miga-base 0.7.26.0 → 1.0.0.1

data/utils/enveomics/enveomics.R/R/growthcurve.R

@@ -0,0 +1,331 @@
+#==============> Define S4 classes
+
+#' Enveomics: Growth Curve S4 Class
+#' 
+#' Enve-omics representation of fitted growth curves.
+#'
+#' @slot design \code{(array)} Experimental design of the experiment.
+#' @slot models \code{(list)} Fitted growth curve models.
+#' @slot predict \code{(list)} Fitted growth curve values.
+#' @slot call \code{(call)} Call producing this object.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#' 
+#' @exportClass
+
+enve.GrowthCurve <- setClass("enve.GrowthCurve",
+                             representation(
+                               design  = "array",
+                               models  = "list",
+                               predict = "list",
+                               call='call')
+                             ,package='enveomics.R');
+
+#' Attribute accessor
+#' 
+#' @param x Object
+#' @param name Attribute name
+setMethod("$", "enve.GrowthCurve", function(x, name) attr(x, name))
+
+#' Enveomics: Plot of Growth Curve
+#' 
+#' Plots an \code{\link{enve.GrowthCurve}} object.
+#' 
+#' @param x An \code{\link{enve.GrowthCurve}} object to plot.
+#' @param col Base colors to use for the different samples. Can be recycled.
+#' By default, grey for one sample or rainbow colors for more than one.
+#' @param pt.alpha Color alpha for the observed data points, using \code{col}
+#' as a base.
+#' @param ln.alpha Color alpha for the fitted growth curve, using \code{col}
+#' as a base.
+#' @param ln.lwd Line width for the fitted curve.
+#' @param ln.lty Line type for the fitted curve.
+#' @param band.alpha Color alpha for the confidence interval band of the 
+#' fitted growth curve, using \code{col} as a base.
+#' @param band.density Density of the filling pattern in the interval band.
+#' If \code{NULL}, a solid color is used.
+#' @param band.angle Angle of the density filling pattern in the interval 
+#' band. Ignored if \code{band.density} is \code{NULL}.
+#' @param xp.alpha Color alpha for the line connecting individual experiments,
+#' using \code{col} as a base.
+#' @param xp.lwd Width of line for the experiments.
+#' @param xp.lty Type of line for the experiments.
+#' @param pch Point character for observed data points.
+#' @param new Should a new plot be generated? If \code{FALSE}, the existing
+#' canvas is used.
+#' @param legend Should the plot include a legend? If \code{FALSE}, no legend
+#' is added. If \code{TRUE}, a legend is added in the bottom-right corner.
+#' Otherwise, a legend is added in the position specified as \code{xy.coords}.
+#' @param add.params Should the legend include the parameters of the fitted 
+#' model?
+#' @param ... Any other graphic parameters.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#' 
+#' @method plot enve.GrowthCurve
+#' @export
+
+#==============> Define S4 methods
+plot.enve.GrowthCurve <- function
+(x,
+ col,
+ pt.alpha=0.9,
+ ln.alpha=1.0,
+ ln.lwd=1,
+ ln.lty=1,
+ band.alpha=0.4,
+ band.density=NULL,
+ band.angle=45,
+ xp.alpha=0.5,
+ xp.lwd=1,
+ xp.lty=1,
+ pch=19,
+ new=TRUE,
+ legend=new,
+ add.params=FALSE,
+ ...
+){
+  
+  # Arguments
+  if(missing(col)){
+    col <-
+      if(length(x$design)==0) grey(0.2)
+    else rainbow(length(x$design), v=3/5, s=3/5)
+  }
+  
+  if(new){
+    # Initiate canvas
+    od.fit.max <- max(sapply(x$predict, function(x) max(x[,"upr"])))
+    od.obs.max <- max(sapply(x$models, function(x) max(x$data[,"od"])))
+    opts <- list(...)
