@@ -87,6 +87,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

+\code{\link{foldIndexR}()},

 \code{\link{meanScaledHydropathy}()},

 \code{\link{scaledHydropathyLocal}()}

 }

@@ -7,8 +7,8 @@

 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

 }

 \arguments{

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

-or vector of single characters.

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

+a vector of single characters, or an AAString object.

 It also supports a single character string that specifies

 the path to a .fasta or .fa file.}

@@ -34,6 +34,17 @@ This is used to calculate the scaled hydropathy of an amino acid

   The output is either a data frame or graph

   showing the matched scores for each residue along the sequence.

 }

+\section{Plot Colors}{

+

+  For users who wish to keep a common aesthetic, the following colors are

+  used when plotResults = TRUE. \cr

+  \itemize{

+  \item Dynamic line colors: \itemize{

+  \item Close to 0 = "skyblue3" or "#6CA6CD"

+  \item Close to 1 = "chocolate1" or "#FF7F24"

+  \item Close to midpoint = "grey65" or "#A6A6A6"}}

+}

+

 \examples{

 #Amino acid sequences can be character strings

 aaString <- "ACDEFGHIKLMNPQRSTVWY"

@@ -42,7 +53,7 @@ aaVector <- c("A", "C", "D", "E", "F",

               "G", "H", "I", "K", "L",

               "M", "N", "P", "Q", "R",

               "S", "T", "V", "W", "Y")

-#Alternativly, .fasta files can also be used by providing

+#Alternatively, .fasta files can also be used by providing

 ##The path to the file as a character string

 exampleDF <- scaledHydropathyGlobal(aaString,

@@ -40,8 +40,8 @@ aaString <- "ACDEFGHIKLMNPQRSTVWY"

 #Amino acid sequences can also be character vectors

 aaVector <- c("A", "C", "D", "E", "F",

               "G", "H", "I", "K", "L",

-           "M", "N", "P", "Q", "R",

-           "S", "T", "V", "W", "Y")

+              "M", "N", "P", "Q", "R",

+              "S", "T", "V", "W", "Y")

 #Alternativly, .fasta files can also be used by providing

 ##The path to the file as a character string

@@ -4,8 +4,6 @@

 \alias{scaledHydropathyGlobal}

 \title{Protein Scaled Hydropathy Calculations}

 \usage{

-scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

-

 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

 }

 \arguments{

@@ -24,12 +22,6 @@ optional setting to include the name in the plot title.}

 \item{...}{any additional parameters, especially those for plotting.}

 }

 \value{

-if \code{plotResults = TRUE}, a graphical representation data.

-  Average is shown by the horizontal line.

-  If \code{plotResults = FALSE}, a dataframe is reported

-  with each amino acid and each residue value shown.

-  Score for each residue shown in the column "Hydropathy".

-

 if \code{plotResults = TRUE}, a graphical representation data.

   Average is shown by the horizontal line.

   If \code{plotResults = FALSE}, a data frame is reported

@@ -37,11 +29,6 @@ if \code{plotResults = TRUE}, a graphical representation data.

   Score for each residue shown in the column "Hydropathy".

 }

 \description{

-This is used to calculate the scaled hydropathy of an amino acid

-  sequence for each residue in the sequence.

-  The output is either a dataframe or graph

-  showing the matched scores for each residue along the sequence.

-

 This is used to calculate the scaled hydropathy of an amino acid

   sequence for each residue in the sequence.

   The output is either a data frame or graph

@@ -67,57 +54,19 @@ exampleDF <- scaledHydropathyGlobal(aaVector,

 head(exampleDF)

 #plotResults = TRUE will output a ggplot

-\dontrun{

-  scaledHydropathyGlobal(aaString,

-                         plot = T)

-

-  #since it is a ggplot, you can change or annotate the plot

-  gg <- scaledHydropathyGlobal(aaVector,

-                               plot = T)

-  gg <- gg + ggplot2::ylab("Local Hydropathy")

-  gg <- gg + ggplot2::geom_text(data = exampleDF,

-                                ggplot2::aes(label = AA,

-                                             y = Hydropathy + 0.1))

-  plot(gg)

-}

-#Amino acid sequences can be character strings

-aaString <- "ACDEFGHIKLMNPQRSTVWY"

-#Amino acid sequences can also be character vectors

-aaVector <- c("A", "C", "D", "E", "F",

-              "G", "H", "I", "K", "L",

-           "M", "N", "P", "Q", "R",

-           "S", "T", "V", "W", "Y")

