% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scaledHydropathy.R
\title{Protein Scaled Hydropathy Calculations}
scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
\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.}

\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.}
if \code{plotResults = TRUE}, a graphical representation data.
  Average is shown by the horizontal line.
  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".
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
  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
  \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"}}

#Amino acid sequences can be character strings
#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")
#Alternatively, .fasta files can also be used by providing
##The path to the file as a character string

exampleDF <- scaledHydropathyGlobal(aaString,
                                    plotResults = FALSE)

exampleDF <- scaledHydropathyGlobal(aaVector,
                                    plotResults = FALSE)

#plotResults = TRUE will output a ggplot
                         plotResults = TRUE)

  #since it is a ggplot, you can change or annotate the plot
  gg <- scaledHydropathyGlobal(aaVector,
                               plotResults = TRUE)
  gg <- gg + ggplot2::ylab("Local Hydropathy")
  gg <- gg + ggplot2::geom_text(data = exampleDF,
                                ggplot2::aes(label = AA,
                                             y = Hydropathy + 0.1))
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.
\code{\link{KDNorm}} for residue values.

Other scaled hydropathy functions: 
\concept{scaled hydropathy functions}