+    plot.defaults <- list(xlab="Time", ylab="Density",
+                          xlim=range(x$predict[[1]][,"t"]), ylim=c(0, max(od.fit.max, od.obs.max)))
+    for(i in names(plot.defaults)){
+      if(is.null(opts[[i]])) opts[[i]] <- plot.defaults[[i]]
+    }
+    opts[["x"]] <- 1
+    opts[["type"]] <- "n"
+    do.call(plot, opts)
+  }
+  
+  # Graphic default
+  pch <- rep(pch, length.out=length(x$design))
+  col <- rep(col, length.out=length(x$design))
+  pt.col   <- enve.col2alpha(col, pt.alpha)
+  ln.col   <- enve.col2alpha(col, ln.alpha)
+  band.col <- enve.col2alpha(col, band.alpha)
+  xp.col   <- enve.col2alpha(col, xp.alpha)
+  band.angle   <- rep(band.angle, length.out=length(x$design))
+  if(!all(is.null(band.density))){
+    band.density <- rep(band.density, length.out=length(x$design))
+  }
+  
+  for(i in 1:length(x$design)){
+    # Observed data
+    d <- x$models[[i]]$data
+    points(d[,"t"], d[,"od"], pch=pch[i], col=pt.col[i])
+    for(j in unique(d[,"replicate"])){
+      sel <- d[,"replicate"]==j
+      lines(d[sel,"t"], d[sel,"od"], col=xp.col[i], lwd=xp.lwd, lty=xp.lty)
+    }
+    # Fitted growth curves
+    if(x$models[[i]]$convInfo$isConv){
+      d <- x$predict[[i]]
+      lines(d[,"t"], d[,"fit"], col=ln.col[i], lwd=ln.lwd, lty=ln.lty)
+      polygon(c(d[,"t"], rev(d[,"t"])), c(d[,"lwr"], rev(d[,"upr"])),
+              border=NA, col=band.col[i], density=band.density[i],
+              angle=band.angle[i])
+    }
+  }
+  
+  if(!all(is.logical(legend)) || legend){
+    if(all(is.logical(legend))) legend <- "bottomright"
+    legend.txt <- names(x$design)
+    if(add.params){
+      for(p in names(coef(x$models[[1]]))){
+        legend.txt <- paste(legend.txt, ", ", p, "=",
+                            sapply(x$models, function(x) signif(coef(x)[p],2)) , sep="")
+      }
+    }
+    legend(legend, legend=legend.txt, pch=pch, col=ln.col)
+  }
+}
+
+#' Enveomics: Summary of Growth Curve
+#' 
+#' Summary of an \code{\link{enve.GrowthCurve}} object.
+#' 
+#' @param object An \code{\link{enve.GrowthCurve}} object.
+#' @param ... No additional parameters are currently supported.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @method summary enve.GrowthCurve
+#' @export
+
+summary.enve.GrowthCurve <- function(
+  object,
+  ...
+){
+  
+  x <- object
+  cat('===[ enve.GrowthCurves ]------------------\n')
+  for(i in names(x$design)){
+    cat(i, ':\n', sep='')
+    if(x$models[[i]]$convInfo$isConv){
+      for(j in names(coef(x$models[[i]]))){
+        cat('  - ', j, ' = ', coef(x$models[[i]])[j], '\n', sep='')
+      }
+    }else{
+      cat('  Model didn\'t converge:\n    ',
+          x$models[[i]]$convInfo$stopMessage, '\n', sep='')
+    }
+    cat('  ', nrow(x$models[[i]]$data), ' observations, ',
+        length(unique(x$models[[i]]$data[,"replicate"])), ' replicates.\n',
+        sep='')
+  }
+  cat('------------------------------------------\n')
+  cat('call:',as.character(attr(x,'call')),'\n')
+  cat('------------------------------------------\n')
+}
+
+#' Enveomics: Growth Curve
+#' 
+#' Calculates growth curves using the logistic growth function.
+#' 
+#' @param x Data frame (or coercible) containing the observed growth data
+#' (e.g., O.D. values). Each column is an independent growth curve and each
+#' row is a time point. \code{NA}'s are allowed.
+#' @param times Vector with the times at which each row was taken. By default,
+#' all rows are assumed to be part of constantly periodic measurements.
+#' @param triplicates If \code{TRUE}, the columns are assumed to be sorted by
+#' sample with three replicates by sample. It requires a number of columns 
+#' multiple of 3.
+#' @param design Experimental design of the data. An \strong{array} of mode list
+#' with sample names as index and the list of column names in each sample as 
+#' the values. By default, each column is assumed to be an independent sample
+#' if \code{triplicates} is \code{FALSE}, or every three columns are assumed 
+#' to be a sample if \code{triplicates} is \code{TRUE}. In the latter case, 
+#' samples are simply numbered.
+#' @param new.times Values of time for the fitted curve.
+#' @param level Confidence (or prediction) interval in the fitted curve.
+#' @param interval Type of interval to be calculated for the fitted curve.
+#' @param plot Should the growth curve be plotted?
+#' @param FUN Function to fit. By default: logistic growth with paramenters
+#' \code{K}: carrying capacity, 
+#' \code{r}: intrinsic growth rate, and
+#' \code{P0}: Initial population.
