First attemt on laydi R package.

R/laydi.R

@@ -1,17 +1,17 @@
 
 write.ftsv <- function(data, con, name="unnamed_dataset", rowdim="rows", coldim="cols") {
-    /* If con is a file name, open it */
+    # If con is a file name, open it 
     opened.here = FALSE
     if (is.character(con)){
         con = file(con, "w")
         opened.here = TRUE 
     }
     
-    /* Substitute all whitespace with underscores in identifiers */
+    # Substitute all whitespace with underscores in identifiers 
     rows <- paste(gsub("\\s", "_", rownames(data)), collapse=" ")
     cols <- paste(gsub("\\s", "_", colnames(data)), collapse=" ")
 
-    /* Write header */
+    # Write header 
     writeLines(c("# type: dataset", 
                  paste("# dimension:", rowdim, rows, collapse=' '), 
                  paste("# dimension:", coldim, cols, collapse=' '), 
@@ -19,10 +19,10 @@ write.ftsv <- function(data, con, name="unnamed_dataset", rowdim="rows", coldim=
                  ""),
                con=con)
 
-    /* Write matrix */
+    # Write matrix 
     write.table(data, file=con, col.names=FALSE, row.names=FALSE, sep="\t")
 
-    /* If con was a string, close file now */
+    # If con was a string, close file now 
     if (opened.here)
         close(con)
 }

R/laydi/DESCRIPTION

@@ -0,0 +1,10 @@
+Package: laydi
+Type: Package
+Title: Interface to Laydi
+Version: 1.0
+Date: 2011-03-05
+Author: Einar Ryeng <einarr@pvv.ntnu.no>
+Maintainer: Einar Ryeng <einarr@pvv.ntnu.no>
+Description: R interface to Laydi
+License: LGPL
+LazyLoad: yes

R/laydi/R/laydi.R

@@ -0,0 +1,30 @@
+
+write.ftsv <- function(data, con, name="unnamed_dataset", rowdim="rows", coldim="cols") {
+    # If con is a file name, open it 
+    opened.here = FALSE
+    if (is.character(con)){
+        con = file(con, "w")
+        opened.here = TRUE 
+    }
+    
+    # Substitute all whitespace with underscores in identifiers 
+    rows <- paste(gsub("\\s", "_", rownames(data)), collapse=" ")
+    cols <- paste(gsub("\\s", "_", colnames(data)), collapse=" ")
+
+    # Write header 
+    writeLines(c("# type: dataset", 
+                 paste("# dimension:", rowdim, rows, collapse=' '), 
+                 paste("# dimension:", coldim, cols, collapse=' '), 
+                 paste("# name:", name, collapse=' '),
+                 ""),
+               con=con)
+
+    # Write matrix 
+    write.table(data, file=con, col.names=FALSE, row.names=FALSE, sep="\t")
+
+    # If con was a string, close file now 
+    if (opened.here)
+        close(con)
+}
+
+

R/laydi/man/laydi-package.Rd

@@ -0,0 +1,39 @@
+\name{laydi-package}
+\alias{laydi-package}
+\alias{laydi}
+\docType{package}
+\title{Interface to Laydi}
+\description{
+Interface to Laydi files and projects. Allows writing R matrices to laydi data files.
+}
+\details{
+\tabular{ll}{
+Package: \tab laydi\cr
+Type: \tab Package\cr
+Version: \tab 0.1.0\cr
+Date: \tab 2011-03-05\cr
+License: \tab LGPL\cr
+LazyLoad: \tab yes\cr
+}
+
+library(laydi)
+
+}
+\author{
+Einar Ryeng <einarr@pvv.org>
+Arnar Flatberg <arnar.flatberg@gmail.com>
+
+Maintainer: Einar Ryeng <einarr@pvv.org>
+}
+\references{
+}
+~~ Optionally other standard keywords, one per line, from file KEYWORDS in ~~
+~~ the R documentation directory ~~
+\keyword{ package }
+\seealso{
+~~ Optional links to other man pages, e.g. ~~
+~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+}
+\examples{
+~~ simple examples of the most important functions ~~
+}

R/laydi/man/write.ftsv.Rd

@@ -0,0 +1,105 @@
+\name{write.ftsv}
+\alias{write.ftsv}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~
+}
+\description{
+Writes a matrix to a ftsv (laydi dataset) file. The matrix must have rownames
+and colnames. Rownames and colnames must be unique, and whitespace characters
+will be replaced with underscores.
+}
+\usage{
+write.ftsv(data, con, name = "unnamed_dataset", rowdim = "rows", coldim = "cols")
+}
+\arguments{
+  \item{data}{
+     A data matrix. All items in rownames(data) and colnames(data) must be
+     unique, and all whitespace characters will be replaced wity underscores in
+     the output. (Laydi requires unique identifiers along a dimension, and does
+     not allow identifiers to contain spaces.)
+  }
+  \item{con}{
+     Connection (or file name) to write the data to. If con is a character
+     string, it will be treated as a file name, and a file by that name will be
+     created, written to and closed. If con is an open connection (file descriptor),
+     the file will remain open.
+  }
+  \item{name}{
+     Datasets in laydi have a name.
+  }
+  \item{rowdim}{
+     Laydi names all dimensions of matrices. rowdim is the dimension
+     name for rows in the the file. E.g. "samples", if rows denotes samples.
+  }
+  \item{coldim}{
+     Laydi names all dimensions of matrices. coldim is the dimension
+     name for columns in the the file. E.g. "gene-ids" if columns represent
+     genes.
+  }
+}
+
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+Laydi and this R package are not published in the litterature. Source code can be found at
+http://dev.pvv.ntnu.no/projects/laydi
+}
+\author{
+Einar Ryeng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or do  help(data=index)  for the standard data sets.
+
+## The function is currently defined as
+function(data, con, name="unnamed_dataset", rowdim="rows", coldim="cols") {
+    # If con is a file name, open it 
+    opened.here = FALSE
+    if (is.character(con)){
+        con = file(con, "w")
+        opened.here = TRUE 
+    }
+    
+    # Substitute all whitespace with underscores in identifiers 
+    rows <- paste(gsub("\\s", "_", rownames(data)), collapse=" ")
+    cols <- paste(gsub("\\s", "_", colnames(data)), collapse=" ")
+
+    # Write header 
+    writeLines(c("# type: dataset", 
+                 paste("# dimension:", rowdim, rows, collapse=' '), 
+                 paste("# dimension:", coldim, cols, collapse=' '), 
+                 paste("# name:", name, collapse=' '),
+                 ""),
+               con=con)
+
+    # Write matrix 
+    write.table(data, file=con, col.names=FALSE, row.names=FALSE, sep="\t")
+
+    # If con was a string, close file now 
+    if (opened.here)
+        close(con)
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line