#### FoldIndexR addition

Package changes implementing the FoldIndexR() equation into idpr and the idprofiles.

WilliamMc authored on 11/03/2022 07:31:29
Showing1 changed files
 ... ... @@ -87,6 +87,7 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for 87 87   88 88  Other scaled hydropathy functions:  89 89  \code{\link{KDNorm}}, 90 +\code{\link{foldIndexR}()}, 90 91  \code{\link{meanScaledHydropathy}()}, 91 92  \code{\link{scaledHydropathyLocal}()} 92 93  }

#### Updating sequenceCheck

WilliamMc authored on 26/08/2020 22:50:34
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 ... ... @@ -7,8 +7,8 @@ 7 7  scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 8 8  } 9 9  \arguments{ 10 -\item{sequence}{amino acid sequence as a single character string 11 -or vector of single characters. 10 +\item{sequence}{amino acid sequence as a single character string, 11 +a vector of single characters, or an AAString object. 12 12  It also supports a single character string that specifies 13 13  the path to a .fasta or .fa file.} 14 14 

#### Proofreading Documentation

WilliamMc authored on 16/07/2020 22:26:29
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 ... ... @@ -34,6 +34,17 @@ This is used to calculate the scaled hydropathy of an amino acid 34 34  The output is either a data frame or graph 35 35  showing the matched scores for each residue along the sequence. 36 36  } 37 +\section{Plot Colors}{ 38 + 39 + For users who wish to keep a common aesthetic, the following colors are 40 + used when plotResults = TRUE. \cr 41 + \itemize{ 42 + \item Dynamic line colors: \itemize{ 43 + \item Close to 0 = "skyblue3" or "#6CA6CD" 44 + \item Close to 1 = "chocolate1" or "#FF7F24" 45 + \item Close to midpoint = "grey65" or "#A6A6A6"}} 46 +} 47 + 37 48  \examples{ 38 49  #Amino acid sequences can be character strings 39 50  aaString <- "ACDEFGHIKLMNPQRSTVWY" ... ... @@ -42,7 +53,7 @@ aaVector <- c("A", "C", "D", "E", "F", 42 53  "G", "H", "I", "K", "L", 43 54  "M", "N", "P", "Q", "R", 44 55  "S", "T", "V", "W", "Y") 45 -#Alternativly, .fasta files can also be used by providing 56 +#Alternatively, .fasta files can also be used by providing 46 57  ##The path to the file as a character string 47 58   48 59  exampleDF <- scaledHydropathyGlobal(aaString,

#### fixing notes by bioccheck

WilliamMc authored on 07/07/2020 20:51:57
Showing1 changed files
 ... ... @@ -40,8 +40,8 @@ aaString <- "ACDEFGHIKLMNPQRSTVWY" 40 40  #Amino acid sequences can also be character vectors 41 41  aaVector <- c("A", "C", "D", "E", "F", 42 42  "G", "H", "I", "K", "L", 43 - "M", "N", "P", "Q", "R", 44 - "S", "T", "V", "W", "Y") 43 + "M", "N", "P", "Q", "R", 44 + "S", "T", "V", "W", "Y") 45 45  #Alternativly, .fasta files can also be used by providing 46 46  ##The path to the file as a character string 47 47 