+#' @param nls.opt Any additional options passed to \code{nls}.
+#' @param ... Any additional parameters to be passed to 
+#' \code{plot.enve.GrowthCurve}.
+#' 
+#' @return Returns an \code{\link{enve.GrowthCurve}} object.
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#' 
+#' @examples 
+#' # Load data
+#' data("growth.curves", package="enveomics.R", envir=environment())
+#' # Generate growth curves with different colors
+#' g <- enve.growthcurve(growth.curves[,-1], growth.curves[,1], triplicates=TRUE)
+#' # Generate black-and-white growth curves with different symbols
+#' plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))
+#'
+#' @export
+
+#==============> Core functions
+enve.growthcurve <- structure(function(
+  x,
+  times=1:nrow(x),
+  triplicates=FALSE,
+  design,
+  new.times=seq(min(times), max(times), length.out=length(times)*10),
+  level=0.95,
+  interval=c("confidence","prediction"),
+  plot=TRUE,
+  FUN=function(t,K,r,P0) K*P0*exp(r*t)/(K+P0*(exp(r*t)-1)),
+  nls.opt=list(),
+  ...
+){
+  
+  # Arguments
+  if(missing(design)){
+    design <-
+      if(triplicates)
+        tapply(colnames(x), colnames(x)[rep(1:(ncol(x)/3)*3-2, each=3)], c,
+               simplify=FALSE)
+    else tapply(colnames(x), colnames(x), c, simplify=FALSE)
+  }
+  mod <- list()
+  fit <- list()
+  interval <- match.arg(interval)
+  enve._growth.fx <- NULL
+  enve._growth.fx <<- FUN
+  
+  for(sample in names(design)){
+    od <- c()
+    for(col in design[[sample]]){
+      od <- c(od, x[,col])
+    }
+    data <- data.frame(t=rep(times, length(design[[sample]])), od=od,
+                       replicate=rep(1:length(design[[sample]]), each=length(times)))
+    data <- data[!is.na(data$od),]
+    opts <- nls.opt
+    opts[["data"]] <- data
+    opt.defaults <- list(formula = od ~ enve._growth.fx(t, K, r, P0),
+                         algorithm="port", lower=list(P0=1e-16),
+                         control=nls.control(warnOnly=TRUE),
+                         start=list(
+                           K  = 2*max(data$od),
+                           r  = length(times)/max(data$t),
+                           P0 = min(data$od[data$od>0])
+                         ))
+    for(i in names(opt.defaults)){
+      if(is.null(opts[[i]])){
+        opts[[i]] <- opt.defaults[[i]]
+      }
+    }
+    mod[[sample]] <- do.call(nls, opts)
+    fit[[sample]] <- cbind(t=new.times,
+                           predFit(mod[[sample]], level=level, interval=interval,
+                                   newdata=data.frame(t=new.times)))
+  }
+  enve._growth.fx <<- NULL
+  gc <- new("enve.GrowthCurve",
+            design=design, models=mod, predict=fit,
+            call=match.call());
+  if(plot) plot(gc, ...);
+  return(gc)
+}, ex=function(){
+  # Load data
+  data("growth.curves", package="enveomics.R", envir=environment())
+  # Generate growth curves with different colors
+  g <- enve.growthcurve(growth.curves[,-1], growth.curves[,1], triplicates=TRUE)
+  # Generate black-and-white growth curves with different symbols
+  plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))
+});
+
+#' Enveomics: Color to Alpha
+#' 
+#' Takes a vector of colors and sets the alpha.
+#' 
+#' @param x A vector of any value base colors.
+#' @param alpha Alpha level to set (in the 0-1 range).
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#' 
+#' @export
+
+enve.col2alpha <- function(
+  x,
+  alpha
+){
+  out <- c()
+  for(i in x){
+    opt <- as.list(col2rgb(i)[,1]/256)
+    opt[["alpha"]] = alpha
+    out <- c(out, do.call(rgb, opt))
+  }
+  names(out) <- names(x)
+  return(out)
+}

data/utils/enveomics/enveomics.R/R/prefscore.R

@@ -0,0 +1,79 @@
+#' Enveomics: Pref Score
+#'
+#' Estimate preference score of species based on occupancy in biased sample sets
+#'
+#' @param x
+#' Occupancy matrix (logical or numeric binary) with species as rows and samples
+#' as columns
+#' @param set
+#' Vector indicating samples in the test set. It can be any selection vector:
+#' boolean (same length as the number of columns in \code{x}), or numeric or
+#' character vector with indexes of the \code{x} columns.