-#Alternativly, .fasta files can also be used by providing

-##The path to the file as a character string

-

-exampleDF <- scaledHydropathyGlobal(aaString,

-                                    plotResults = FALSE)

-head(exampleDF)

-

-exampleDF <- scaledHydropathyGlobal(aaVector,

-                                    plotResults = FALSE)

-head(exampleDF)

-

-#plotResults = TRUE will output a ggplot

-\dontrun{

   scaledHydropathyGlobal(aaString,

-                         plot = T)

+                         plotResults = TRUE)

   #since it is a ggplot, you can change or annotate the plot

   gg <- scaledHydropathyGlobal(aaVector,

-                               plot = T)

+                               plotResults = TRUE)

   gg <- gg + ggplot2::ylab("Local Hydropathy")

   gg <- gg + ggplot2::geom_text(data = exampleDF,

                                 ggplot2::aes(label = AA,

                                              y = Hydropathy + 0.1))

   plot(gg)

 }

-}

 \references{

-Kyte, J., & Doolittle, R. F. (1982). A simple method for

-  displaying the hydropathic character of a protein.

-  Journal of molecular biology, 157(1), 105-132.

-

 Kyte, J., & Doolittle, R. F. (1982). A simple method for

   displaying the hydropathic character of a protein.

   Journal of molecular biology, 157(1), 105-132.

@@ -125,13 +74,6 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 \seealso{

 \code{\link{KDNorm}} for residue values.

-\code{\link{KDNorm}} for residue values.

-

-Other scaled hydropathy functions: 

-\code{\link{KDNorm}},

-\code{\link{meanScaledHydropathy}()},

-\code{\link{scaledHydropathyLocal}()}

-

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

 \code{\link{meanScaledHydropathy}()},

@@ -12,7 +12,7 @@ scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

 \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.}

+the path to a .fasta or .fa file.}

 \item{plotResults}{logical value, FALSE by default.

 If \code{plotResults = TRUE} a plot will be the output.

@@ -32,7 +32,7 @@ if \code{plotResults = TRUE}, a graphical representation data.

 if \code{plotResults = TRUE}, a graphical representation data.

   Average is shown by the horizontal line.

-  If \code{plotResults = FALSE}, a dataframe is reported

+  If \code{plotResults = FALSE}, a data frame is reported

   with each amino acid and each residue value shown.

   Score for each residue shown in the column "Hydropathy".

 }

@@ -44,7 +44,7 @@ This is used to calculate the scaled hydropathy of an amino acid

 This is used to calculate the scaled hydropathy of an amino acid

   sequence for each residue in the sequence.

-  The output is either a dataframe or graph

+  The output is either a data frame or graph

   showing the matched scores for each residue along the sequence.

 }

 \examples{

@@ -1,9 +1,11 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/scaledHydropathyGlobal.R

+% Please edit documentation in R/scaledHydropathy.R

 \name{scaledHydropathyGlobal}

 \alias{scaledHydropathyGlobal}

 \title{Protein Scaled Hydropathy Calculations}

 \usage{

+scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

+

 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

 }

 \arguments{

@@ -22,6 +24,12 @@ optional setting to include the name in the plot title.}

 \item{...}{any additional parameters, especially those for plotting.}

 }

 \value{

+if \code{plotResults = TRUE}, a graphical representation data.

+  Average is shown by the horizontal line.

+  If \code{plotResults = FALSE}, a dataframe is reported

+  with each amino acid and each residue value shown.

+  Score for each residue shown in the column "Hydropathy".

+

 if \code{plotResults = TRUE}, a graphical representation data.

   Average is shown by the horizontal line.

   If \code{plotResults = FALSE}, a dataframe is reported

@@ -31,9 +39,85 @@ if \code{plotResults = TRUE}, a graphical representation data.

 \description{

 This is used to calculate the scaled hydropathy of an amino acid

   sequence for each residue in the sequence.

-  Results are based on the

+  The output is either a dataframe or graph

+  showing the matched scores for each residue along the sequence.

+

+This is used to calculate the scaled hydropathy of an amino acid

+  sequence for each residue in the sequence.

+  The output is either a dataframe or graph

+  showing the matched scores for each residue along the sequence.

