miga-base 1.2.15.2 → 1.2.15.4

data/utils/enveomics/enveomics.R/R/recplot2.R

@@ -1,1631 +0,0 @@
-#==============> Define S4 classes
-
-#' Enveomics: Recruitment Plot (2) - S4 Class
-#'
-#' Enve-omics representation of Recruitment plots. This object can
-#' be produced by \code{\link{enve.recplot2}} and supports S4 method plot.
-#'
-#' @slot counts \code{(matrix)} Counts as a two-dimensional histogram.
-#' @slot pos.counts.in \code{(numeric)} Counts of in-group hits per position bin.
-#' @slot pos.counts.out \code{(numeric)} Counts of out-group hits per position bin.
-#' @slot id.counts \code{(numeric)} Counts per ID bin.
-#' @slot id.breaks \code{(numeric)} Breaks of identity bins.
-#' @slot pos.breaks \code{(numeric)} Breaks of position bins.
-#' @slot pos.names \code{(character)} Names of the position bins.
-#' @slot seq.breaks \code{(numeric)} Breaks of input sequences.
-#' @slot peaks \code{(list)} Peaks identified in the recplot.
-#' Limits of the subject sequences after concatenation.
-#' @slot seq.names \code{(character}) Names of the subject sequences.
-#' @slot id.metric \code{(character}) Metric used as 'identity'.
-#' @slot id.ingroup \code{(logical}) Identity bins considered in-group.
-#' @slot call \code{(call)} Call producing this object.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @exportClass
-
-enve.RecPlot2 <- setClass("enve.RecPlot2",
-                          representation(
-                            # slots = list(
-                            counts='matrix',
-                            pos.counts.in='numeric',
-                            pos.counts.out='numeric',
-                            id.counts='numeric',
-                            id.breaks='numeric',
-                            pos.breaks='numeric',
-                            pos.names='character',
-                            seq.breaks='numeric',
-                            peaks='list',
-                            seq.names='character',
-                            id.metric='character',
-                            id.ingroup='logical',
-                            call='call')
-                          ,package='enveomics.R'
-);
-
-#' Enveomics: Recruitment Plot (2) Peak - S4 Class
-#'
-#' Enve-omics representation of a peak in the sequencing depth histogram
-#' of a Recruitment plot (see \code{\link{enve.recplot2.findPeaks}}).
-#'
-#' @slot dist \code{(character)}
-#' Distribution of the peak. Currently supported: \code{norm} (normal) and \code{sn}
-#' (skew-normal).
-#' @slot values \code{(numeric)}
-#' Sequencing depth values predicted to conform the peak.
-#' @slot values.res \code{(numeric)}
-#' Sequencing depth values not explained by this or previously identified
-#' peaks.
-#' @slot mode \code{(numeric)}
-#' Seed-value of mode anchoring the peak.
-#' @slot param.hat \code{(list)}
-#' Parameters of the distribution. A list of two values if dist=\code{norm} (sd
-#' and mean), or three values if dist=\code{sn}(omega=scale, alpha=shape, and
-#' xi=location). Note that the "dispersion" parameter is always first and
-#' the "location" parameter is always last.
-#' @slot n.hat \code{(numeric)}
-#' Number of bins estimated to be explained by this peak. This should
-#' ideally be equal to the length of  \code{values}, but it's not an integer.
-#' @slot n.total \code{(numeric)}
-#' Total number of bins from which the peak was extracted. I.e., total
-#' number of position bins with non-zero sequencing depth in the recruitment
-#' plot (regardless of peak count).
-#' @slot err.res \code{(numeric)}
-#' Error left after adding the peak (mower) or log-likelihood (em or emauto).
-#' @slot merge.logdist \code{(numeric)}
-#' Attempted \code{merge.logdist} parameter.
-#' @slot seq.depth \code{(numeric)}
-#' Best estimate available for the sequencing depth of the peak (centrality).
-#' @slot log \code{(logical)}
-#' Indicates if the estimation was performed in natural logarithm space.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @exportClass
-
-enve.RecPlot2.Peak <- setClass("enve.RecPlot2.Peak",
-                               representation(
-                                 # slots = list(
-                                 dist='character',
-                                 values='numeric',
-                                 values.res='numeric',
-                                 mode='numeric',
-                                 param.hat='list',
-                                 n.hat='numeric',
-                                 n.total='numeric',
-                                 err.res='numeric',
-                                 merge.logdist='numeric',
-                                 seq.depth='numeric',
-                                 log='logical'
-                               ));
-
-#' Attribute accessor
-#'
-#'
-#' @param x Object
-#' @param name Attribute name
-setMethod("$", "enve.RecPlot2", function(x, name) attr(x, name))
-
-#' Attribute accessor
-#'
-#'
-#' @param x Object
-#' @param name Attribute name
-setMethod("$", "enve.RecPlot2.Peak", function(x, name) attr(x, name))
-
-#==============> Define S4 methods
-
-#' Enveomics: Recruitment Plot (2)
-#'
-#' Plots an \code{\link{enve.RecPlot2}} object.
-#'
-#' @param x
-#' \code{\link{enve.RecPlot2}} object to plot.
-#' @param layout
-#' Matrix indicating the position of the different panels in the layout,
-#' where:
-#' \itemize{
-#'   \item 0: Empty space
-#'   \item 1: Counts matrix
-#'   \item 2: position histogram (sequencing depth)
-#'   \item 3: identity histogram
-#'   \item 4: Populations histogram (histogram of sequencing depths)
-#'   \item 5: Color scale for the counts matrix (vertical)
-#'   \item 6: Color scale of the counts matrix (horizontal)
-#' }
-#' Only panels indicated here will be plotted. To plot only one panel
-#' simply set this to the number of the panel you want to plot.
-#' @param panel.fun
-#' List of functions to be executed after drawing each panel. Use the
-#' indices in \code{layout} (as characters) as keys. Functions for indices
-#' missing in \code{layout} are ignored. For example, to add a vertical line
-#' at the 3Mbp mark in both the position histogram and the counts matrix:
-#' \code{list('1'=function() abline(v=3), '2'=function() abline(v=3))}.
-#' Note that the X-axis in both panels is in Mbp by default. To change
-#' this behavior, set \code{pos.units} accordingly.
-#' @param widths
-#' Relative widths of the columns of \code{layout}.
-#' @param heights
-#' Relative heights of the rows of \code{layout}.
-#' @param palette
-#' Colors to be used to represent the counts matrix, sorted from no hits
-#' to the maximum sequencing depth.
-#' @param underlay.group
-#' If TRUE, it indicates the in-group and out-group areas couloured based
-#' on \code{in.col} and \code{out.col}. Requires support for semi-transparency.
-#' @param peaks.col
-#' If not \code{NA}, it attempts to represent peaks in the population histogram
-#' in the specified color. Set to \code{NA} to avoid peak-finding.
-#' @param use.peaks
-#' A list of \code{\link{enve.RecPlot2.Peak}} objects, as returned by
-#' \code{\link{enve.recplot2.findPeaks}}. If passed, \code{peaks.opts} is ignored.
-#' @param id.lim
-#' Limits of identities to represent.
-#' @param pos.lim
-#' Limits of positions to represent (in bp, regardless of \code{pos.units}).
-#' @param pos.units
-#' Units in which the positions should be represented (powers of 1,000
-#' base pairs).
-#' @param mar
-#' Margins of the panels as a list, with the character representation of
-#' the number of the panel as index (see \code{layout}).
-#' @param pos.splines
-#' Smoothing parameter for the splines in the position histogram. Zero
-#' (0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
-#' cross-validation.
-#' @param id.splines
-#' Smoothing parameter for the splines in the identity histogram. Zero
-#' (0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
-#' cross-validation.
-#' @param in.lwd
-#' Line width for the sequencing depth of in-group matches.
-#' @param out.lwd
-#' Line width for the sequencing depth of out-group matches.
