@@ -10,6 +10,7 @@ export(scaledHydropathyGlobal)

 export(scaledHydropathyLocal)

 export(sequenceCheck)

 export(sequenceMap)

+export(sequenceMapCoordinates)

 export(sequencePlot)

 export(structuralTendency)

 export(structuralTendencyPlot)

@@ -46,6 +46,7 @@

 #' @return A ggplot. Can be plotted immediatly or

 #'   additional layers can be added.

 #' @export

+#' @seealso \code{\link{sequenceMapCoordinates}} for mapping coordinates

 #'

 sequenceMap <- function(

@@ -1,3 +1,27 @@

+#' Sequence Map Coordinates

+#'

+#' This is a function used to create a coordinate grid for the

+#'   \code{\link{sequenceMap}} function. It is based on the length of the

+#'   sequence being mapped, and how many residues per line are specified.

+#'   The function wraps the sequence to have a number of columns that is

+#'   the sequence length / number of residues per row, rounded up. \cr\cr

+#'   This is intended for use within the sequenceMap function, however, this

+#'   can also be used to identify the coordinates of residues within the ggplot

+#'   coordinate plane for addition annotations.

+#'

+#' @inheritParams sequenceMap

+#' @inheritParams sequenceCheck

+#'

+#' @return A data frame with rows containing the amino acid sequence, residue

+#'   position within the sequence, as well as the row and column of each

+#'   residue within the ggplot output of sequenceMap().

+#'

+#' @seealso \code{\link{sequenceMapCoordinates}} for mapping coordinates

+#' @export

+

+

+

+

 sequenceMapCoordinates <-

   function(sequence,

            nbResidues = 30) {

@@ -73,3 +73,6 @@ A ggplot. Can be plotted immediatly or

 This is a graphical function used to visualize data along an

   amino acid sequence.

 }

+\seealso{

+\code{\link{sequenceMapCoordinates}} for mapping coordinates

+}

new file mode 100644

@@ -0,0 +1,37 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/sequenceMapCoordinates.R

+\name{sequenceMapCoordinates}

+\alias{sequenceMapCoordinates}

+\title{Sequence Map Coordinates}

+\usage{

+sequenceMapCoordinates(sequence, nbResidues = 30)

+}

+\arguments{

+\item{sequence}{amino acid sequence as a single character string

+or vector of single characters.

+It also supports a single character string that specifies

+the locaion of a .fasta or .fa file.}

+

+\item{nbResidues}{numeric value, 30 by default.

+The number of residues to display on each row of the plot.

+It is not reccomended to be over 50 or under 10 for standard sequences.

+Optimal value may vary between sequences of extreme lengths.}

+}

+\value{

+A data frame with rows containing the amino acid sequence, residue

+  position within the sequence, as well as the row and column of each

+  residue within the ggplot output of sequenceMap().

+}

+\description{

+This is a function used to create a coordinate grid for the

+  \code{\link{sequenceMap}} function. It is based on the length of the

+  sequence being mapped, and how many residues per line are specified.

+  The function wraps the sequence to have a number of columns that is

+  the sequence length / number of residues per row, rounded up. \cr\cr

+  This is intended for use within the sequenceMap function, however, this

+  can also be used to identify the coordinates of residues within the ggplot

+  coordinate plane for addition annotations.

+}

+\seealso{

+\code{\link{sequenceMapCoordinates}} for mapping coordinates

+}