plotProfile.R

## this is identical to the plotProfile function from Timecourse with the addition of a line to 
## write the results to a file. 

plotProfile <- function (object, 
                         stats = c("HotellingT2", "MB"), 
                         ranking = 1, 
                         gid = NULL, 
                         gnames = NULL, 
                         desc = NULL, 
                         type = c("p", "l", "b"), 
                         col = 2:100, 
                         lty = 1:100, 
                         pch = 1:100, 
                         lwd = 2,
                         xlab = "Time",
                         ylab = "Expression", 
                         legloc = NULL, 
                         xlim = NULL,
                         ylim = NULL, 
                         cex.main = 1, 
                         outputList=NULL
                         ) 
{
  if (!is.null(object$geneNames)) 
    gnames <- object$geneNames
  if (!is.null(object$descriptions)) 
    desc <- object$descriptions
  indx <- order(object$con.group, object$rep.group, object$time.group)
  M <- object$M[, indx]
  G <- nrow(M)
  if (!is.character(desc)) 
    desc <- as.character(desc)
  stats <- match.arg(stats, c("HotellingT2", "MB"))
  type <- match.arg(type, c("p", "l", "b"))
  if (!is.null(gid)) 
    ranking <- NULL
  if (stats == "HotellingT2" & !is.null(ranking)) {
    pos <- object$pos.HotellingT2[ranking]
    val <- object$HotellingT2[pos]
    gid <- gnames[pos]
    #### Write//append to file here?
    #print(gid)
    print(outputList)
    write.table(gid,file=outputList,sep=",",row.names=FALSE, col.names = FALSE, append=TRUE)
  }
  if (stats == "MB" & !is.null(ranking)) {
    pos <- object$pos.MB[ranking]
    val <- object$MB[pos]
    gid <- gnames[pos]
  }
  if (stats == "HotellingT2" & is.null(ranking)) {
    pos <- c(1:G)[gnames == gid]
    if (length(pos) > 1) {
      pos <- pos[1]
      warning(length(pos), " genes have the same gene ID...only the first gene is plotted!")
    }
    val <- object$HotellingT2[pos]
    ranking <- G - rank(object$HotellingT2)[pos] + 1
    write(c(gid,val),file="../data/rankedTimecourseGenes.txt",append=TRUE)
  }
  if (stats == "MB" & is.null(ranking)) {
    pos <- c(1:G)[gnames == gid]
    if (length(pos) > 1) {
      pos <- pos[1]
      warning(length(pos), " genes have the same gene ID...only the first gene is plotted!")
    }
    val <- object$MB[pos]
    ranking <- G - rank(object$MB)[pos] + 1
  }
  x <- M[pos, ]
  desc <- desc[pos]
  size <- as.matrix(object$size)[pos, ]
  D <- length(size)
  k <- length(unique(object$time.group))
  y <- matrix(x, byrow = TRUE, ncol = k)
  yulim <- max(y, na.rm = TRUE) + 0.4 * (max(y, na.rm = TRUE) - 
                                           min(y, na.rm = TRUE))
  yllim <- min(y, na.rm = TRUE) - 0.4 * (max(y, na.rm = TRUE) - 
                                           min(y, na.rm = TRUE))
  ?max
  #print(max(unique(object$time.group),na.rm=TRUE))
  xulim <- max(unique(object$time.group), na.rm = TRUE) + 1
  xllim <- min(unique(object$time.group), na.rm = TRUE) - 1
  if (is.null(ylim)) 
    ylim <- c(yllim, yulim)
  if (is.null(xlim)) 
    xlim <- c(xllim, xulim)
  if (!is.null(desc)) {
    plot(sort(unique(object$time.group)), y[1, ], type = "n", 
         main = paste(gid, "", stats, "=", round(val, 1), 
                      "", "\n rank=", ranking), xlim = xlim, ylim = ylim, 
         xlab = xlab, ylab = ylab, cex.main =cex.main,cex.axis=1.5)
    mtext(substr(desc, 1, 10), 4)
  }
  if (is.null(desc)) 
    plot(sort(unique(object$time.group)), y[1, ], type = "n", 
         main = paste(gid, "", stats, "=", round(val, 1), 