-#' @param id.lwd
-#' Line width for the identity histogram.
-#' @param in.col
-#' Color associated to in-group matches.
-#' @param out.col
-#' Color associated to out-group matches.
-#' @param id.col
-#' Color for the identity histogram.
-#' @param breaks.col
-#' Color of the vertical lines indicating sequence breaks.
-#' @param peaks.opts
-#' Options passed to \code{\link{enve.recplot2.findPeaks}},
-#' if \code{peaks.col} is not \code{NA}.
-#' @param ...
-#' Any other graphic parameters (currently ignored).
-#'
-#' @return
-#' Returns a list of \code{\link{enve.RecPlot2.Peak}} objects (see
-#' \code{\link{enve.recplot2.findPeaks}}). If \code{peaks.col=NA} or
-#' \code{layout} doesn't include 4, returns \code{NA}.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @method plot enve.RecPlot2
-#' @export
-
-plot.enve.RecPlot2 <- function
-(x,
- layout=matrix(c(5,5,2,1,4,3), nrow=2),
- panel.fun=list(),
- widths=c(1,7,2),
- heights=c(1,2),
- palette=grey((100:0)/100),
- underlay.group=TRUE,
- peaks.col='darkred',
- use.peaks,
- id.lim=range(x$id.breaks),
- pos.lim=range(x$pos.breaks),
- pos.units=c('Mbp','Kbp','bp'),
- mar=list('1'=c(5,4,1,1)+.1, '2'=c(ifelse(any(layout==1),1,5),4,4,1)+.1,
-          '3'=c(5,ifelse(any(layout==1),1,4),1,2)+0.1,
-          '4'=c(ifelse(any(layout==1),1,5),ifelse(any(layout==2),1,4),4,2)+0.1,
-          '5'=c(5,3,4,1)+0.1, '6'=c(5,4,4,2)+0.1),
- pos.splines=0,
- id.splines=1/2,
- in.lwd=ifelse(is.null(pos.splines) || pos.splines>0, 1/2, 2),
- out.lwd=ifelse(is.null(pos.splines) || pos.splines>0, 1/2, 2),
- id.lwd=ifelse(is.null(id.splines) || id.splines>0, 1/2, 2),
- in.col='darkblue',
- out.col='lightblue',
- id.col='black',
- breaks.col='#AAAAAA40',
- peaks.opts=list(),
- ...
-){
-  pos.units	<- match.arg(pos.units);
-  pos.factor	<- ifelse(pos.units=='bp',1,ifelse(pos.units=='Kbp',1e3,1e6));
-  pos.lim	<- pos.lim/pos.factor;
-  lmat <- layout;
-  for(i in 1:6) if(!any(layout==i)) lmat[layout>i] <- lmat[layout>i]-1;
-
-  layout(lmat, widths=widths, heights=heights);
-  ori.mar <- par('mar');
-
-  # Essential vars
-  counts	<- x$counts
-
-  id.ingroup	<- x$id.ingroup
-  id.counts	<- x$id.counts
-  id.breaks	<- x$id.breaks
-  id.mids	<- (id.breaks[-length(id.breaks)]+id.breaks[-1])/2
-  id.binsize	<- id.breaks[-1] - id.breaks[-length(id.breaks)]
-
-  pos.counts.in  <- x$pos.counts.in
-  pos.counts.out <- x$pos.counts.out
-  pos.breaks   <- x$pos.breaks/pos.factor
-  pos.mids     <- (pos.breaks[-length(pos.breaks)]+pos.breaks[-1])/2
-  pos.binsize  <- (pos.breaks[-1] - pos.breaks[-length(pos.breaks)])*pos.factor
-
-  seqdepth.in  <- pos.counts.in/pos.binsize
-  seqdepth.out <- pos.counts.out/pos.binsize
-  seqdepth.lim <- range(c(seqdepth.in[seqdepth.in>0],
-                          seqdepth.out[seqdepth.out>0]))*c(1/2,2)
-
-  if(underlay.group){
-    in.bg  <- do.call(rgb, c(as.list(col2rgb(in.col)),
-                             list(maxColorValue=256, alpha=62)));
-    out.bg <- do.call(rgb, c(as.list(col2rgb(out.col)[,1]),
-                             list(maxColorValue=256, alpha=52)));
-  }
-
-  # [1] Counts matrix
-  if(any(layout==1)){
-    par(mar=mar[['1']]);
-    plot(1, t='n', bty='l',
-         xlim=pos.lim, xlab=paste('Position in genome (',pos.units,')',sep=''),
-         xaxs='i', ylim=id.lim,  ylab=x$id.metric, yaxs='i');
-    if(underlay.group){
-      rect(pos.lim[1], id.lim[1], pos.lim[2],
-           min(id.breaks[c(id.ingroup,TRUE)]), col=out.bg, border=NA);
-      rect(pos.lim[1], min(id.breaks[c(id.ingroup,TRUE)]), pos.lim[2],
-           id.lim[2], col=in.bg,  border=NA);
-    }
-    abline(v=x$seq.breaks/pos.factor, col=breaks.col);
-    image(x=pos.breaks, y=id.breaks, z=log10(counts),col=palette,
-          bg=grey(1,0), breaks=seq(-.1,log10(max(counts)),
-                                   length.out=1+length(palette)), add=TRUE);
-    if(exists('1',panel.fun)) panel.fun[['1']]();
-  }
-
-  # [2] Position histogram
-  if(any(layout==2)){
-    par(mar=mar[['2']]);
-    if(any(layout==1)){
-      xlab=''
-      xaxt='n'
-    }else{
-      xlab=paste('Position in genome (',pos.units,')',sep='')
-      xaxt='s'
-    }
-    plot(1,t='n', bty='l', log='y',
-         xlim=pos.lim, xlab=xlab, xaxt=xaxt, xaxs='i',
-         ylim=seqdepth.lim, yaxs='i', ylab='Sequencing depth (X)');
-    abline(v=x$seq.breaks/pos.factor, col=breaks.col)
-    pos.x <- rep(pos.breaks,each=2)[-c(1,2*length(pos.breaks))]
-    pos.f <- rep(seqdepth.in,each=2)
-    lines(pos.x, rep(seqdepth.out,each=2), lwd=out.lwd, col=out.col);
-    lines(pos.x, pos.f, lwd=in.lwd, col=in.col);
-    if(is.null(pos.splines) || pos.splines > 0){
-      pos.spline <- smooth.spline(pos.x[pos.f>0], log(pos.f[pos.f>0]),
-                                  spar=pos.splines)
-      lines(pos.spline$x, exp(pos.spline$y), lwd=2, col=in.col)
-    }
-    if(any(pos.counts.out==0)) rect(pos.breaks[c(pos.counts.out==0,FALSE)],
-                                    seqdepth.lim[1], pos.breaks[c(FALSE,pos.counts.out==0)],
-                                    seqdepth.lim[1]*3/2, col=out.col, border=NA);
-    if(any(pos.counts.in==0))  rect(pos.breaks[c(pos.counts.in==0,FALSE)],
-                                    seqdepth.lim[1], pos.breaks[c(FALSE,pos.counts.in==0)],
-                                    seqdepth.lim[1]*3/2, col=in.col,  border=NA);
-    if(exists('2',panel.fun)) panel.fun[['2']]();
-  }
-
-  # [3] Identity histogram
-  if(any(layout==3)){
-    par(mar=mar[['3']]);
-    if(any(layout==1)){
-      ylab=''
-      yaxt='n'
-    }else{
-      ylab=x$id.metric
-      yaxt='s'
-    }
-    if(sum(id.counts>0) >= 4){
-      id.counts.range <- range(id.counts[id.counts>0])*c(1/2,2);
-      plot(1,t='n', bty='l', log='x',
-           xlim=id.counts.range, xlab='bps per bin', xaxs='i',
-           ylim=id.lim, yaxs='i', ylab=ylab, yaxt=yaxt);
-      if(underlay.group){
-        rect(id.counts.range[1], id.lim[1], id.counts.range[2],
-             min(id.breaks[c(id.ingroup,TRUE)]), col=out.bg, border=NA);
-        rect(id.counts.range[1], min(id.breaks[c(id.ingroup,TRUE)]),
-             id.counts.range[2], id.lim[2], col=in.bg,  border=NA);
-      }
-      id.f <- rep(id.counts,each=2)
-      id.x <- rep(id.breaks,each=2)[-c(1,2*length(id.breaks))]