#### Updating based on BiocCheck

WilliamMc authored on 07/07/2020 16:12:39
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 ... ... @@ -4,8 +4,6 @@ 4 4  \alias{scaledHydropathyGlobal} 5 5  \title{Protein Scaled Hydropathy Calculations} 6 6  \usage{ 7 -scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 8 - 9 7  scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 10 8  } 11 9  \arguments{ ... ... @@ -24,12 +22,6 @@ optional setting to include the name in the plot title.} 24 22  \item{...}{any additional parameters, especially those for plotting.} 25 23  } 26 24  \value{ 27 -if \code{plotResults = TRUE}, a graphical representation data. 28 - Average is shown by the horizontal line. 29 - If \code{plotResults = FALSE}, a dataframe is reported 30 - with each amino acid and each residue value shown. 31 - Score for each residue shown in the column "Hydropathy". 32 - 33 25  if \code{plotResults = TRUE}, a graphical representation data. 34 26  Average is shown by the horizontal line. 35 27  If \code{plotResults = FALSE}, a data frame is reported ... ... @@ -37,11 +29,6 @@ if \code{plotResults = TRUE}, a graphical representation data. 37 29  Score for each residue shown in the column "Hydropathy". 38 30  } 39 31  \description{ 40 -This is used to calculate the scaled hydropathy of an amino acid 41 - sequence for each residue in the sequence. 42 - The output is either a dataframe or graph 43 - showing the matched scores for each residue along the sequence. 44 - 45 32  This is used to calculate the scaled hydropathy of an amino acid 46 33  sequence for each residue in the sequence. 47 34  The output is either a data frame or graph ... ... @@ -67,57 +54,19 @@ exampleDF <- scaledHydropathyGlobal(aaVector, 67 54  head(exampleDF) 68 55   69 56  #plotResults = TRUE will output a ggplot 70 -\dontrun{ 71 - scaledHydropathyGlobal(aaString, 72 - plot = T) 73 - 74 - #since it is a ggplot, you can change or annotate the plot 75 - gg <- scaledHydropathyGlobal(aaVector, 76 - plot = T) 77 - gg <- gg + ggplot2::ylab("Local Hydropathy") 78 - gg <- gg + ggplot2::geom_text(data = exampleDF, 79 - ggplot2::aes(label = AA, 80 - y = Hydropathy + 0.1)) 81 - plot(gg) 82 -} 83 -#Amino acid sequences can be character strings 84 -aaString <- "ACDEFGHIKLMNPQRSTVWY" 85 -#Amino acid sequences can also be character vectors 86 -aaVector <- c("A", "C", "D", "E", "F", 87 - "G", "H", "I", "K", "L", 88 - "M", "N", "P", "Q", "R", 89 - "S", "T", "V", "W", "Y") 90 -#Alternativly, .fasta files can also be used by providing 91 -##The path to the file as a character string 92 - 93 -exampleDF <- scaledHydropathyGlobal(aaString, 94 - plotResults = FALSE) 95 -head(exampleDF) 96 - 97 -exampleDF <- scaledHydropathyGlobal(aaVector, 98 - plotResults = FALSE) 99 -head(exampleDF) 100 - 101 -#plotResults = TRUE will output a ggplot 102 -\dontrun{ 103 57  scaledHydropathyGlobal(aaString, 104 - plot = T) 58 + plotResults = TRUE) 105 59   106 60  #since it is a ggplot, you can change or annotate the plot 107 61  gg <- scaledHydropathyGlobal(aaVector, 108 - plot = T) 62 + plotResults = TRUE) 109 63  gg <- gg + ggplot2::ylab("Local Hydropathy") 110 64  gg <- gg + ggplot2::geom_text(data = exampleDF, 111 65  ggplot2::aes(label = AA, 112 66  y = Hydropathy + 0.1)) 113 67  plot(gg) 114 68  } 115 -} 116 69  \references{ 117 -Kyte, J., & Doolittle, R. F. (1982). A simple method for 118 - displaying the hydropathic character of a protein. 119 - Journal of molecular biology, 157(1), 105-132. 120 - 121 70  Kyte, J., & Doolittle, R. F. (1982). A simple method for 122 71  displaying the hydropathic character of a protein. 123 72  Journal of molecular biology, 157(1), 105-132. ... ... @@ -125,13 +74,6 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for 125 74  \seealso{ 126 75  \code{\link{KDNorm}} for residue values. 127 76   128 -\code{\link{KDNorm}} for residue values. 129 - 130 -Other scaled hydropathy functions:  131 -\code{\link{KDNorm}}, 132 -\code{\link{meanScaledHydropathy}()}, 133 -\code{\link{scaledHydropathyLocal}()} 134 - 135 77  Other scaled hydropathy functions:  136 78  \code{\link{KDNorm}}, 137 79  \code{\link{meanScaledHydropathy}()},

