#' IDp PRofile From idpr Package
#'
#' The IDPRofile is a summation of many features of the idpr package,
#' conveniently grouped into one function for quick analysis. This combines
#' many plotting functions in this package. These include:\cr
#' \code{\link{chargeHydropathyPlot}}\cr
#' \code{\link{chargeCalculationLocal}}\cr
#' \code{\link{scaledHydropathyLocal}}\cr
#' \code{\link{structuralTendencyPlot}}\cr
#' \code{\link{foldIndexR}}\cr
#' All of the above linked functions only require the sequence argument
#' to output plots of characteristics associated with IDPs. The function also
#' includes options for IUPred functions. The function does one of the
#' following based on user-specified parameters:\cr
#' \code{\link{iupred}}\cr
#' \code{\link{iupredAnchor}}\cr
#' \code{\link{iupredRedox}}\cr
#' The IUPred function used depends on the argument of iupredType. All
#' require the UniProt Accession to make a proper connection to the IUPred2A
#' REST API. If the UniProt Accession is not specified, the IUPred plot is
#' skipped.
#'
#' Described in McFadden, W. M., & Yanowitz, J. L. (2022).
#' idpr: A package for profiling and analyzing Intrinsically Disordered
#' Proteins in R. PloS one,
#' \href{https://doi.org/10.1371/journal.pone.0266929}{17(4), e0266929}
#' @param sequence amino acid sequence as a single character string or vector of
#' single characters. It also supports a single character string that
#' specifies the location of a .fasta or .fa file.
#' @param uniprotAccession character string specifying the UniProt Accession of
#' the protein of interest. Used to fetch predictions from IUPreds REST API.
#' Default is NA. Keep as NA if you do not have a UniProt Accession.
#' @param window a positive, odd integer. 9 by default.
#' Sets the size of sliding window, must be an odd number.
#' The window determines the number of residues to be analyzed and averaged
#' for each position along the sequence. For chargeCalculationLocal and
#' scaledHydropathyLocal.
#' @param proteinName character string, optional.
#' Used to add protein name to the title in ggplot.
#' @inheritParams chargeCalculationLocal
#' @inheritParams structuralTendencyPlot
#' @param structuralTendencyType a character string specifying the type of plot
#' the \code{\link{structuralTendencyPlot}} should output.
#' Can be "bar" or "pie".
#' Equivalent argument to graphType= in the linked function.
#' "bar" by default.
#' @param structuralTendencySummarize a logical value specifying the
#' \code{\link{structuralTendencyPlot}} should be summarized into broad
#' categories. Equivalent argument to summarize= in the linked function.
#' FALSE by default
#' @param disorderPromoting,disorderNeutral,orderPromoting character vectors
#' of individual residues to be matched with the input sequence. Defaults:
#' \itemize{
#' \item disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G")
#' \item orderPromoting =
#' c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C")
#' \item disorderNeutral = c("D", "T", "R")
#' }
#' It is not recommended to change these. Arguments passed to
#' \code{\link{structuralTendencyPlot}}
#' @param iupredType character string specifying the type of IUPred2 prediction
#' to retrieve. Can be c("long", "short", "glob", "anchor", "redox"). "long"
#' by default. "long", "short", and "glob" use the \code{\link{iupred}}
#' function and specify the type of plot. Both "redox" and "anchor" use "long"
#' for predictions, but are context dependent. "anchor" uses
#' \code{\link{iupredAnchor}} to get predictions of disorder with IUPred2 and
#' predictions of induced folding based on ANCHOR2 predictions (Shown with a
#' red line). "redox" uses \code{\link{iupredRedox}} to make predictions of
#' disorder based on environmental conditions. Regions of predicted
#' environmental sensitivity are highlighted. See the respective functions
#' for more details. This is skipped if uniprotAccession = NA.
#' @param foldIndexWindowSize a positive, odd integer. 51 by default.
#' Sets the size of sliding window, must be an odd number.
#' The window determines the number of residues to be scored and averaged
#' for each position along the sequence.
#' @param foldIndex_pH numeric value, 7.0 by default.
#' The environmental pH used to calculate residue charge.
#' FoldIndex specifically uses pH = 7.0 in settings and thus, is distinct
#' from changing pH in the other calculations.
#'
#' @return 4 or 5 plots, depending if a UniProt Accession is provided.
#' @export
#' @seealso
#' \code{\link{chargeHydropathyPlot}}\cr
#' \code{\link{chargeCalculationLocal}}\cr
#' \code{\link{scaledHydropathyLocal}}\cr
#' \code{\link{structuralTendencyPlot}}\cr
#' \code{\link{foldIndexR}}\cr
#' \code{\link{iupred}}\cr
#' \code{\link{iupredAnchor}}\cr
#' \code{\link{iupredRedox}}
#'
#' @section Citations for each Plot:
#' \itemize{
#' \item \code{\link{chargeHydropathyPlot}}
#' \itemize{
#' \item{Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator.
#' Biology Direct, 11(1), 55.
#' https://doi.org/10.1186/s13062-016-0159-9}
#' \item{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.}
#' \item{Uversky, V. N. (2016). Paradoxes and wonders of intrinsic
#' disorder: Complexity of simplicity. Intrinsically Disordered
#' Proteins, 4(1), e1135015.
#' https://doi.org/10.1080/21690707.2015.1135015}
#' \item{Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000).
#' Why are “natively unfolded” proteins unstructured under
#' physiologic conditions?. Proteins: structure, function,
#' and bioinformatics, 41(3), 415-427.