-      lines(id.f, id.x, lwd=id.lwd, col=id.col);
-      if(is.null(id.splines) || id.splines > 0){
-        id.spline <- smooth.spline(id.x[id.f>0], log(id.f[id.f>0]),
-                                   spar=id.splines)
-        lines(exp(id.spline$y), id.spline$x, lwd=2, col=id.col)
-      }
-    }else{
-      plot(1,t='n',bty='l',xlab='', xaxt='n', ylab='', yaxt='n')
-      text(1,1,labels='Insufficient data', srt=90)
-    }
-    if(exists('3',panel.fun)) panel.fun[['3']]();
-  }
-
-  # [4] Populations histogram
-  peaks <- NA;
-  if(any(layout==4)){
-    par(mar=mar[['4']]);
-    if(any(layout==2)){
-      ylab=''
-      yaxt='n'
-    }else{
-      ylab='Sequencing depth (X)'
-      yaxt='s'
-    }
-    h.breaks <- seq(log10(seqdepth.lim[1]*2), log10(seqdepth.lim[2]/2),
-                    length.out=200);
-    h.in <- hist(log10(seqdepth.in), breaks=h.breaks, plot=FALSE);
-    h.out <- hist(log10(seqdepth.out), breaks=h.breaks, plot=FALSE);
-    plot(1, t='n', log='y',
-         xlim=range(c(h.in$counts,h.out$counts,sum(pos.counts.in==0))),
-         xaxs='r', xlab='', xaxt='n', ylim=seqdepth.lim, yaxs='i', ylab=ylab,
-         yaxt=yaxt)
-    y.tmp.in <- c(rep(10^h.in$breaks,each=2),seqdepth.lim[1]*c(1,1,3/2,3/2))
-    y.tmp.out <- c(rep(10^h.out$breaks,each=2),seqdepth.lim[1]*c(1,1,3/2,3/2))
-    lines(c(0,rep(h.out$counts,each=2),0,0,rep(sum(pos.counts.out==0),2),0),
-          y.tmp.out, col=out.col)
-    polygon(c(0,rep(h.in$counts,each=2),0,0,rep(sum(pos.counts.in==0),2),0),
-            y.tmp.in, border=NA, col=in.col)
-    if(!is.na(peaks.col)){
-      o <- peaks.opts; o$x = x;
-      if(missing(use.peaks)){
-        peaks <- do.call(enve.recplot2.findPeaks, o)
-      }else{
-        peaks <- use.peaks
-      }
-      h.mids <- (10^h.breaks[-1] + 10^h.breaks[-length(h.breaks)])/2
-      if(!is.null(peaks) & length(peaks)>0){
-        pf <- h.mids*0;
-        for(i in 1:length(peaks)){
-          cnt <- enve.recplot2.__peakHist(peaks[[i]], h.mids)
-          lines(cnt, h.mids, col='red');
-          pf <- pf+cnt;
-          axis(4, at=peaks[[i]]$seq.depth, letters[i], las=1, hadj=1/2)
-        }
-        lines(pf, h.mids, col='red',lwd=1.5);
-        dpt <- signif(as.numeric(lapply(peaks, function(x) x$seq.depth)),2)
-        frx <- signif(100*as.numeric(
-          lapply(peaks,
-                 function(x) ifelse(length(x$values)==0, x$n.hat,
-                                    length(x$values))/x$n.total)), 2)
-        if(peaks[[1]]$err.res < 0){
-          err <- paste(', LL:', signif(peaks[[1]]$err.res, 3))
-        }else{
-          err <- paste(', err:',
-                       signif(as.numeric(lapply(peaks, function(x) x$err.res)), 2))
-        }
-        legend('topright', bty='n', cex=1/2,
-               legend=paste(letters[1:length(peaks)],'. ',
-                            dpt,'X (', frx, '%', err, ')', sep=''))
-      }
-    }
-    if(exists('4',panel.fun)) panel.fun[['4']]();
-  }
-
-  # [5] Color scale of the counts matrix (vertical)
-  count.bins <- 10^seq(log10(min(counts[counts>0])), log10(max(counts)),
-                       length.out=1+length(palette))
-  if(any(layout==5)){
-    par(mar=mar[['5']]);
-    plot(1,t='n',log='y',xlim=0:1,xaxt='n',xlab='',xaxs='i',
-         ylim=range(count.bins), yaxs='i', ylab='')
-    rect(0,count.bins[-length(count.bins)],1,count.bins[-1],col=palette,
-         border=NA)
-    if(exists('5',panel.fun)) panel.fun[['5']]();
-  }
-
-  # [6] Color scale of the coutnts matrix (horizontal)
-  if(any(layout==6)){
-    par(mar=mar[['6']]);
-    plot(1,t='n',log='x',ylim=0:1,yaxt='n',ylab='',yaxs='i',
-         xlim=range(count.bins), xaxs='i',xlab='');
-    rect(count.bins[-length(count.bins)],0,count.bins[-1],1,col=palette,
-         border=NA);
-    if(exists('6',panel.fun)) panel.fun[['6']]();
-  }
-
-  par(mar=ori.mar);
-  return(peaks);
-}
-
-#==============> Define core functions
-
-#' Enveomics: Recruitment Plot (2)
-#'
-#' Produces recruitment plots provided that \code{BlastTab.catsbj.pl} has
-#' been previously executed.
-#'
-#' @param prefix
-#' Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
-#' least the files .rec and .lim must exist with this prefix.
-#' @param plot
-#' Should the object be plotted?
-#' @param pos.breaks
-#' Breaks in the positions histogram. It can also be a vector of break
-#' points, and values outside the range are ignored. If zero (0), it
-#' uses the sequence breaks as defined in the .lim file, which means
-#' one bin per contig (or gene, if the mapping is agains genes). Ignored
-#' if `pos.breaks.tsv` is passed.
-#' @param pos.breaks.tsv
-#' Path to a list of (absolute) coordinates to use as position breaks.
-#' This tab-delimited file can be produced by \code{GFF.catsbj.pl}, and it
-#' must contain at least one column: coordinates of the break positions of
-#' each position bin. If it has a second column, this is used as the name
-#' of the position bin that ends at the given coordinate (the first row is
-#' ignored). Any additional columns are currently ignored. If \code{NA},
-#' position bins are determined by \code{pos.breaks}.
-#' @param id.breaks
-#' Breaks in the identity histogram. It can also be a vector of break
-#' points, and values outside the range are ignored.
-#' @param id.free.range
-#' Indicates that the range should be freely set from the observed
-#' values. Otherwise, 70-100\% is included in the identity histogram
-#' (default).
-#' @param id.metric
-#' Metric of identity to be used (Y-axis). Corrected identity is only
-#' supported if the original BLAST file included sequence lengths.
-#' @param id.summary
-#' Function summarizing the identity bins. Other recommended options
-#' include: \code{median} to estimate the median instead of total bins, and
-#' \code{function(x) mlv(x,method='parzen')$M} to estimate the mode.
-#' @param id.cutoff
-#' Cutoff of identity metric above which the hits are considered
-#' \code{in-group}. The 95\% identity corresponds to the expectation of
-#' ANI<95\% within species.
-#' @param threads
-#' Number of threads to use.
-#' @param verbose
-#' Indicates if the function should report the advance.
-#' @param ...
-#' Any additional parameters supported by \code{\link{plot.enve.RecPlot2}}.