+#' @param ignore
+#' Vector indicating species to ignore. It can be any selection vector with
+#' respect to the rows in \code{x} (see \code{set}).
+#' @param signif.thr Absolute value of the significance threshold
+#' @param plot Indicates if a plot should be generated
+#' @param col.above Color for points significantly above zero
+#' @param col.equal Color for points not significantly different from zero
+#' @param col.below Color for points significantly below zero
+#' @param ... Any additional parameters supported by \code{plot}
+#'
+#' @return Returns a named vector of preference scores.
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.prefscore <- function
+(
+  x,
+  set,
+  ignore = NULL,
+  signif.thr,
+  plot = TRUE,
+  col.above = rgb(148, 17, 0, maxColorValue = 255),
+  col.equal = rgb(189, 189, 189, maxColorValue = 255),
+  col.below = rgb(47, 84, 150, maxColorValue = 255),
+  ...
+) {
+  # Normalize classes and filter universe
+  x <- !!as.matrix(x)
+  if(is.null(colnames(x))) colnames(x) <- 1:ncol(x)
+  if(is.null(rownames(x))) rownames(x) <- 1:nrow(x)
+  set <- enve.selvector(set, colnames(x))
+  universe <- !enve.selvector(ignore, rownames(x))
+  x.u <- x[universe, ]
+  if(missing(signif.thr)) signif.thr <- 1 + 100 / length(universe)
+
+  # Base (null) probabilities
+  p_a <- (rowSums(x.u) + 1) / (ncol(x.u) + 2)
+  p_b <- (colSums(x.u) + 1) / (nrow(x.u) + 2)
+  p_p <- p_a %*% t(p_b)
+
+  # Set preference score
+  expected <- (rowSums(p_p[, set]) - rowSums(p_p[, !set])) / sum(p_p)
+  observed <- (rowSums(x.u[, set]) - rowSums(x.u[, !set])) / sum(x.u)
+  y <- observed / abs(expected)
+  names(y) <- rownames(x)[universe]
+  y.code <- cut(y, c(-Inf, -signif.thr, signif.thr, Inf), 1:3)
+
+  # Plot
+  if(plot) {
+    idx <- (1:nrow(x))[universe]
+    opts.def <- list(x = idx, y = y, ylim = c(-1, 1) * max(abs(y)),
+      xlab = 'Species', ylab = 'Preference score', xlim = c(0, nrow(x)+1),
+      col = c(col.above, col.equal, col.below)[y.code],
+      las = 1, xaxs = 'i', pch = 15)
+    opts <- list(...)
+    for(i in names(opts.def)) if(is.null(opts[[i]])) opts[[i]] <- opts.def[[i]]
+    do.call('plot', opts)
+    abline(h = 0, lty = 1, col = rgb(0, 0, 0, 1/4))
+    abline(h = c(-1, 1) * signif.thr, lty = 2, col = rgb(0, 0, 0, 1/4))
+  }
+
+  # Print and return
+  print(table(c(c('<', '=', '>')[y.code], rep('Tot', length(y.code)))))
+  cat('---------\n')
+  return(y)
+}

data/utils/enveomics/enveomics.R/R/recplot.R

@@ -0,0 +1,354 @@
+#' Enveomics: Recruitment Plots
+#' 
+#' @description 
+#' Produces recruitment plots provided that BlastTab.catsbj.pl has
+#' been previously executed. Requires the \pkg{gplots} library.
+#' 
+#' @param prefix
+#' Path to the prefix of the BlastTab.catsbj.pl output files. At
+#' least the files \strong{.rec} and \strong{.lim} must exist with this prefix.
+#' @param id.min
+#' Minimum identity to be considered. By default, the minimum detected
+#' identity. This value is a percentage.
+#' @param id.max
+#' Maximum identity to be considered. By default, 100\%.
+#' @param id.binsize
+#' Size of the identity bins (vertical histograms). By default, 0.1 for
+#' identity metrics and 5 for bit score.
+#' @param id.splines
+#' Smoothing parameter for the splines in the identity histogram. Zero (0) for no
+#' splines. A generally good value is 1/2. If non-zero, requires the \pkg{stats} package.
+#' @param id.metric
+#' Metric of identity to be used (Y-axis). 
+#' It can be any unambiguous prefix of:
+#' \itemize{
+#' \item "identity"
+#' \item "corrected identity" 
+#' \item "bit score"}
+#' @param id.summary
+#' Method used to build the identity histogram (Horizontal axis of the right panel).