                      "", "\n rank=", ranking), xlim = xlim, ylim = ylim, 
         xlab = xlab, ylab = ylab, cex.main = cex.main)
  rep.pch <- rep.lty <- con <- matrix(rep(0, max(as.matrix(object$size)) * 
                                            ncol(as.matrix(object$size))), ncol = ncol(as.matrix(object$size)))
  con2 <- NULL
  if (D != 2) {
    rep.indx <- unique(cbind(object$con.group, object$rep.group))
    tmp <- sapply(1:D, function(z) rep.indx[, 1] == sort(unique(object$con.group))[z])
    for (z in 1:D) {
      con <- con1 <- sort(rep.indx[tmp[, z], 2])
      con2[z] <- length(con)
      if (z == 1) {
        rep.pch[1:con2[z], z] <- pch[1:cumsum(con2)[z]]
        rep.lty[1:con2[z], z] <- lty[1:cumsum(con2)[z]]
      }
      if (z > 1) {
        rep.pch[1:con2[z], z] <- pch[(cumsum(con2)[z - 
                                                     1] + 1):cumsum(con2)[z]]
        rep.lty[1:con2[z], z] <- lty[(cumsum(con2)[z - 
                                                     1] + 1):cumsum(con2)[z]]
      }
    }
  }
  if (D == 2) {
    rep.indx <- unique(cbind(object$con.group, object$rep.group))
    tmp <- (rep.indx[, 1] == sort(unique(object$con.group))[1])
    con1 <- sort(rep.indx[tmp, 2])
    tmp <- (rep.indx[, 1] == sort(unique(object$con.group))[2])
    con2 <- sort(rep.indx[tmp, 2])
    if (length(con1) < length(con2)) 
      con1[(length(con1) + 1):length(con2)] <- NA
    if (length(con2) < length(con1)) 
      con2[(length(con2) + 1):length(con1)] <- NA
    con <- data.frame(con1, con2)
    rep.pch[1:nrow(con[!is.na(con[, 1]), ]), 1] <- pch[1:nrow(con[!is.na(con[, 
                                                                             1]), ])]
    rep.lty[1:nrow(con[!is.na(con[, 1]), ]), 1] <- lty[1:nrow(con[!is.na(con[, 
                                                                             1]), ])]
    both <- intersect(con[, 1], con[, 2])
    if (length(both) > 0) {
      for (i in 1:length(both)) {
        for (j in 1:nrow(con)) {
          if (con[j, 2] == both[i] & !is.na(con[j, 2])) 
            rep.pch[j, 2] <- rep.pch[con[, 1] == both[i], 
                                     1]
          if (con[j, 2] == both[i] & !is.na(con[j, 2])) 
            rep.lty[j, 2] <- rep.lty[con[, 1] == both[i], 
                                     1]
        }
      }
    }
    for (j in 1:nrow(con)) {
      if (rep.pch[j, 2] == 0) 
        rep.pch[j, 2] <- pch[nrow(con[!is.na(con[, 1]), 
                                      ]) + j]
      if (rep.lty[j, 2] == 0) 
        rep.lty[j, 2] <- lty[nrow(con[!is.na(con[, 1]), 
                                      ]) + j]
    }
  }
  tmp <- NULL
  con.indx <- cumsum(apply(as.matrix(object$size), 2, max))
  for (j in 1:D) {
    if (j == 1) 
      mydata <- y[1:con.indx[j], ]
    if (j > 1) 
      mydata <- y[(con.indx[j - 1] + 1):con.indx[j], ]
    for (i in 1:nrow(mydata)) {
      if (length(size) == 1) {
        lines(sort(unique(object$time.group)), mydata[i, 
                                                      ], type = type, col = col[i], lty = rep.lty[i, 
                                                                                                  j], pch = rep.pch[i, j], lwd = lwd)
        tmp <- cbind(tmp, sort(unique(object$time.group)), 
                     mydata[i, ])
      }
      if (D > 1) {
        lines(sort(unique(object$time.group)), mydata[i, 
                                                      ], type = type, col = col[j], lty = rep.lty[i, 
                                                                                                  j], pch = rep.pch[i, j], lwd = lwd)
        tmp <- cbind(tmp, sort(unique(object$time.group)), 