-#'
-#' @return Returns an object of class \code{\link{enve.RecPlot2}}.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#' @author Kenji Gerhardt [aut]
-#'
-#' @export
-
-enve.recplot2 <- function(
-  prefix,
-  plot = TRUE,
-  pos.breaks = 1e3,
-  pos.breaks.tsv = NA,
-  id.breaks = 60,
-  id.free.range = FALSE,
-  id.metric = c('identity', 'corrected identity', 'bit score'),
-  id.summary = sum,
-  id.cutoff = 95,
-  threads = 2,
-  verbose = TRUE,
-  ...
-){
-  # Settings
-  id.metric <- match.arg(id.metric);
-
-  #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 = "", as.is = TRUE);
-
-  # Build matrix
-  if (verbose) cat("Building counts matrix.\n")
-  if (id.metric == "corrected identity" & ncol(rec) < 6) {
-    stop("Requesting corr. identity, but .rec file doesn't have 6th column")
-  }
-  rec.idcol <- ifelse(id.metric == "identity", 3,
-                      ifelse(id.metric == "corrected identity", 6, 4))
-  pos.names <- as.character(NULL)
-  if (!is.na(pos.breaks.tsv)){
-    tmp <- read.table(pos.breaks.tsv, sep = "\t", header = FALSE, as.is = TRUE)
-    pos.breaks <- as.numeric(tmp[, 1])
-    if (ncol(tmp) > 1) pos.names <- as.character(tmp[-1, 2])
-  } else if (length(pos.breaks) == 1) {
-    if (pos.breaks > 0){
-      pos.breaks <- seq(min(lim[, 2]), max(lim[, 3]), length.out = pos.breaks + 1)
-    } else {
-      pos.breaks <- c(lim[1, 2], lim[, 3])
-      pos.names  <- lim[, 1]
-    }
-  }
-  if (length(id.breaks) == 1) {
-    id.range.v <- rec[, rec.idcol]
-    if (!id.free.range) id.range.v <- c(id.range.v, 70, 100)
-    id.range.v <- range(id.range.v)
-    id.breaks <- seq(id.range.v[1], id.range.v[2], length.out = id.breaks + 1)
-  }
-
-  # Run in parallel
-  # If they already set threads to 1 manually, there's no point in launching
-  # clusters, it's just slower. Ditto for small files.
-  if (nrow(rec) < 75000 | threads == 1) {
-    # Coerces rec into a form that __counts is happy about
-    rec.l <- list()
-    rec.l[[1]] <- list(rec = rec, verbose = FALSE)
-
-    # No need to make a temporary variable, there's only one return for sure
-    # and it's not a list because it isn't coming back from an apply
-    counts <- enve.recplot2.__counts(
-      rec.l[[1]], pos.breaks = pos.breaks, id.breaks = id.breaks,
-      rec.idcol = rec.idcol)
-  } else {
-    cl <- makeCluster(threads)
-    rec.l <- list()
-    thl <- ceiling(nrow(rec)/threads)
-    for (i in 0:(threads - 1)) {
-      rec.l[[i + 1]] <- list(
-        rec = rec[(i * thl + 1):min(((i + 1) * thl), nrow(rec)), ],
-        verbose = ifelse(i == 0, verbose, FALSE))
-    }
-    counts.l <- clusterApply(
-      cl, rec.l, enve.recplot2.__counts, pos.breaks = pos.breaks,
-      id.breaks = id.breaks, rec.idcol = rec.idcol)
-    stopCluster(cl) # No spooky ghost clusters
-
-    counts <- counts.l[[1]]
-    for (i in 2:threads) counts <- counts + counts.l[[i]]
-  }
-
-  # Estimate 1D histograms
-  if (verbose) cat("Building histograms.\n")
-  id.mids	<- (id.breaks[-length(id.breaks)] + id.breaks[-1])/2;
-  id.ingroup	<- (id.mids > id.cutoff);
-  id.counts	<- apply(counts, 2, id.summary);
-  pos.counts.in   <- apply(counts[, id.ingroup], 1, sum);
-  pos.counts.out  <- apply(counts[, !id.ingroup], 1, sum);
-
-  # Plot and return
-  recplot <- new('enve.RecPlot2',
-                 counts = counts, id.counts = id.counts,
-                 pos.counts.in = pos.counts.in, pos.counts.out = pos.counts.out,
-                 id.breaks = id.breaks, pos.breaks = pos.breaks,
-                 pos.names = pos.names, seq.breaks = c(lim[1, 2], lim[, 3]),
-                 seq.names = lim[, 1], id.ingroup = id.ingroup,
-                 id.metric = id.metric, call = match.call());
-  if (plot) {
-    if (verbose) cat("Plotting.\n")
-    peaks <- plot(recplot, ...);
-    attr(recplot, "peaks") <- peaks
-  }
-  return(recplot);
-}
-
-#' Enveomics: Recruitment Plot (2) Peak Finder
-#'
-#' Identifies peaks in the population histogram potentially indicating
-#' sub-population mixtures.
-#'
-#' @param x
-#' An \code{\link{enve.RecPlot2}} object.
-#' @param method
-#' Peak-finder method. This should be one of:
-#' \itemize{
-#'    \item \strong{emauto}
-#'    (Expectation-Maximization with auto-selection of components)
-#'    \item \strong{em}
-#'    (Expectation-Maximization)
-#'    \item \strong{mower}
-#'    (Custom distribution-mowing method)
-#' }
-#' @param ...
-#' Any additional parameters supported by
-#' \code{\link{enve.recplot2.findPeaks}}.
-#'
-#' @return Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' export
-
-enve.recplot2.findPeaks <- function(
-  x,
-  method="emauto",
-  ...
-){
-  if(method == "emauto"){
-    peaks <- enve.recplot2.findPeaks.emauto(x, ...)
-  }else if(method == "em"){
-    peaks <- enve.recplot2.findPeaks.em(x, ...)
-  }else if(method == "mower"){
-    peaks <- enve.recplot2.findPeaks.mower(x, ...)
-  }else{
-    stop("Invalid peak-finder method ", method)
-  }
-  return(peaks)
-}
-
-#' Enveomics: Recruitment Plot (2) Emauto Peak Finder
-#'
-#' Identifies peaks in the population histogram using a Gaussian Mixture
-#' Model Expectation Maximization (GMM-EM) method with number of components
-#' automatically detected.
-#'
-#' @param x
-#' An \code{\link{enve.RecPlot2}} object.
-#' @param components
-#' A vector of number of components to evaluate.
-#' @param criterion
-#' Criterion to use for components selection. Must be one of:
-#' \code{aic} (Akaike Information Criterion), \code{bic} or \code{sbc}
-#' (Bayesian Information Criterion or Schwarz Criterion).
-#' @param merge.tol
-#' When attempting to merge peaks with very similar sequencing depth, use
-#' this number of significant digits (in log-scale).
-#' @param verbose
-#' Display (mostly debugging) information.
-#' @param ...
-#' Any additional parameters supported by
-#' \code{\link{enve.recplot2.findPeaks.em}}.
-#'
-#' @return Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.emauto <- function(
-  x,
-  components = seq(1, 5),
-  criterion = 'aic',
-  merge.tol = 2L,
-  verbose = FALSE,
-  ...
-){
-  best <- list(crit=0, pstore=list())
-  if(criterion == 'aic'){
-    do_crit <- function(ll, k, n) 2*k - 2*ll
-  }else if(criterion %in% c('bic', 'sbc')){
-    do_crit <- function(ll, k, n) log(n)*k - 2*ll
-  }else{
-    stop('Invalid criterion ', criterion)
-  }
-  for(comp in components){
-    if(verbose) cat('Testing:',comp,'\n')
-    best <- enve.recplot2.findPeaks.__emauto_one(x, comp, do_crit, best,
-                                                 verbose, ...)