+#' It can be any unambiguous prefix of: 
+#' \itemize{
+#' \item "sum"
+#' \item "average" 
+#' \item "median"
+#' \item "90\% lower bound"
+#' \item "90\% upper bound"
+#' \item "95\% lower bound"
+#' \item "95\% upper bound" }
+#' The last four options
+#' correspond to the upper and lower boundaries of the 90\% and 95\% empirical confidence
+#' intervals.
+#' @param pos.min
+#' Minimum (leftmost) position in the reference (concatenated) genome (in bp).
+#' @param pos.max
+#' Maximum (rightmost) position in the reference (concatenated) genome (in bp).
+#' By default: Length of the genome.
+#' @param pos.binsize
+#' Size of the position bins (horizontal histograms) in bp.
+#' @param pos.splines
+#' Smoothing parameter for the splines in the position histogram. Zero (0) for no splines.
+#' If non-zero, requires the stats package.
+#' @param rec.col1
+#' Lightest color in the recruitment plot.
+#' @param rec.col2
+#' Darkest color in the recruitment plot.
+#' @param main
+#' Title of the plot.
+#' @param contig.col
+#' Color of the Contig boundaries. Set to \code{NA} to ignore Contig boundaries.
+#' @param ret.recplot
+#' Indicates if the matrix of the recruitment plot is to be returned.
+#' @param ret.hist
+#' Ignored, for backwards compatibility.
+#' @param ret.mode
+#' Indicates if the mode of the identity is to be computed. It requires the 
+#' \pkg{modeest} package.
+#' @param id.cutoff
+#' Minimum identity to consider an alignment as "top". By default, it is 0.95 for the
+#' identity metrics and 95\% of the best scoring alignment for bit score.
+#' @param verbose
+#' Indicates if the function should report the advance.
+#' @param ...
+#' Any additional graphic parameters to be passed to plot for all panels except the
+#' recruitment plot (lower-left).
+#' 
+#' @return 
+#' 
+#' Returns a list with the following elements:
+#' 
+#' \describe{
+#' \item{\code{pos.marks}}{Midpoints of the position histogram.}
+#' \item{\code{id.matrix}}{Midpoints of the identity histogram.}
+#' \item{\code{recplot}}{Matrix containing the recruitment plot values 
+#'      (if \code{ret.recplot=TRUE}).}
+#' \item{\code{id.mean}}{Mean identity.}
+#' \item{\code{id.median}}{Median identity.}
+#' \item{\code{id.mode}}{Mode of the identity (if \code{ret.mode=TRUE}). Deprecated.}
+#' \item{\code{id.hist}}{Values of the identity histogram (if \code{ret.hist=TRUE}).}
+#' \item{\code{pos.hist.low}}{Values of the position histogram (depth) with "low"
+#'      identity (i.e., below id.cutoff) (if \code{ret.hist=TRUE}).}
+#' \item{\code{pos.hist.top}}{Values of the position histogram (depth) with "top"
+#'      identity (i.e., above id.cutoff) (if \code{ret.hist=TRUE}).}
+#' \item{\code{id.max}}{Value of \code{id.max}. This is returned because 
+#'      \code{id.max=NULL} may vary.}
+#' \item{\code{id.cutoff}}{Value of \code{id.cutoff}. 
+#'      This is returned because \code{id.cutoff=NULL} may vary.}
+#' \item{\code{seqdepth.mean.top}}{Average sequencing depth with identity above 
+#'      \code{id.cutoff}.}
+#' \item{\code{seqdepth.mean.low}}{Average sequencing depth with identity below 
+#'      \code{id.cutoff}.} 
+#' \item{\code{seqdepth.mean.all}}{Average sequencing depth without identity filtering.}
+#' \item{\code{seqdepth.median.top}}{Median sequencing depth with identity above 
+#'      \code{id.cutoff}.}
+#' \item{\code{seqdepth.median.low}}{Median sequencing depth with identity below 
+#'      \code{id.cutoff}.}
+#' \item{\code{seqdepth.median.all}}{Median sequencing depth without identity filtering.}
+#' \item{\code{id.metric}}{Full name of the used identity metric.}
+#' \item{\code{id.summary}}{Full name of the summary method used to build the identity plot.}}
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.recplot <- structure(function(
+  prefix,
+  
+  # Id. hist.
+  id.min=NULL,
+  id.max=NULL,
+  id.binsize=NULL,
+  id.splines=0,
+  id.metric='id',
+  id.summary='sum',
+  
+  # Pos. hist.
