% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/scaledHydropathy.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,
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.}
}
\value{
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".
}
\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 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"
#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
scaledHydropathyGlobal(aaString,
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))
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.
}
\seealso{