+}

+\examples{

+#Amino acid sequences can be character strings

+aaString <- "ACDEFGHIKLMNPQRSTVWY"

+#Amino acid sequences can also be character vectors

+aaVector <- c("A", "C", "D", "E", "F",

+              "G", "H", "I", "K", "L",

+           "M", "N", "P", "Q", "R",

+           "S", "T", "V", "W", "Y")

+#Alternativly, .fasta files can also be used by providing

+##The path to the file as a character string

+

+exampleDF <- scaledHydropathyGlobal(aaString,

+                                    plotResults = FALSE)

+head(exampleDF)

+

+exampleDF <- scaledHydropathyGlobal(aaVector,

+                                    plotResults = FALSE)

+head(exampleDF)

+

+#plotResults = TRUE will output a ggplot

+\dontrun{

+  scaledHydropathyGlobal(aaString,

+                         plot = T)

+

+  #since it is a ggplot, you can change or annotate the plot

+  gg <- scaledHydropathyGlobal(aaVector,

+                               plot = T)

+  gg <- gg + ggplot2::ylab("Local Hydropathy")

+  gg <- gg + ggplot2::geom_text(data = exampleDF,

+                                ggplot2::aes(label = AA,

+                                             y = Hydropathy + 0.1))

+  plot(gg)

+}

+#Amino acid sequences can be character strings

+aaString <- "ACDEFGHIKLMNPQRSTVWY"

+#Amino acid sequences can also be character vectors

+aaVector <- c("A", "C", "D", "E", "F",

+              "G", "H", "I", "K", "L",

+           "M", "N", "P", "Q", "R",

+           "S", "T", "V", "W", "Y")

+#Alternativly, .fasta files can also be used by providing

+##The path to the file as a character string

+

+exampleDF <- scaledHydropathyGlobal(aaString,

+                                    plotResults = FALSE)

+head(exampleDF)

+

+exampleDF <- scaledHydropathyGlobal(aaVector,

+                                    plotResults = FALSE)

+head(exampleDF)

+

+#plotResults = TRUE will output a ggplot

+\dontrun{

+  scaledHydropathyGlobal(aaString,

+                         plot = T)

+

+  #since it is a ggplot, you can change or annotate the plot

+  gg <- scaledHydropathyGlobal(aaVector,

+                               plot = T)

+  gg <- gg + ggplot2::ylab("Local Hydropathy")

+  gg <- gg + ggplot2::geom_text(data = exampleDF,

+                                ggplot2::aes(label = AA,

+                                             y = Hydropathy + 0.1))

+  plot(gg)

+}

 }

 \references{

+Kyte, J., & Doolittle, R. F. (1982). A simple method for

+  displaying the hydropathic character of a protein.

+  Journal of molecular biology, 157(1), 105-132.

+

 Kyte, J., & Doolittle, R. F. (1982). A simple method for

   displaying the hydropathic character of a protein.

   Journal of molecular biology, 157(1), 105-132.

@@ -41,6 +125,13 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for

 \seealso{

 \code{\link{KDNorm}} for residue values.

+\code{\link{KDNorm}} for residue values.

+

+Other scaled hydropathy functions: 

+\code{\link{KDNorm}},

+\code{\link{meanScaledHydropathy}()},

+\code{\link{scaledHydropathyLocal}()}

+

 Other scaled hydropathy functions: 

 \code{\link{KDNorm}},

 \code{\link{meanScaledHydropathy}()},

new file mode 100644

@@ -0,0 +1,49 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/scaledHydropathyGlobal.R

+\name{scaledHydropathyGlobal}

+\alias{scaledHydropathyGlobal}

+\title{Protein Scaled Hydropathy Calculations}

+\usage{

+scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

+}

+\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{plotResults}{logical value, FALSE by default.

+If \code{plotResults = TRUE} a plot will be the output.

+If \code{plotResults = FALSE} the output is a data frame for each residue.}

+

+\item{proteinName}{character string with length = 1.

+optional setting to include the name in the plot title.}

+

+\item{...}{any additional parameters, especially those for plotting.}

+}

+\value{

+if \code{plotResults = TRUE}, a graphical representation data.

+  Average is shown by the horizontal line.

+  If \code{plotResults = FALSE}, a dataframe is reported

+  with each amino acid and each residue value shown.

+  Score for each residue shown in the column "Hydropathy".

+}

+\description{

+This is used to calculate the scaled hydropathy of an amino acid

+  sequence for each residue in the sequence.

+  Results are based on the

+}

+\references{

+Kyte, J., & Doolittle, R. F. (1982). A simple method for

+  displaying the hydropathic character of a protein.

+  Journal of molecular biology, 157(1), 105-132.

+}

+\seealso{

+\code{\link{KDNorm}} for residue values.

+

+Other scaled hydropathy functions: 

+\code{\link{KDNorm}},

+\code{\link{meanScaledHydropathy}()},

+\code{\link{scaledHydropathyLocal}()}

+}

+\concept{scaled hydropathy functions}