+  pos.min=1,
+  pos.max=NULL,
+  pos.binsize=1e3,
+  pos.splines=0,
+  
+  # Rec. plot
+  rec.col1='white',
+  rec.col2='black',
+  
+  # General
+  main=NULL,
+  contig.col=grey(0.85),
+  
+  # Return
+  ret.recplot=FALSE,
+  ret.hist=FALSE,
+  ret.mode=FALSE,
+  
+  # General
+  id.cutoff=NULL,
+  verbose=TRUE,
+  ...
+){
+  
+  # Settings
+  METRICS <- c('identity', 'corrected identity', 'bit score');
+  SUMMARY <- c('sum', 'average', 'median', '');
+  if(is.null(prefix)) stop('Parameter prefix is mandatory.');
+  if(!requireNamespace("gplots", quietly=TRUE)) stop('Unavailable gplots library.');
+  
+  # Read files
+  if(verbose) cat("Reading files.\n")
+  rec <- read.table(paste(prefix, '.rec', sep=''), sep="\t", comment.char='', quote='');
+  lim <- read.table(paste(prefix, '.lim', sep=''), sep="\t", comment.char='', quote='');
+  
+  # Configure ID summary
+  id.summary <- pmatch(id.summary, SUMMARY);
+  if(is.na(id.summary)) stop('Invalid identity summary.');
+  if(id.summary == -1) stop('Ambiguous identity summary.');
+  if(id.summary==1){
+    id.summary.func <- function(x) colSums(x);
+    id.summary.name <- 'sum'
+  }else if(id.summary==2){
+    id.summary.func <- function(x) colMeans(x);
+    id.summary.name <- 'mean'
+  }else if(id.summary==3){
+    id.summary.func <- function(x) apply(x,2,median);
+    id.summary.name <- 'median'
+  }else if(id.summary==4){
+    id.summary.func <- function(x) apply(x,2,quantile,probs=0.05,names=FALSE);
+    id.summary.name <- '90% LB'
+  }else if(id.summary==5){
+    id.summary.func <- function(x) apply(x,2,quantile,probs=0.95,names=FALSE);
+    id.summary.name <- '90% UB'
+  }else if(id.summary==6){
+    id.summary.func <- function(x) apply(x,2,quantile,probs=0.025,names=FALSE);
+    id.summary.name <- '95% LB'
+  }else if(id.summary==7){
+    id.summary.func <- function(x) apply(x,2,quantile,probs=0.975,names=FALSE);
+    id.summary.name <- '95% UB'
+  }
+  
+  # Configure metrics
+  id.metric <- pmatch(id.metric, METRICS);
+  if(is.na(id.metric)) stop('Invalid identity metric.');
+  if(id.metric == -1) stop('Ambiguous identity metric.');
+  if(id.metric==1){
+    id.reccol <- 3
+    id.shortname <- 'Id.'
+    id.fullname  <- 'Identity'
+    id.units     <- '%'
+    id.hallmarks <- seq(0, 100, by=5)
+    if(is.null(id.max)) id.max <- 100
+    if(is.null(id.cutoff)) id.cutoff <- 95
+    if(is.null(id.binsize)) id.binsize <- 0.1
+  }else if(id.metric==2){
+    if(ncol(rec)<6) stop("Requesting corrected identity, but .rec file doesn't have 6th column")
+    id.reccol <- 6
+    id.shortname <- 'cId.'
+    id.fullname  <- 'Corrected identity'
+    id.units     <- '%'
+    id.hallmarks <- seq(0, 100, by=5)
+    if(is.null(id.max)) id.max <- 100
+    if(is.null(id.cutoff)) id.cutoff <- 95
+    if(is.null(id.binsize)) id.binsize <- 0.1
+  }else if(id.metric==3){
+    id.reccol <- 4
+    id.shortname <- 'BSc.'