-  }
-  if(length(best[['peaks']])==0) return(list())
-
-  seqdepths.r <- signif(log(sapply(best[['peaks']],
-                                   function(x) x$seq.depth)), merge.tol)
-  distinct <- length(unique(seqdepths.r))
-  if(distinct < length(best[['peaks']])){
-    if(verbose) cat('Attempting merge to', distinct, 'components\n')
-    init <- apply(sapply(best[['peaks']],
-                         function(x) c(x$param.hat, alpha=x$n.hat/x$n.total)), 1, as.numeric)
-    init <- init[!duplicated(seqdepths.r),]
-    init <- list(mu=init[,'mean'], sd=init[,'sd'],
-                 alpha=init[,'alpha']/sum(init[,'alpha']))
-    best <- enve.recplot2.findPeaks.__emauto_one(x, distinct, do_crit, best,
-                                                 verbose, ...)
-  }
-  return(best[['peaks']])
-}
-
-#' Enveomics: Recruitment Plot (2) Em Peak Finder
-#'
-#' Identifies peaks in the population histogram using a Gaussian Mixture
-#' Model Expectation Maximization (GMM-EM) method.
-#'
-#' @param x
-#' An \code{\link{enve.RecPlot2}} object.
-#' @param max.iter
-#' Maximum number of EM iterations.
-#' @param ll.diff.res
-#' Maximum Log-Likelihood difference to be considered as convergent.
-#' @param components
-#' Number of distributions assumed in the mixture.
-#' @param rm.top
-#' Top-values to remove before finding peaks, as a quantile probability.
-#' This step is useful to remove highly conserved regions, but can be
-#' turned off by setting \code{rm.top=0}. The quantile is determined
-#' \strong{after} removing zero-coverage windows.
-#' @param verbose
-#' Display (mostly debugging) information.
-#' @param init
-#' Initialization parameters. By default, these are derived from k-means
-#' clustering. A named list with vectors for \code{mu}, \code{sd}, and
-#' \code{alpha}, each of length \code{components}.
-#' @param log
-#' Logical value indicating if the estimations should be performed in
-#' natural logarithm units. Do not change unless you know what you're
-#' doing.
-#'
-#' @return Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.em <- function(
-  x,
-  max.iter = 1000,
-  ll.diff.res = 1e-8,
-  components = 2,
-  rm.top = 0.05,
-  verbose = FALSE,
-  init,
-  log = TRUE
-){
-
-  # Essential vars
-  pos.binsize  <- x$pos.breaks[-1] - x$pos.breaks[-length(x$pos.breaks)]
-  lsd1  <- (x$pos.counts.in/pos.binsize)[ x$pos.counts.in > 0 ]
-  lsd1 <- lsd1[ lsd1 < quantile(lsd1, 1-rm.top, names = FALSE) ]
-  if(log) lsd1 <- log(lsd1)
-
-  # 1. Initialize
-  if(missing(init)){
-    km.clust <- kmeans(lsd1, components)$cluster
-    init <- list(
-      mu = tapply(lsd1, km.clust, mean),
-      sd = tapply(lsd1, km.clust, sd),
-      alpha = table(km.clust) / length(km.clust)
-    )
-  }
-  m.step <- init
-  ll <- c()
-  cur.ll <- -Inf
-
-  for(i in 1:max.iter){
-    # 2/3. EM
-    e.step <- enve.recplot2.findPeaks.__em_e(lsd1, m.step)
-    m.step <- enve.recplot2.findPeaks.__em_m(lsd1, e.step[['posterior']])
-    # 4. Convergence
-    ll <- c(ll, e.step[["ll"]])
-    ll.diff <- abs(cur.ll - e.step[["ll"]])
-    cur.ll <- e.step[["ll"]]
-    if(verbose) cat(i, '\t| LL =', cur.ll, '\t| LL.diff =', ll.diff, '\n')
-    if(is.na(ll.diff) || ll.diff == Inf) break
-    if(ll.diff <= ll.diff.res) break
-  }
-
-  # Return
-  peaks <- list()
-  for(i in 1:components){
-    n.hat <- m.step[['alpha']][i]*length(lsd1)
-    peaks[[i]] <- new('enve.RecPlot2.Peak', dist='norm', values=as.numeric(),
-                      values.res=0, mode=m.step[['mu']][i],
-                      param.hat=list(sd=m.step[['sd']][i], mean=m.step[['mu']][i]),
-                      n.hat=n.hat, n.total=length(lsd1), err.res=cur.ll,
-                      merge.logdist=as.numeric(), log=log,
-                      seq.depth=ifelse(log, exp(m.step[['mu']][i]), m.step[['mu']][i]))
-  }
-  return(peaks)
-}
-
-#' Enveomics: Recruitment Plot (2) Mowing Peak Finder
-#'
-#' Identifies peaks in the population histogram potentially indicating
-#' sub-population mixtures, using a custom distribution-mowing method.
-#'
-#' @param x
-#' An \code{\link{enve.RecPlot2}} object.
-#' @param min.points
-#' Minimum number of points in the quantile-estimation-range
-#' \code{(quant.est)} to estimate a peak.
-#' @param quant.est
-#' Range of quantiles to be used in the estimation of a peak's
-#' parameters.
-#' @param mlv.opts
-#' Ignored. For backwards compatibility.
-#' @param fitdist.opts.sn
-#' Options passed to \code{fitdist} to estimate the standard deviation if
-#' \code{with.skewness=TRUE}. Note that the \code{start} parameter will be
-#' ammended with \code{xi=estimated} mode for each peak.
-#' @param fitdist.opts.norm
-#' Options passed to \code{fitdist} to estimate the standard deviation if
-#' \code{with.skewness=FALSE}. Note that the \code{start} parameter will be
-#' ammended with \code{mean=estimated} mode for each peak.
-#' @param rm.top
-#' Top-values to remove before finding peaks, as a quantile probability.
-#' This step is useful to remove highly conserved regions, but can be
-#' turned off by setting \code{rm.top=0}. The quantile is determined
-#' \strong{after} removing zero-coverage windows.
-#' @param with.skewness
-#' Allow skewness correction of the peaks. Typically, the
-#' sequencing-depth distribution for a single peak is left-skewed, due
-#' partly (but not exclusively) to fragmentation and mapping sensitivity.
-#' See \emph{Lindner et al 2013, Bioinformatics 29(10):1260-7} for an
-#' alternative solution for the first problem (fragmentation) called
-#' "tail distribution".
-#' @param optim.rounds
-#' Maximum rounds of peak optimization.
-#' @param optim.epsilon
-#' Trace change at which optimization stops (unless \code{optim.rounds} is
-#' reached first). The trace change is estimated as the sum of square
-#' differences between parameters in one round and those from two rounds
-#' earlier (to avoid infinite loops from approximation).
-#' @param merge.logdist
-#' Maximum value of \code{|log-ratio|} between centrality parameters in peaks
-#' to attempt merging. The default of ~0.22 corresponds to a maximum
-#' difference of 25\%.
-#' @param verbose
-#' Display (mostly debugging) information.
-#' @param log
-#' Logical value indicating if the estimations should be performed in
-#' natural logarithm units. Do not change unless you know what you're
-#' doing.