#### Vignette and Documentation Updates

Proofreading and updating documentation for the package

WilliamMc authored on 17/06/2020 18:50:56
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 ... ... @@ -12,7 +12,7 @@ scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 12 12  \item{sequence}{amino acid sequence as a single character string 13 13  or vector of single characters. 14 14  It also supports a single character string that specifies 15 -the locaion of a .fasta or .fa file.} 15 +the path to a .fasta or .fa file.} 16 16   17 17  \item{plotResults}{logical value, FALSE by default. 18 18  If \code{plotResults = TRUE} a plot will be the output. ... ... @@ -32,7 +32,7 @@ if \code{plotResults = TRUE}, a graphical representation data. 32 32   33 33  if \code{plotResults = TRUE}, a graphical representation data. 34 34  Average is shown by the horizontal line. 35 - If \code{plotResults = FALSE}, a dataframe is reported 35 + If \code{plotResults = FALSE}, a data frame is reported 36 36  with each amino acid and each residue value shown. 37 37  Score for each residue shown in the column "Hydropathy". 38 38  } ... ... @@ -44,7 +44,7 @@ This is used to calculate the scaled hydropathy of an amino acid 44 44   45 45  This is used to calculate the scaled hydropathy of an amino acid 46 46  sequence for each residue in the sequence. 47 - The output is either a dataframe or graph 47 + The output is either a data frame or graph 48 48  showing the matched scores for each residue along the sequence. 49 49  } 50 50  \examples{

#### Added example documentation and combined similar scripts into the same file

WilliamMc authored on 05/06/2020 22:41:26
Showing1 changed files
 ... ... @@ -1,9 +1,11 @@ 1 1  % Generated by roxygen2: do not edit by hand 2 -% Please edit documentation in R/scaledHydropathyGlobal.R 2 +% Please edit documentation in R/scaledHydropathy.R 3 3  \name{scaledHydropathyGlobal} 4 4  \alias{scaledHydropathyGlobal} 5 5  \title{Protein Scaled Hydropathy Calculations} 6 6  \usage{ 7 +scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 8 + 7 9  scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 8 10  } 9 11  \arguments{ ... ... @@ -22,6 +24,12 @@ optional setting to include the name in the plot title.} 22 24  \item{...}{any additional parameters, especially those for plotting.} 23 25  } 24 26  \value{ 27 +if \code{plotResults = TRUE}, a graphical representation data. 28 + Average is shown by the horizontal line. 29 + If \code{plotResults = FALSE}, a dataframe is reported 30 + with each amino acid and each residue value shown. 31 + Score for each residue shown in the column "Hydropathy". 32 + 25 33  if \code{plotResults = TRUE}, a graphical representation data. 26 34  Average is shown by the horizontal line. 27 35  If \code{plotResults = FALSE}, a dataframe is reported ... ... @@ -31,9 +39,85 @@ if \code{plotResults = TRUE}, a graphical representation data. 31 39  \description{ 32 40  This is used to calculate the scaled hydropathy of an amino acid 33 41  sequence for each residue in the sequence. 34 - Results are based on the 42 + The output is either a dataframe or graph 43 + showing the matched scores for each residue along the sequence. 44 + 45 +This is used to calculate the scaled hydropathy of an amino acid 46 + sequence for each residue in the sequence. 47 + The output is either a dataframe or graph 48 + showing the matched scores for each residue along the sequence. 49 +} 50 +\examples{ 51 +#Amino acid sequences can be character strings 52 +aaString <- "ACDEFGHIKLMNPQRSTVWY" 53 +#Amino acid sequences can also be character vectors 54 +aaVector <- c("A", "C", "D", "E", "F", 55 + "G", "H", "I", "K", "L", 56 + "M", "N", "P", "Q", "R", 57 + "S", "T", "V", "W", "Y") 58 +#Alternativly, .fasta files can also be used by providing 59 +##The path to the file as a character string 60 + 61 +exampleDF <- scaledHydropathyGlobal(aaString, 62 + plotResults = FALSE) 63 +head(exampleDF) 64 + 65 +exampleDF <- scaledHydropathyGlobal(aaVector, 66 + plotResults = FALSE) 67 +head(exampleDF) 68 + 69 +#plotResults = TRUE will output a ggplot 70 +\dontrun{ 71 + scaledHydropathyGlobal(aaString, 72 + plot = T) 73 + 74 + #since it is a ggplot, you can change or annotate the plot 75 + gg <- scaledHydropathyGlobal(aaVector, 76 + plot = T) 77 + gg <- gg + ggplot2::ylab("Local Hydropathy") 78 + gg <- gg + ggplot2::geom_text(data = exampleDF, 79 + ggplot2::aes(label = AA, 80 + y = Hydropathy + 0.1)) 81 + plot(gg) 82 +} 83 +#Amino acid sequences can be character strings 84 +aaString <- "ACDEFGHIKLMNPQRSTVWY" 85 +#Amino acid sequences can also be character vectors 86 +aaVector <- c("A", "C", "D", "E", "F", 87 + "G", "H", "I", "K", "L", 88 + "M", "N", "P", "Q", "R", 89 + "S", "T", "V", "W", "Y") 90 +#Alternativly, .fasta files can also be used by providing 91 +##The path to the file as a character string 92 + 93 +exampleDF <- scaledHydropathyGlobal(aaString, 94 + plotResults = FALSE) 95 +head(exampleDF) 96 + 97 +exampleDF <- scaledHydropathyGlobal(aaVector, 98 + plotResults = FALSE) 99 +head(exampleDF) 100 + 101 +#plotResults = TRUE will output a ggplot 102 +\dontrun{ 103 + scaledHydropathyGlobal(aaString, 104 + plot = T) 105 + 106 + #since it is a ggplot, you can change or annotate the plot 107 + gg <- scaledHydropathyGlobal(aaVector, 108 + plot = T) 109 + gg <- gg + ggplot2::ylab("Local Hydropathy") 110 + gg <- gg + ggplot2::geom_text(data = exampleDF, 111 + ggplot2::aes(label = AA, 112 + y = Hydropathy + 0.1)) 113 + plot(gg) 114 +} 35 115  } 36 116  \references{ 117 +Kyte, J., & Doolittle, R. F. (1982). A simple method for 118 + displaying the hydropathic character of a protein. 119 + Journal of molecular biology, 157(1), 105-132. 120 + 37 121  Kyte, J., & Doolittle, R. F. (1982). A simple method for 38 122  displaying the hydropathic character of a protein. 39 123  Journal of molecular biology, 157(1), 105-132. ... ... @@ -41,6 +125,13 @@ Kyte, J., & Doolittle, R. F. (1982). A simple method for 41 125  \seealso{ 42 126  \code{\link{KDNorm}} for residue values. 43 127   128 +\code{\link{KDNorm}} for residue values. 129 + 130 +Other scaled hydropathy functions:  131 +\code{\link{KDNorm}}, 132 +\code{\link{meanScaledHydropathy}()}, 133 +\code{\link{scaledHydropathyLocal}()} 134 + 44 135  Other scaled hydropathy functions:  45 136  \code{\link{KDNorm}}, 46 137  \code{\link{meanScaledHydropathy}()},

