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--- fst_matrix [2007/12/21 13:56] – heidi
+++ fst_matrix [2008/07/22 13:31] (current) – external edit 127.0.0.1
@@ Line 114: / Line 114: @@
         box()
 </code>
 ===== read data from a XML file =====
@@ Line 206: / Line 207: @@
         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>