-#'
-#' @return Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.mower <- function(
-  x,
-  min.points=10,
-  quant.est=c(0.002, 0.998),
-  mlv.opts=list(method='parzen'),
-  fitdist.opts.sn=list(distr='sn', method='qme', probs=c(0.1,0.5,0.8),
-                       start=list(omega=1, alpha=-1), lower=c(0, -Inf, -Inf)),
-  fitdist.opts.norm=list(distr='norm', method='qme', probs=c(0.4,0.6),
-                         start=list(sd=1), lower=c(0, -Inf)),
-  rm.top=0.05,
-  with.skewness=TRUE,
-  optim.rounds=200,
-  optim.epsilon=1e-4,
-  merge.logdist=log(1.75),
-  verbose=FALSE,
-  log=TRUE
-){
-
-  # Essential vars
-  pos.binsize	<- x$pos.breaks[-1] - x$pos.breaks[-length(x$pos.breaks)];
-  seqdepth.in	<- x$pos.counts.in/pos.binsize;
-  lsd1 <- seqdepth.in[seqdepth.in>0];
-  lsd1 <- lsd1[ lsd1 < quantile(lsd1, 1-rm.top, names=FALSE) ]
-  if(log) lsd1 <- log(lsd1)
-  if(with.skewness){
-    fitdist.opts <- fitdist.opts.sn
-  }else{
-    fitdist.opts <- fitdist.opts.norm
-  }
-  peaks.opts <- list(lsd1=lsd1, min.points=min.points, quant.est=quant.est,
-                     mlv.opts=mlv.opts, fitdist.opts=fitdist.opts, with.skewness=with.skewness,
-                     optim.rounds=optim.rounds, optim.epsilon=optim.epsilon, verbose=verbose,
-                     n.total=length(lsd1), merge.logdist=merge.logdist, log=log)
-
-  # Find seed peaks
-  if(verbose) cat('Mowing peaks for n =',length(lsd1),'\n')
-  peaks <- enve.recplot2.findPeaks.__mower(peaks.opts);
-
-  # Merge overlapping peaks
-  if(verbose) cat('Trying to merge',length(peaks),'peaks\n')
-  merged <- (length(peaks)>1)
-  while(merged){
-    merged <- FALSE
-    ignore <- c()
-    peaks2 <- list();
-    for(i in 1:length(peaks)){
-      if(i %in% ignore) next
-      p <- peaks[[ i ]]
-      j <- enve.recplot2.__whichClosestPeak(p, peaks)
-      p2 <- peaks[[ j ]]
-      dst.a <- p$param.hat[[ length(p$param.hat) ]]
-      dst.b <- p2$param.hat[[ length(p2$param.hat) ]]
-      if( abs(log(dst.a/dst.b)) < merge.logdist ){
-        if(verbose) cat('==> Attempting a merge at',
-                        p$param.hat[[ length(p$param.hat) ]],'&',
-                        p2$param.hat[[ length(p2$param.hat) ]],'X\n');
-        peaks.opts$lsd1 <- c(p$values, p2$values)
-        p.new <- enve.recplot2.findPeaks.__mower(peaks.opts)
-        if(length(p.new)==1){
-          peaks2[[ length(peaks2)+1 ]] <- p.new[[ 1 ]]
-          ignore <- c(ignore, j)
-          merged <- TRUE
-        }
-      }
-      if(!merged) peaks2[[ length(peaks2)+1 ]] <- p
-    }
-    peaks <- peaks2
-    if(length(peaks)==1) break
-  }
-
-  if(verbose) cat('Found',length(peaks),'peak(s)\n')
-  return(peaks);
-}
-
-#==============> Define utils
-
-#' Enveomics: Recruitment Plot (2) Core Peak Finder
-#'
-#' Finds the peak in a list of peaks that is most likely to represent the
-#' "core genome" of a population.
-#'
-#' @param x \code{list} of \code{\link{enve.RecPlot2.Peak}} objects.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.corePeak <- function
-(x
-){
-  # Find the peak with maximum depth (centrality)
-  maxPeak <- x[[
-    which.max(as.numeric(lapply(x,
-                                function(y) y$param.hat[[ length(y$param.hat) ]])))
-    ]]
-  # If a "larger" peak (a peak explaining more bins of the genome) is within
-  # the default "merge.logdist" distance, take that one instead.
-  corePeak <- maxPeak
-  for(p in x){
-    p.len <- ifelse(length(p$values)==0, p$n.hat, length(p$values))
-    corePeak.len <- ifelse(
-      length(corePeak$values)==0, corePeak$n.hat, length(corePeak$values))
-    sz.d <- log(p.len/corePeak.len)
-    if(is.nan(sz.d) || sz.d < 0) next
-    sq.d.a <- as.numeric(tail(p$param.hat, n=1))
-    sq.d.b <- as.numeric(tail(maxPeak$param.hat, n=1))
-    if(p$log) sq.d.a <- exp(sq.d.a)
-    if(corePeak$log) sq.d.b <- exp(sq.d.b)
-    if(abs(log(sq.d.a/sq.d.b)) < log(1.75)+sz.d/5) corePeak <- p
-  }
-  return(corePeak)
-}
-
-#' Enveomics: Recruitment Plot (2) Change Cutoff
-#'
-#' Change the intra-species cutoff of an existing recruitment plot.
-#'
-#' @param rp
-#' \code{\link{enve.RecPlot2}} object.
-#' @param new.cutoff
-#' New cutoff to use.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.changeCutoff <- function
-(rp,
- new.cutoff=98
-){
-  # Re-calculate vectors
-  id.mids	<- (rp$id.breaks[-length(rp$id.breaks)]+rp$id.breaks[-1])/2
-  id.ingroup	<- (id.mids > new.cutoff)
-  pos.counts.in  <- apply(rp$counts[,id.ingroup], 1, sum)
-  pos.counts.out <- apply(rp$counts[,!id.ingroup], 1, sum)
-  # Update object
-  attr(rp, "id.ingroup")     <- id.ingroup
-  attr(rp, "pos.counts.in")  <- pos.counts.in
-  attr(rp, "pos.counts.out") <- pos.counts.out
-  attr(rp, "call")           <- match.call()
-  return(rp)
-}
-
-#' Enveomics: Recruitment Plot (2) Window Depth Threshold
-#'
-#' Identifies the threshold below which windows should be identified as
-#' variable or absent.
-#'
-#' @param rp
-#' Recruitment plot, an \code{\link{enve.RecPlot2}} object.
-#' @param peak
-#' Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
-#' list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
-#' used (see \code{\link{enve.recplot2.corePeak}}).
-#' @param lower.tail
-#' If \code{FALSE}, it returns windows significantly above the peak in
-#' sequencing depth.
-#' @param significance
-#' Significance threshold (alpha) to select windows.
-#'
-#' @return
-#' Returns a float. The units are depth if the peaks were estimated in
-#' linear scale, or log-depth otherwise (\code{peak$log}).
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.windowDepthThreshold <- function
-(rp,
- peak,
- lower.tail=TRUE,
- significance=0.05
-){
-  if(is.list(peak)) peak <- enve.recplot2.corePeak(peak)
-  par <- peak$param.hat
-  par[["p"]] <- ifelse(lower.tail, significance, 1-significance)
-  thr <- do.call(ifelse(length(par)==4, qsn, qnorm), par)
-  if(peak$log) thr <- exp(thr)
-
-  return(thr)
-}
-
-#' Enveomics: Recruitment Plot (2) Extract Windows
-#'
-#' Extract windows significantly below (or above) the peak in sequencing
-#' depth.
-#'
-#' @param rp
-#' Recruitment plot, a \code{\link{enve.RecPlot2}} object.
-#' @param peak
-#' Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
-#' list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
-#' used (see \code{\link{enve.recplot2.corePeak}}).
-#' @param lower.tail
-#' If \code{FALSE}, it returns windows significantly above the peak in
-#' sequencing depth.
-#' @param significance
-#' Significance threshold (alpha) to select windows.
-#' @param seq.names
-#' Returns subject sequence names instead of a vector of Booleans. If
-#' the recruitment plot was generated with named position bins (e.g, using
-#' \code{pos.breaks=0} or a two-column \code{pos.breaks.tsv}), it returns a
-#' vector of characters (the sequence identifiers), otherwise it returns a
-#' data.frame with a name column and two columns of coordinates.
-#'
-#' @return
-#' Returns a vector of logicals if \code{seq.names = FALSE}.
-#' If \code{seq.names = TRUE}, it returns a data.frame with five columns:
-#' \code{name.from}, \code{name.to}, \code{pos.from}, \code{pos.to}, and
-#' \code{seq.name} (see \code{\link{enve.recplot2.coordinates}}).