+    id.fullname  <- 'Bit score'
+    id.units     <- 'bits'
+    max.bs <- max(rec[, id.reccol])
+    id.hallmarks <- seq(0, max.bs*1.2, by=50)
+    if(is.null(id.max)) id.max <- max.bs
+    if(is.null(id.cutoff)) id.cutoff <- 0.95 * max.bs
+    if(is.null(id.binsize)) id.binsize <- 5
+  }
+  if(is.null(id.min)) id.min <- min(rec[, id.reccol]);
+  if(is.null(pos.max)) pos.max <- max(lim[, 3]);
+  id.lim <- c(id.min, id.max);
+  pos.lim <- c(pos.min, pos.max)/1e6;
+  id.breaks <- round((id.max-id.min)/id.binsize);
+  pos.breaks <- round((pos.max-pos.min)/pos.binsize);
+  if(is.null(main)) main <- paste('Recruitment plot of ', prefix, sep='');
+  pos.marks=seq(pos.min, pos.max, length.out=pos.breaks+1)/1e6;
+  id.marks=seq(id.min, id.max, length.out=id.breaks+1);
+  id.topclasses <- 0;
+  for(i in length(id.marks):1) if(id.marks[i]>id.cutoff) id.topclasses <- id.topclasses + 1;
+  
+  # Set-up image
+  layout(matrix(c(3,4,1,2), nrow=2, byrow=TRUE), widths=c(2,1), heights=c(1,2));
+  out <- list();
+  
+  # Recruitment plot
+  if(verbose) cat("Rec. plot.\n")
+  par(mar=c(5,4,0,0)+0.1);
+  rec.hist <- matrix(0, nrow=pos.breaks, ncol=id.breaks);
+  for(i in 1:nrow(rec)){
+    id.class <- ceiling((id.breaks)*((rec[i, id.reccol]-id.min)/(id.max-id.min)));
+    if(id.class<=id.breaks & id.class>0){
+      for(pos in rec[i, 1]:rec[i, 2]){
+        pos.class <- ceiling((pos.breaks)*((pos-pos.min)/(pos.max-pos.min)));
+        if(pos.class<=pos.breaks & pos.class>0) rec.hist[pos.class, id.class] <- rec.hist[pos.class, id.class]+1;
+      }
+    }
+  }
+  id.top <- c((1-id.topclasses):0) + id.breaks;
+  rec.col=gplots::colorpanel(256, rec.col1, rec.col2);
+  image(x=pos.marks, y=id.marks, z=log10(rec.hist),
+        breaks=seq(0, log10(max(rec.hist)), length.out=1+length(rec.col)), col=rec.col,
+        xlim=pos.lim, ylim=id.lim, xlab='Position in genome (Mbp)',
+        ylab=paste(id.fullname, ' (',id.units,')', sep=''), xaxs='i', yaxs='r');
+  if(!is.na(contig.col)) abline(v=c(lim$V2, lim$V3)/1e6, lty=1, col=contig.col);
+  abline(h=id.hallmarks, lty=2, col=grey(0.7));
+  abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
+  legend('bottomleft', 'Rec. plot', bg=rgb(1,1,1,2/3));
+  out <- c(out, list(pos.marks=pos.marks, id.marks=id.marks));
+  if(ret.recplot) out <- c(out, list(recplot=rec.hist));
+  
+  # Identity histogram
+  if(verbose) cat(id.shortname, " hist.\n", sep='')
+  par(mar=c(5,0,0,2)+0.1);
+  id.hist <- id.summary.func(rec.hist);
+  plot(1, t='n', xlim=c(1, max(id.hist)), ylim=id.lim, ylab='', yaxt='n', xlab=paste('Sequences (bp),', id.summary.name), log='x', ...);
+  id.x <- rep(id.marks, each=2)[2:(id.breaks*2+1)]
+  id.f <- rep(id.hist, each=2)[1:(id.breaks*2)]
+  if(sum(id.f)>0){
+    lines(id.f, id.x, lwd=ifelse(id.splines>0, 1/2, 2), type='o', pch='.');
+    if(id.splines>0){
+      id.spline <- smooth.spline(id.x[id.f>0], log(id.f[id.f>0]), spar=id.splines)
+      lines(exp(id.spline$y), id.spline$x, lwd=2)
+    }
+  }
+  
+  abline(h=id.hallmarks, lty=2, col=grey(0.7));
+  abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
+  legend('bottomright', paste(id.shortname, 'histogram'), bg=rgb(1,1,1,2/3));
+  out <- c(out, list(id.mean=mean(rec[, id.reccol])));
+  out <- c(out, list(id.median=median(rec[, id.reccol])));
+  if(ret.hist)  out <- c(out, list(id.hist=id.hist));
+  
+  # Position histogram
