R/markerProfilePlot.r

In mooredf22/protlocassign0p1p1: Compute constrained proportional assignments for fractionated protein abundance

#' Plot profiles of reference proteins
#'
#' This function plots profiles of reference proteins and also the average profile for each compartment
#'
#' @param refLoc  the name of the reference subcellular compartment to plot
#' @param markerList List of reference proteins
#' @param profile data frame of protein names (as row names) and relative abundance levels.
#' @param ylab label for y-axis of plot, e.g., NSA or RSA or Acup
#' @param refLocationProfiles A matrix refLocationProfiles giving the abundance level profiles of the subcellular locations
#' @param ylab label for y=axis, eg, "NSA"
#' @param refProtPlot indices of reference proteins to plot; default is NULL
#' @importFrom graphics par
#' @importFrom graphics axis
#' @importFrom graphics text
#' @importFrom graphics lines
#' @importFrom graphics title
#' @export
#' @return plot only
#' @examples
#' refLocationProfilesNSA <- locationProfileSetup(profile=protNSA_AT5tmtMS2,
#'    markerList=markerListJadot, numDataCols=9)
#' markerProfilePlot(refLoc="PM", profile=protNSA_AT5tmtMS2, markerList=markerListJadot,
#'    refLocationProfiles=refLocationProfilesNSA, ylab="NSA")


markerProfilePlot <- function(refLoc,  profile, markerList,
                           refLocationProfiles, ylab="", refProtPlot=NULL)  {
  n.channels <- ncol(refLocationProfiles)
  protNames <- rownames(profile)
  # add protName column for merge
  profileWithProteins <- data.frame(protNames, profile)
  names(profileWithProteins)[1] <- "protName"
  meanReferenceProts <- merge(x=markerList, y=profileWithProteins,
                            by.x="protName", by.y="protName", all.x=FALSE, sort=FALSE)
  markerLoc <- t(refLocationProfiles)
  max.val <- max(markerLoc)

  fractions.list <- rownames(markerLoc)
  compartments.list <- rownames(refLocationProfiles)

  # stop if refLoc not found
  if (!(refLoc %in% compartments.list)) {
    cat("reference compartment not found\n")
    return(NULL)
  }

  location.list <- colnames(markerLoc)

  n.loc <- ncol(markerLoc)

    # i=1
    #loc.i <- location.list[i]
    loc.i <- refLoc

    # channels.i <- meanReferenceProts[meanReferenceProts$referenceCompartment == loc.i,2+1:n.channels]
     channels.i <- meanReferenceProts[meanReferenceProts$referenceCompartment == loc.i,2+seq_len(n.channels)]
     refprotsvec.i <- as.character(meanReferenceProts[meanReferenceProts$referenceCompartment == loc.i,1])
     n.refprots.i <- length(refprotsvec.i)

    mean.i <- as.numeric(markerLoc[, {loc.i == location.list}] )
    xvals <- seq_len(length(mean.i))

    max.val <- max(channels.i)
    # ylim=c(0,max.val),
    par(mar = c(6.1, 4.1, 4.1, 4.1)) # change the margins
    plot(mean.i ~ xvals,ylim=c(0,max.val), axes="F", type="n", ylab=ylab,
          xlab="")

    axis(1,at=xvals,labels=fractions.list, cex.axis=1, las=2)

    axis(2, las=1)
    lines(mean.i ~ xvals, lwd=5, lty=1, col="black")
    lines(mean.i ~ xvals, lwd=2, lty=2, col="yellow")
    for (j in seq_len(nrow(channels.i))) {

      means.j <- as.numeric(channels.i[j,])

      if (is.null(refProtPlot)) {
        lines(as.numeric(means.j) ~ xvals, col="red")
        }
      if (!is.null(refProtPlot)) {
        if (refProtPlot == j) {
          lines(as.numeric(means.j) ~ xvals, col="red")
          refprot.j <- refprotsvec.i[j]
        }
      }
    }


    if (is.null(refProtPlot)) {
      title(main=paste(loc.i,"profiles\n", as.character(n.refprots.i), " reference proteins"))
    }
    if (!is.null(refProtPlot)) {
      title(main=paste(loc.i,"profiles\n", "reference protein ",as.character(refprot.j)))
    }

 # }
return(NULL)

  }