[Seqinr-commits] r1629 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-08-26 14:21:46 +0200 (Wed, 26 Aug 2009)
New Revision: 1629

Modified:
   pkg/man/read.abif.Rd
Log:
new example

Modified: pkg/man/read.abif.Rd
===================================================================
--- pkg/man/read.abif.Rd	2009-08-26 12:20:02 UTC (rev 1628)
+++ pkg/man/read.abif.Rd	2009-08-26 12:21:46 UTC (rev 1629)
@@ -15,8 +15,7 @@
   \item{verbose}{logical [FALSE]. If TRUE verbose mode is on.}	
 }
 \details{
-This function is experiemental and has not been intensively tested. All data are imported
-into memory, there is no attempt to read items on the fly.
+All data are imported into memory, there is no attempt to read items on the fly.
 }
 \value{
 A list with three components: \code{Header} which is a list that contains various low-level information,
@@ -32,14 +31,49 @@
 Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
 Available at \url{http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf}.
 Last visited on 03-NOV-2008.
+
+The figure in the example section is an attempt to reproduce figure 1A from:
+
+Krawczyk, J.,  Goesmann, A., Nolte, R., Werber, M., Weisshaar, B. (2009)
+Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format.
+\emph{Source Code for Biology and Medicine}, \bold{4}:4.
+
 }
 \author{J.R. Lobry}
-\seealso{\code{\link{readBin}} which is used here to import the binary file and \code{\link{file.info}} to
-get the size of the file.}
+
+\seealso{
+\code{\link{readBin}} which is used here to import the binary file and \code{\link{file.info}} to
+get the size of the file. See \code{\link{JLO}} for the files used in quality check.
+}
+
 \examples{
+#
 # Quality check:
+#
+
 data(JLO)
 JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa", 
   package = "seqinr"))
 stopifnot(identical(JLO, JLO.check))
+
+#
+# Try to reproduce figure 1A from Krawczyk et al. 2009:
+#
+
+Krawczyk <- read.abif(system.file("abif/samplefsa2ps.fsa", 
+  package = "seqinr"))$Data
+x <- 1:length(Krawczyk[["DATA.1"]])
+par(mar = c(2,4,2,0)+0.1, cex = 0.5)
+plot(x, Krawczyk[["DATA.1"]], type = "l", col = "blue",
+  ylab = "", xlab = "",
+  ylim = c(-2000, 10000), cex = 0.5,
+  main = "Figure 1A from Krawczyk et al. 2009",
+  xaxs = "i", yaxs = "i",
+  xaxt = "n", yaxt = "n")
+axis(1, at = seq(2000, 24000, by = 2000))
+axis(2, at = seq(-1000, 10000, by = 1000), las = 1)
+lines(x, Krawczyk[["DATA.2"]], col = "green")
+lines(x, Krawczyk[["DATA.3"]], col = "black")
+lines(x, Krawczyk[["DATA.4"]], col = "red")
+
 }