+  if(verbose) cat("Pos. hist.\n")
+  par(mar=c(0,4,4,0)+0.1);
+  h1<-rep(0,nrow(rec.hist)) ;
+  h2<-rep(0,nrow(rec.hist)) ;
+  pos.winsize <- (pos.max-pos.min+1)/pos.breaks;
+  if(sum(rec.hist[, id.top])>0) h1 <- rowSums(matrix(rec.hist[, id.top], nrow=nrow(rec.hist)))/pos.winsize;
+  if(sum(rec.hist[,-id.top])>0) h2 <- rowSums(matrix(rec.hist[,-id.top], nrow=nrow(rec.hist)))/pos.winsize;
+  
+  ymin <- min(1, h1[h1>0], h2[h2>0]);
+  ymax <- max(10, h1, h2);
+  if(is.na(ymin) || ymin<=0) ymin <- 1e-10;
+  if(is.na(ymax) || ymax<=0) ymax <- 1;
+  plot(1, t='n', xlab='', xaxt='n', ylab='Sequencing depth (X)', log='y', xlim=pos.lim,
+       ylim=c(ymin, ymax), xaxs='i', main=main, ...);
+  if(!is.na(contig.col)) abline(v=c(lim[,2], lim[,3])/1e6, lty=1, col=contig.col);
+  abline(h=10^c(0:5), lty=2, col=grey(0.7));
+  if(sum(h2)>0){
+    h2.x <- rep(pos.marks, each=2)[2:(pos.breaks*2+1)]
+    h2.y <- rep(h2, each=2)[1:(pos.breaks*2)]
+    lines(h2.x, h2.y, lwd=ifelse(pos.splines>0, 1/2, 2), col=grey(0.5));
+    if(pos.splines>0){
+      h2.spline <- smooth.spline(h2.x[h2.y>0], log(h2.y[h2.y>0]), spar=pos.splines)
+      lines(h2.spline$x, exp(h2.spline$y), lwd=2, col=grey(0.5))
+    }
+    if(ret.hist) out <- c(out, list(pos.hist.low=h2.y));
+  }
+  if(sum(h1)>0){
+    h1.x <- rep(pos.marks, each=2)[2:(pos.breaks*2+1)]
+    h1.y <- rep(h1, each=2)[1:(pos.breaks*2)]
+    lines(h1.x, h1.y, lwd=ifelse(pos.splines>0, 1/2, 2), col=grey(0));
+    if(pos.splines>0){
+      h1.spline <- smooth.spline(h1.x[h1.y>0], log(h1.y[h1.y>0]), spar=pos.splines)
+      lines(h1.spline$x, exp(h1.spline$y), lwd=2, col=grey(0))
+    }
+    if(ret.hist) out <- c(out, list(pos.hist.top=h1.y));
+  }
+  legend('topleft', 'Pos. histogram', bg=rgb(1,1,1,2/3));
+  out <- c(out, list(id.max=id.max, id.cutoff=id.marks[id.top[1]]));
+  out <- c(out, list(seqdepth.mean.top=mean(h1)));
+  out <- c(out, list(seqdepth.mean.low=mean(h2)));
+  out <- c(out, list(seqdepth.mean=mean(h1+h2)));
+  out <- c(out, list(seqdepth.median.top=median(h1)));
+  out <- c(out, list(seqdepth.median.low=median(h2)));
+  out <- c(out, list(seqdepth.median=median(h1+h2)));
+  out <- c(out, list(id.metric=id.fullname));
+  out <- c(out, list(id.summary=id.summary.name));
+  
+  # Legend
+  par(mar=c(0,0,4,2)+0.1);
+  plot(1, t='n', xlab='', xaxt='n', ylab='', yaxt='n', xlim=c(0,1), ylim=c(0,1), xaxs='r', yaxs='i', ...);
+  text(1/2, 5/6, labels=paste('Reads per ', signif((pos.max-pos.min)/pos.breaks, 2), ' bp (rec. plot)', sep=''), pos=3);
+  leg.col <- gplots::colorpanel(100, rec.col1, rec.col2);
+  leg.lab <- signif(10^seq(0, log10(max(rec.hist)), length.out=10), 2);
+  for(i in 1:10){
+    for(j in 1:10){
+      k <- (i-1)*10 + j;
+      polygon(c(k-1, k, k, k-1)/100, c(2/3, 2/3, 5/6, 5/6), border=leg.col[k], col=leg.col[k]);
+    }
+    text((i-0.5)/10, 2/3, labels=paste(leg.lab[i], ''), srt=90, pos=2, offset=0, cex=3/4);
+  }
+  legend('bottom',
+         legend=c('Contig boundary', 'Hallmark', paste(id.fullname, 'cutoff'),
+                  paste('Pos. hist.: ',id.shortname,' > ',signif(id.marks[id.top[1]],2),id.units,sep=''),
+                  paste('Pos. hist.: ',id.shortname,' < ',signif(id.marks[id.top[1]],2),id.units,sep='')), ncol=2,
+         col=grey(c(0.85, 0.7, 0.5, 0, 0.5)), lty=c(1,2,3,1,1), lwd=c(1,1,1,2,2), bty='n', inset=0.05, cex=5/6);
+  return(out);
+});
+