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.extractWindows <- function
-(rp,
- peak,
- lower.tail = TRUE,
- significance = 0.05,
- seq.names = FALSE
-){
-  # Determine the threshold
-  thr <- enve.recplot2.windowDepthThreshold(rp, peak, lower.tail, significance)
-
-  # Select windows past the threshold
-  seqdepth.in <- enve.recplot2.seqdepth(rp)
-  if(lower.tail){
-    sel <- seqdepth.in < thr
-  }else{
-    sel <- seqdepth.in > thr
-  }
-
-  # seq.names = FALSE
-  if(!seq.names) return(sel)
-  # seq.names = TRUE
-  return(enve.recplot2.coordinates(rp, sel))
-}
-
-#' Enveomics: Recruitment Plot (2) Compare Identities
-#'
-#' Compare the distribution of identities between two
-#' \code{\link{enve.RecPlot2}} objects.
-#'
-#' @param x
-#' First \code{\link{enve.RecPlot2}} object.
-#' @param y
-#' Second \code{\link{enve.RecPlot2}} object.
-#' @param method
-#' Distance method to use. This should be (an unambiguous abbreviation of)
-#' one of:
-#' \itemize{
-#'    \item{"hellinger" (\emph{Hellinger, 1090, doi:10.1515/crll.1909.136.210}),}
-#'    \item{"bhattacharyya" (\emph{Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35}),}
-#'    \item{"kl" or "kullback-leibler" (\emph{Kullback & Leibler, 1951,
-#'    doi:10.1214/aoms/1177729694}), or}
-#'    \item{"euclidean"}
-#' }
-#' @param smooth.par
-#' Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
-#' Use \code{NULL} to automatically determine this value using leave-one-out
-#' cross-validation (see \code{smooth.spline} parameter \code{spar}).
-#' @param pseudocounts
-#' Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
-#' 1 for add-one smoothing.
-#' @param max.deviation
-#' Maximum mean deviation between identity breaks tolerated (as percent
-#' identity). Difference in number of \code{id.breaks} is never tolerated.
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.compareIdentities <- function
-(x,
- y,
- method="hellinger",
- smooth.par=NULL,
- pseudocounts=0,
- max.deviation=0.75
-){
-  METHODS <- c("hellinger","bhattacharyya","kullback-leibler","kl","euclidean")
-  i.meth <- pmatch(method, METHODS)
-  if (is.na(i.meth)) stop("Invalid distance ", method)
-  if(!inherits(x, "enve.RecPlot2"))
-    stop("'x' must inherit from class `enve.RecPlot2`")
-  if(!inherits(y, "enve.RecPlot2"))
-    stop("'y' must inherit from class `enve.RecPlot2`")
-  if(length(x$id.breaks) != length(y$id.breaks))
-    stop("'x' and 'y' must have the same number of `id.breaks`")
-  dev <- mean(abs(x$id.breaks - y$id.breaks))
-  if(dev > max.deviation)
-    stop("'x' and 'y' must have similar `id.breaks`; exceeding max.deviation: ",
-         dev)
-  x.cnt <- x$id.counts
-  y.cnt <- y$id.counts
-  if(is.null(smooth.par) || smooth.par > 0){
-    x.mids <- (x$id.breaks[-1] + x$id.breaks[-length(x$id.breaks)])/2
-    y.mids <- (y$id.breaks[-1] + y$id.breaks[-length(y$id.breaks)])/2
-    p.spline <- smooth.spline(x.mids, x.cnt, spar=smooth.par)
-    q.spline <- smooth.spline(y.mids, y.cnt, spar=smooth.par)
-    x.cnt <- pmax(p.spline$y, 0)
-    y.cnt <- pmax(q.spline$y, 0)
-  }
-  a <- as.numeric(pseudocounts)
-  p <- (x.cnt + a) / sum(x.cnt + a)
-  q <- (y.cnt + a) / sum(y.cnt + a)
-  d <- NA
-  if(i.meth %in% c(1L, 2L)){
-    d <- sqrt(sum((sqrt(p) - sqrt(q))**2))/sqrt(2)
-    if(i.meth==2L) d <- 1 - d**2
-  }else if(i.meth %in% c(3L, 4L)){
-    sel <- p>0
-    if(any(q[sel]==0))
-      stop("Undefined distance without absolute continuity, use pseudocounts")
-    d <- -sum(p[sel]*log(q[sel]/p[sel]))
-  }else if(i.meth == 5L){
-    d <- sqrt(sum((q-p)**2))
-  }
-  return(d)
-}
-
-#' Enveomics: Recruitment Plot (2) Coordinates
-#'
-#' Returns the sequence name and coordinates of the requested position bins.
-#'
-#' @param x
-#' \code{\link{enve.RecPlot2}} object.
-#' @param bins
-#' Vector of selected bins to return. It can be a vector of logical values
-#' with the same length as \code{x$pos.breaks-1} or a vector of integers. If
-#' missing, returns the coordinates of all windows.
-#'
-#' @return
-#' Returns a data.frame with five columns: \code{name.from} (character),
-#' \code{pos.from} (numeric), \code{name.to} (character), \code{pos.to}
-#' (numeric), and \code{seq.name} (character).
-#' The first two correspond to sequence and position of the start point of the
-#' bin. The next two correspond to the sequence and position of the end point of
-#' the bin. The last one indicates the name of the sequence (if defined).
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.coordinates <- function
-(x,
- bins
-){
-  if(!inherits(x, "enve.RecPlot2"))
-    stop("'x' must inherit from class `enve.RecPlot2`")
-  if(missing(bins)) bins <- rep(TRUE, length(x$pos.breaks)-1)
-  if(!is.vector(bins)) stop("'bins' must be a vector")
-  if(inherits(bins, "logical")) bins <- which(bins)
-
-  y <- data.frame(stringsAsFactors = FALSE, row.names = bins)
-
-  for(i in 1:length(bins)){
-    j <- bins[i]
-    # Concatenated coordinates
-    cc <- x$pos.breaks[c(j, j+1)]
-    # Find the corresponding `seq.breaks`
-    sb.from <- which(
-      cc[1] >= x$seq.breaks[-length(x$seq.breaks)] &
-        cc[1] <  x$seq.breaks[-1])
-    sb.to   <- which(
-      cc[2] >  x$seq.breaks[-length(x$seq.breaks)] &
-        cc[2] <= x$seq.breaks[-1])
-    # Translate coordinates
-    if(length(sb.from)==1 & length(sb.to)==1){
-      y[i, 'name.from'] <- x$seq.names[sb.from]
-      y[i, 'pos.from']  <- floor(x$seq.breaks[sb.from] + cc[1] - 1)
-      y[i, 'name.to']   <- x$seq.names[sb.to]
-      y[i, 'pos.to']    <- ceiling(x$seq.breaks[sb.to] + cc[2] - 1)
-      y[i, 'seq.name']  <- x$pos.names[i]
-    }
-  }
-
-  return(y)
-}
-
-#' Enveomics: Recruitment Plot (2) Sequencing Depth
-#'
-#' Calculate the sequencing depth of the given window(s).
-#'
-#' @param x
-#' \code{\link{enve.RecPlot2}} object.
-#' @param sel
-#' Window(s) for which the sequencing depth is to be calculated. If not
-#' passed, it returns the sequencing depth of all windows.
-#' @param low.identity
-#' A logical indicating if the sequencing depth is to be estimated only
-#' with low-identity matches. By default, only high-identity matches are
-#' used.
-#'
-#' @return
-#' Returns a numeric vector of sequencing depths (in bp/bp).