#' https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}
#' \item{If a pKa set is specified, see \code{\link{pKaData}}}
#' }
#' \item \code{\link{chargeCalculationLocal}}
#' \itemize{
#' \item{Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator.
#' Biology Direct, 11(1), 55.
#' https://doi.org/10.1186/s13062-016-0159-9}
#' \item{If a pKa set is specified, see \code{\link{pKaData}}}
#' }
#' \item \code{\link{scaledHydropathyLocal}}
#' \itemize{
#' \item{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.}
#' }
#' \item \code{\link{structuralTendencyPlot}}
#' \itemize{
#' \item{Uversky, V. N. (2013).
#' A decade and a half of protein intrinsic disorder:
#' Biology still waits for physics.
#' Protein Science, 22(6), 693-724.
#' doi:10.1002/pro.2261 }
#' }
#' \item \code{\link{foldIndexR}}
#' \itemize{
#' \item{Prilusky, J., Felder, C. E., et al. (2005).
#' FoldIndex: a simple tool to predict whether
#' a given protein sequence is intrinsically unfolded.
#' Bioinformatics, 21(16), 3435-3438.}
#' \item{Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000).
#' Why are “natively unfolded” proteins unstructured under
#' physiologic conditions?. Proteins: structure, function,
#' and bioinformatics, 41(3), 415-427.
#' https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7}
#' \item{Also see citations for hydrapthy and charge plots above}
#' }
#' \item \code{\link{iupred}},
#' \code{\link{iupredAnchor}},
#' \code{\link{iupredRedox}}
#' \itemize{
#' \item{Bálint Mészáros, Gábor Erdős, Zsuzsanna Dosztányi, IUPred2A:
#' context-dependent prediction of protein disorder as a function of
#' redox state and protein binding, Nucleic Acids Research, Volume 46,
#' Issue W1, 2 July 2018, Pages W329–W337,
#' https://doi.org/10.1093/nar/gky384}
#' \item{Erdős, G., & Dosztányi, Z. (2020). Analyzing protein disorder
#' with IUPred2A. Current Protocols in Bioinformatics, 70, e99.
#' https://doi.org/10.1002/cpbi.99}
#' }
#' }
#' @examples
#' #For most functions, a protein sequence is all that is needed.
#'
#' #The UniProt ID is optional but recommended for IUPred results.
#' proteinID <- "P04637"
#' p53Seq <- idpr:::TP53Sequences[2]
#' \dontrun{
#' idprofile(
#' sequence = p53Seq,
#' uniprotAccession = proteinID)
#'
#'
#' #changing the iupred to redox
#' ## and getting a pie chart for structuralTendency.
#' idprofile(
#' sequence = p53Seq,
#' uniprotAccession = proteinID,
#' pKaSet = EMBOSS,
#' iupredType = "redox",
#' structuralTendencyType = "pie")
#' }
#'
idprofile <- function(
sequence,
uniprotAccession = NA,
proteinName = NA,
iupredType = "long",
window = 9,
foldIndexWindowSize = 51,
pH = 7.0,
foldIndex_pH = 7.0,
pKaSet = "IPC_protein",
structuralTendencyType = "bar",
structuralTendencySummarize = FALSE,
disorderPromoting = c("P", "E", "S", "Q", "K", "A", "G"),
disorderNeutral = c("D", "T", "R"),
orderPromoting = c("M", "N", "V", "H", "L", "F", "Y", "I", "W", "C")) {
#---- General Plots
rhPlot <- chargeHydropathyPlot(
sequence = sequence,
pH = pH,
pKaSet = pKaSet,
proteinName = proteinName)
chargePlot <- chargeCalculationLocal(
sequence = sequence,
window = window,
plotResults = TRUE, pH = pH,
proteinName = proteinName)
hydropPlot <- scaledHydropathyLocal(
sequence = sequence,
window = window,
plotResults = TRUE,
pKaSet = pKaSet,
proteinName = proteinName)
tendencyPlot <- structuralTendencyPlot(
sequence = sequence,
graphType = structuralTendencyType,
summarize = structuralTendencySummarize,
disorderPromoting = disorderPromoting,
disorderNeutral = disorderNeutral,
orderPromoting = orderPromoting,
proteinName = proteinName)
foldIndexPlot <- foldIndexR(sequence = sequence,
window = foldIndexWindowSize,
pH = foldIndex_pH,
proteinName = proteinName,
pKaSet = pKaSet)
#-------- Adding IUPred Plot based on which type
if (!is.na(uniprotAccession)) {
if (iupredType %in% c("long", "short", "glob")) {
iupredPlot <- iupred(
uniprotAccession,
iupredType = iupredType,
plotResults = TRUE,
proteinName = proteinName)
}
if (iupredType == "anchor") {
iupredPlot <- iupredAnchor(
uniprotAccession,
plotResults = TRUE,
proteinName = proteinName)
}
if (iupredType == "redox") {
iupredPlot <- iupredRedox(
uniprotAccession,
plotResults = TRUE,
proteinName = proteinName)
}
} else {
iupredPlot <- ggplot2::ggplot() +
ggplot2::annotate("text", x = 1, y = 1,
label = "No Uniprot Accession provided...IUPred plot skipped") +
ggplot2::theme_void()
}
plotList <- list(rhPlot, tendencyPlot, chargePlot, hydropPlot,
foldIndexPlot, iupredPlot)
return(plotList)
}
