man/scaledHydropathyGlobal.Rd
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 % Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/scaledHydropathy.R
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 \name{scaledHydropathyGlobal}
 \alias{scaledHydropathyGlobal}
 \title{Protein Scaled Hydropathy Calculations}
 \usage{
 scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)
 }
 \arguments{
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 \item{sequence}{amino acid sequence as a single character string,
 a vector of single characters, or an AAString object.
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 It also supports a single character string that specifies
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 the path to a .fasta or .fa file.}
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 \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.
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   If \code{plotResults = FALSE}, a data frame is reported
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   with each amino acid and each residue value shown.
   Score for each residue shown in the column "Hydropathy".
 }
 \description{
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 This is used to calculate the scaled hydropathy of an amino acid
   sequence for each residue in the sequence.
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   The output is either a data frame or graph
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   showing the matched scores for each residue along the sequence.
 }
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 \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"}}
 }
 
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 \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",
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               "M", "N", "P", "Q", "R",
               "S", "T", "V", "W", "Y")
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 #Alternatively, .fasta files can also be used by providing
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 ##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
   scaledHydropathyGlobal(aaString,
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                          plotResults = TRUE)
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   #since it is a ggplot, you can change or annotate the plot
   gg <- scaledHydropathyGlobal(aaVector,
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                                plotResults = TRUE)
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   gg <- gg + ggplot2::ylab("Local Hydropathy")
   gg <- gg + ggplot2::geom_text(data = exampleDF,
                                 ggplot2::aes(label = AA,
                                              y = Hydropathy + 0.1))
   plot(gg)
 }
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 \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}},
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 \code{\link{foldIndexR}()},
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 \code{\link{meanScaledHydropathy}()},
 \code{\link{scaledHydropathyLocal}()}
 }
 \concept{scaled hydropathy functions}