#### Initial commit

WilliamMc authored on 13/05/2020 00:45:34
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 1 1 new file mode 100644 ... ... @@ -0,0 +1,49 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/scaledHydropathyGlobal.R 3 +\name{scaledHydropathyGlobal} 4 +\alias{scaledHydropathyGlobal} 5 +\title{Protein Scaled Hydropathy Calculations} 6 +\usage{ 7 +scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...) 8 +} 9 +\arguments{ 10 +\item{sequence}{amino acid sequence as a single character string 11 +or vector of single characters. 12 +It also supports a single character string that specifies 13 +the locaion of a .fasta or .fa file.} 14 + 15 +\item{plotResults}{logical value, FALSE by default. 16 +If \code{plotResults = TRUE} a plot will be the output. 17 +If \code{plotResults = FALSE} the output is a data frame for each residue.} 18 + 19 +\item{proteinName}{character string with length = 1. 20 +optional setting to include the name in the plot title.} 21 + 22 +\item{...}{any additional parameters, especially those for plotting.} 23 +} 24 +\value{ 25 +if \code{plotResults = TRUE}, a graphical representation data. 26 + Average is shown by the horizontal line. 27 + If \code{plotResults = FALSE}, a dataframe is reported 28 + with each amino acid and each residue value shown. 29 + Score for each residue shown in the column "Hydropathy". 30 +} 31 +\description{ 32 +This is used to calculate the scaled hydropathy of an amino acid 33 + sequence for each residue in the sequence. 34 + Results are based on the 35 +} 36 +\references{ 37 +Kyte, J., & Doolittle, R. F. (1982). A simple method for 38 + displaying the hydropathic character of a protein. 39 + Journal of molecular biology, 157(1), 105-132. 40 +} 41 +\seealso{ 42 +\code{\link{KDNorm}} for residue values. 43 + 44 +Other scaled hydropathy functions:  45 +\code{\link{KDNorm}}, 46 +\code{\link{meanScaledHydropathy}()}, 47 +\code{\link{scaledHydropathyLocal}()} 48 +} 49 +\concept{scaled hydropathy functions}