                     mydata[i, ])
      }
    }
  }
  corner <- matrix(c(xlim[1], ylim[1], xlim[1], ylim[2], xlim[2], 
                     ylim[1], xlim[2], ylim[2]), byrow = TRUE, ncol = 2)
  tmp <- matrix(as.numeric(t(tmp)), byrow = TRUE, ncol = 2)
  loc <- NULL
  for (m in 1:nrow(corner)) {
    tt <- rbind(corner[m, ], tmp)
    corner.dist <- dist(tt)
    loc[m] <- min(as.matrix(corner.dist)[-1, 1])
  }
  if (is.null(legloc)) {
    legloc <- corner[order(loc, decreasing = TRUE)[1], ]
    if (order(loc, decreasing = TRUE)[1] == 1) 
      legloc[2] <- legloc[2] + loc[1]
    if (order(loc, decreasing = TRUE)[1] == 2) 
      legloc[2] <- legloc[2] - loc[2]
    if (order(loc, decreasing = TRUE)[1] == 3) {
      legloc[1] <- legloc[1] - loc[3]
      legloc[2] <- legloc[2] + loc[3]
    }
    if (order(loc, decreasing = TRUE)[1] == 4) 
      legloc[1] <- legloc[1] - loc[4]
  }
  if (type == "b") {
    rep.pch <- as.vector(rep.pch)[as.vector(rep.pch) > 0]
    rep.lty <- as.vector(rep.lty)[as.vector(rep.lty) > 0]
    if (D == 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      rep.lty <- rep.lty[1:max(object$size)][!na.indx]
      rep.pch <- rep.pch[1:max(object$size)][!na.indx]
      col <- col[1:max(object$size)][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], lty = rep.lty, 
             lwd = lwd, col = col, pch = rep.pch, text.col = col, 
             cex = 0.75)
    }
    if (D > 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      tmp <- sum(apply(object$size, 2, max))
      rep.lty <- rep.lty[1:tmp][!na.indx]
      rep.pch <- rep.pch[1:tmp][!na.indx]
      col <- col[rep(1:length(unique(object$con.group)), 
                     apply(object$size, 2, max))][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], lty = rep.lty, 
             lwd = lwd, col = col, pch = rep.pch, text.col = col, 
             cex = 0.75)
    }
  }
  if (type == "p") {
    rep.pch <- as.vector(rep.pch)[as.vector(rep.pch) > 0]
    rep.lty <- as.vector(rep.lty)[as.vector(rep.lty) > 0]
    if (D == 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      rep.pch <- rep.pch[1:max(object$size)][!na.indx]
      col <- col[1:max(object$size)][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], col = col, pch = rep.pch, 
             text.col = col, cex = 0.75)
    }
    if (D > 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      tmp <- sum(apply(object$size, 2, max))
      rep.pch <- rep.pch[1:tmp][!na.indx]
      col <- col[rep(1:length(unique(object$con.group)), 
                     apply(object$size, 2, max))][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], col = col, pch = rep.pch, 
             text.col = col, cex = 0.75)
    }
  }
  if (type == "l") {
    rep.pch <- as.vector(rep.pch)[as.vector(rep.pch) > 0]
    rep.lty <- as.vector(rep.lty)[as.vector(rep.lty) > 0]
    if (D == 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      rep.lty <- rep.lty[1:max(object$size)][!na.indx]
      col <- col[1:max(object$size)][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], lty = rep.lty, 
             lwd = lwd, col = col, text.col = col, cex = 0.75)
    }
    if (D > 1) {
      na.indx <- apply(y, 1, is.na)[1, ]
      tmp <- sum(apply(object$size, 2, max))
      rep.lty <- rep.lty[1:tmp][!na.indx]
      col <- col[rep(1:length(unique(object$con.group)), 
                     apply(object$size, 2, max))][!na.indx]
      legend(legloc[1], legloc[2], legend = sort(unique(paste(object$con.group, 
                                                              object$rep.group)))[!na.indx], lty = rep.lty, 
             lwd = lwd, col = col, text.col = col, cex = 0.75)
    }
  }
}