R/plot_ave_tp.R

In mkajano/HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

#' Preparatory function for average plot
#'
#' Returns plots with average deuteration at each peptide.
#'
#' @param df output from functions output_tp or output_tp or output_tp_proc.
#' @param cola color pallette for different Protein States. As default Paired pallette from color.Brewer is used.
#' @importFrom RColorBrewer brewer.pal
#' @return plots of averages
#' @export
av_tp<-function(df, cola) {
  if(missing(cola)) cola=c(1, brewer.pal(n = max((dim(df)[2]-7), 3), name = "Paired"));
  n1=max((dim(df)[2]-7), 3)
  #cola<-c(1, brewer.pal(n = n1, name = "Paired"))
  plot(df[,7], type="n", xlab="", ylab="", lwd=2, col=cola[1], ylim=c(0, max(df[,7:dim(df)[2]])+10))

  for ( i in 7:dim(df)[2]){
    points(df[,i], type="l", xlab="", ylab="", col=cola[i-6])}
  axis(1, at=seq(0, 1000, by=10), cex.axis=1, labels=FALSE,tcl=-0.2)
  axis(2, at=seq(0, 1000, by=5), cex.axis=1, labels=FALSE,tcl=-0.2)}


#' Legend for average plot.
#'
#' Returns legend with average plots. Preparatory function.
#'
#' @param df output from functions output_tp or output_tp_proc.
#' @param cola color pallette for different Protein States. As default Paired pallette from color.Brewer is used.
#' @importFrom stringr str_sub
#' @return legend for average plot for time points
#' @export
legend_raw_ave<-function(df, cola){
  if(missing(cola)) cola=c(1, brewer.pal(n = max((dim(df)[2]-7), 3), name = "Paired"));
  yloc =1
  yadj =0
  xloc =getCoords1(1, input = "p")
  xadj =0
  n1=max((dim(df)[2]-7), 3)
  #cola<-c(1, brewer.pal(n = n1, name = "Paired"))
  ##draw boxplots ave and sd1
  nm1<-str_sub(colnames(df[7:dim(df)[2]]), start = 4, end = -9)
  legend(x = xloc, y = yloc,  legend = nm1,xjust = xadj,
         yjust = yadj,
         fill=cola,  bty="n", cex=0.6, xpd = TRUE, border = cola )
}

#' Returns average deuteration plot for timepoints in the data frame
#'
#' Returns plots with average deuteration at each peptide.
#'
#' @param df output from functions output_tp or output_tp_proc.
#' @param replicates number of replicates in set as default set to 3.
#' @param cola color pallette for different Protein States. As default Paired pallette from color.Brewer is used.
#' @return average deuteration plots
#' @examples
#' file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
#' a<- output_tp(file_nm)
#' plots_av_tp(df=a, replicates=3, cola=c(1:4))
#' plots_av_tp(df=a)
#' @export
plots_av_tp<-function(df,replicates=3, cola){
  if(missing(cola)) cola=c(1, brewer.pal(n = max((dim(ave_timepoint(df, replicates))[2]-7), 3), name = "Paired"));
  oldpar<-par(no.readonly = TRUE)
  on.exit(par(oldpar))


  par(mfrow=c(length(unique(df$Deut.Time)), 1),mar = c(1, 1, 1, 10), oma=c(4,4,1,0.1), cex.axis=1, cex.main=1, cex.lab=1.1,
      mgp=c(0.1, 0.4, 0), ps=14, font=2, bg="white", font.lab=2, font.axis=2)

  av1<-ave_timepoint(df, replicates)
  for ( i in(unique(df$Deut.Time))){
    av_tp(av1[av1$Deut.Time==i,], cola)

    mtext(i,  c(NORTH<-3),line=-1, outer=FALSE, cex=0.5, adj=1)}
  exp_du<-expression('D'[2]*'O uptake')
  mtext(c("Index"),  c(SOUTH<-1),line=0.7, outer=TRUE, adj=0.36)
  mtext(exp_du,  c(WEST<-2),line=0.7, outer=TRUE)
  par(mfrow=c(1, 1),mar = c(1, 1, 1, 10), oma=c(4,4,1,0.1), cex.axis=1, cex.main=1, cex.lab=1.1,
      mgp=c(0.1, 0.4, 0), ps=14, font=2, bg="white", font.lab=2, font.axis=2)
  legend_raw_ave(av1, cola)

}