FST)",
+            xlab="Population", ylab="Population", legend.args=list( text="Number of different Allels (FST)",
+            cex=1.0, side=4, line=2), axes = FALSE)
+        contour(Matrix, add = TRUE)
+        axis(1, at = c(1:a))
+        axis(2, at = c(1:b), labels=c(b:1))
+        box()
+</code>