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--- half_matrix [2008/01/29 10:28] – created heidi
+++ half_matrix [2008/09/23 09:44] (current) – heidi
@@ Line 1: / Line 1: @@
-====== read data between XML tags ======
+====== read half matrix data  ======
-  * file: Node auslesen_BspTabelle.r
+  * file: read_tag-halfMatrix.r
-  * document page: 19
+  * document page: 37
 \\
 **code:**
 <code>
+#----open XML package-------------------------------------------------
+library(XML)
+#----read data between an XML tag-------------------------------------
+filename = "D:/Heidi/Master/R_Daten/XML/PairwiseFst_XML2.xml"
+tag = "//Fst"
+doc = xmlTreeParse(filename, useInternal = TRUE)
+ch = getNodeSet(doc, tag)
+subDoc = xmlDoc(ch[[1]])
+tagData <- xpathApply(subDoc, tag, xmlValue)
+free(subDoc)
+#----convert string data (half matrix) 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)]
+tagMatrix  <- gsub(" + ", " ", tagMatrix)   # trim white space
+Data <- strsplit(tagMatrix, " ")
+#----to numeric matrix----
+Row <- length(Data)
+Matrix <- as.matrix(as.data.frame(Data[1]))
+Matrix <- rbind(Matrix, matrix(NA, ncol=1, nrow=(Row-1)))
+Matrix <- Matrix[3:nrow(Matrix),]
+numericList <- as.numeric(Matrix)
+numericMatrix <- t(as.matrix(numericList))
+for(n in 2:(Row)){
+  nextrow <- as.matrix(as.data.frame(Data[n]))
+  nextrow <- rbind(nextrow, matrix(NA, ncol=1, nrow=(Row-n)))
+  nextrow <- nextrow[3:nrow(nextrow),]
+  numericList <- as.numeric(nextrow)
+  numericMatrix <- rbind(numericMatrix, t(as.matrix(numericList)))
+}
+numericMatrix
+</code>
+===== read half matrix out of full matrix =====
+  * file: read_tag-halfOutOfFullMatrix.r
+\\
+**code:**
+<code>
+#----open XML package-----------------------------------------------------------
+library(XML)
+#----read data between an XML tag-----------------------------------------------
+filename = "D:/Master/R_Daten/XML/PairwiseFst_XML2.xml"   #not correct!!!!
+tag = "//Fst"
+doc = xmlTreeParse(filename, useInternal = TRUE)
+ch = getNodeSet(doc, tag)
+subDoc = xmlDoc(ch[[1]])
+tagData <- xpathApply(subDoc, tag, xmlValue)
+free(subDoc)
+ #----convert string data (half out of a full matrix) to a numeric matrix------
+  #----split string----
+  tagData2 <- as.character(xmlText)
+  tagData3 <- strsplit(tagData2, "\n")
+  tagMatrix <- as.matrix(as.data.frame(tagData3))
+  tagMatrix <- gsub(" + ", " ", tagMatrix)   # trim white space
+  tagMatrix <- tagMatrix[4:(nrow(tagMatrix)-1)]
+  Data <- strsplit(tagMatrix, " ")
+  #----to numeric matrix----
+  Row <- length(Data)
+  Matrix <- matrix(NA, ncol=1, nrow=Row)
+  numericList <- as.numeric(Matrix)
+  numericMatrix <- t(as.matrix(numericList))
+  for(n in 2:(Row)){
+    nextrow <- as.matrix(as.data.frame(Data[[n]][3:(n+1)]))
+    nextrow <- rbind(nextrow, matrix(NA, ncol=1, nrow=(Row-(n-1))))
+    #nextrow <- nextrow[3:nrow(nextrow),]
+    numericList <- as.numeric(nextrow)
+    numericMatrix <- rbind(numericMatrix, t(as.matrix(numericList)))
+  }
+  numericMatrix
+</code>