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.seqdepth <- function
-
-(x,
- sel,
- low.identity=FALSE
-){
-  if(!inherits(x, "enve.RecPlot2"))
-    stop("'x' must inherit from class `enve.RecPlot2`")
-  if(low.identity){
-    pos.cnts.in <- x$pos.counts.out
-  }else{
-    pos.cnts.in <- x$pos.counts.in
-  }
-  pos.breaks  <- x$pos.breaks
-  pos.binsize <- (pos.breaks[-1] - pos.breaks[-length(pos.breaks)])
-  seqdepth.in <- pos.cnts.in/pos.binsize
-  if(missing(sel)) return(seqdepth.in)
-  return(seqdepth.in[sel])
-}
-
-#' Enveomics: Recruitment Plot (2) ANI Estimate
-#'
-#' Estimate the Average Nucleotide Identity from reads (ANIr) from a
-#' recruitment plot.
-#'
-#' @param x
-#' \code{\link{enve.RecPlot2}} object.
-#' @param range
-#' Range of identities to be considered. By default, the full range
-#' is used (note that the upper boundary is \code{Inf} and not 100 because
-#' recruitment plots can also be built with bit-scores). To use only
-#' intra-population matches (with identities), use c(95,100). To use only
-#' inter-population values, use c(0,95).
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.ANIr <- function
-(x,
- range=c(0,Inf)
-){
-  if(!inherits(x, "enve.RecPlot2"))
-    stop("'x' must inherit from class `enve.RecPlot2`")
-  id.b <- x$id.breaks
-  id <- (id.b[-1]+id.b[-length(id.b)])/2
-  cnt <- x$id.counts
-  cnt[id < range[1]] <- 0
-  cnt[id > range[2]] <- 0
-  return(sum(id*cnt/sum(cnt)))
-}
-
-#==============> Define internal functions
-
-#' Enveomics: Recruitment Plot (2) Internal Ancillary Function
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2}}).
-#'
-#' @param x \code{\link{enve.RecPlot2}} object
-#' @param pos.breaks Position breaks
-#' @param id.breaks Identity breaks
-#' @param rec.idcol Identity column to use
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#' @author Kenji Gerhardt [aut]
-#'
-#' @export
-
-enve.recplot2.__counts <- function
-(x, pos.breaks, id.breaks, rec.idcol) {
-  rec2 <- x$rec
-  verbose <- x$verbose
-
-  # get counts of how many occurrences of each genome pos.bin there are per read
-  x.bins <- mapply(
-    function(start, end) {
-      list(rle(findInterval(start:end, pos.breaks, left.open = T)))
-    }, rec2[, 1], rec2[, 2])
-
-  # find the single y bin for each row, replicates it at the correct places to
-  # the number of distinct bins found in its row
-  y.bins <- rep(findInterval(rec2[, rec.idcol], id.breaks, left.open = T),
-                times = unlist(lapply(x.bins, function(a) length(a$lengths))))
-
-  # x.bins_counts is the number of occurrences of each bin a row contains,
-  # per row, then unlisted
-  x.bins_counts <- unlist(lapply(x.bins, function(a) a$lengths))
-
-  # these are the pos. in. genome bins that each count in x.bins_counts falls into
-  x.bins <- unlist(lapply(x.bins, function(a) a$values))
-
-  # much more efficient counts implementation in R using lists instead of a matrix:
-  counts <- lapply(
-    1:(length(pos.breaks) - 1),
-    function(col_len) rep(0, length(id.breaks) - 1))
-
-  # accesses the correct list in counts by x.bin, then
-  # accesses the position in that row by y.bins and adds the new count
-  for(i in 1:length(x.bins)){
-    counts[[x.bins[i]]][y.bins[i]] <- counts[[x.bins[i]]][y.bins[i]] + x.bins_counts[i]
-  }
-
-  counts <- do.call(rbind, counts)
-  return(counts)
-}
-
-#' Enveomics: Recruitment Plot (2) EMauto Peak Finder - Internal Ancillary Function
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.emauto}}).
-#'
-#' @param x \code{\link{enve.RecPlot2}} object
-#' @param comp Components
-#' @param do_crit Function estimating the criterion
-#' @param best Best solution thus far
-#' @param verbose If verbose
-#' @param ... Additional parameters for \code{\link{enve.recplot2.findPeaks.em}}
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.__emauto_one <- function
-(x, comp, do_crit, best, verbose, ...){
-  peaks <- enve.recplot2.findPeaks.em(x=x, components=comp, ...)
-  if(length(peaks)==0) return(best)
-  k <- comp*3 - 1 # mean & sd for each component, and n-1 free alpha parameters
-  crit <- do_crit(peaks[[1]]$err.res, k, peaks[[1]]$n.total)
-  if(verbose) cat(comp,'\t| LL =', peaks[[1]]$err.res, '\t| Estimate =', crit,
-                  ifelse(crit > best[['crit']], '*', ''), '\n')
-  if(crit > best[['crit']]){
-    best[['crit']] <- crit
-    best[['peaks']] <- peaks
-  }
-  best[['pstore']][[comp]] <- peaks
-  return(best)
-}
-
-#' Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectation
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
-#'
-#' @param x Vector of log-transformed sequencing depths
-#' @param theta Parameters list
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.__em_e <- function
-(x, theta){
-  components <- length(theta[['mu']])
-  product <- do.call(cbind,
-                     lapply(1:components,
-                            function(i) dnorm(x, theta[['mu']][i],
-                                              theta[['sd']][i])*theta[['alpha']][i]))
-  sum.of.components <- rowSums(product)
-  posterior <- product / sum.of.components
-  for(i in which(sum.of.components == Inf)) {
-    cat(i,'/',nrow(product), ':', product[i,], '\n')
-  }
-
-  return(list(ll=sum(log(sum.of.components)), posterior=posterior))
-}
-
-#' Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximization
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
-#'
-#' @param x Vector of log-transformed sequencing depths
-#' @param posterior Posterior probability
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.__em_m <- function
-(x, posterior){
-  components <- ncol(posterior)
-  n <- colSums(posterior)
-  mu <- colSums(posterior * x) / n
-  sd <- sqrt( colSums(
-    posterior * (matrix(rep(x,components), ncol=components) - mu)^2) / n )
-  alpha <- n/length(x)
-  return(list(mu=mu, sd=sd, alpha=alpha))
-}
-
-#' Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Function
-#'
-#' Internal ancillary function (see \code{\link{enve.RecPlot2.Peak}}).
-#'
-#' @param x \code{\link{enve.RecPlot2.Peak}} object
-#' @param mids Midpoints
-#' @param counts Counts
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.__peakHist <- function
-(x, mids, counts=TRUE){
-  d.o <- x$param.hat
-  if(length(x$log)==0) x$log <- FALSE
-  if(x$log){
-    d.o$x <- log(mids)
-  }else{
-    d.o$x <- mids
-  }
-  prob  <- do.call(paste('d', x$dist, sep=''), d.o)
-  if(!counts) return(prob)
-  if(length(x$values)>0) return(prob*length(x$values)/sum(prob))
-  return(prob*x$n.hat/sum(prob))
-}
-
-#' Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1
-#'
-#' Internall ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
-#'
-#' @param lsd1 Vector of log-transformed sequencing depths
-#' @param min.points Minimum number of points
-#' @param quant.est Quantile estimate
-#' @param mlv.opts List of options for \code{mlv}
-#' @param fitdist.opts List of options for \code{fitdist}
-#' @param with.skewness If skewed-normal should be used
-#' @param optim.rounds Maximum number of optimization rounds
-#' @param optim.epsilon Minimum difference considered negligible
-#' @param n.total Global number of windows
-#' @param merge.logdist Attempted \code{merge.logdist} parameter
-#' @param verbose If verbose
-#' @param log If log-transformed depths
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.__mow_one <- function
-(lsd1, min.points, quant.est, mlv.opts, fitdist.opts, with.skewness,
- optim.rounds, optim.epsilon, n.total, merge.logdist, verbose, log
-){
-  dist	<- ifelse(with.skewness, 'sn', 'norm');
-
-  # Find peak
-  o <- mlv.opts; o$x = lsd1;
-  mode1 <- median(lsd1); # mode1 <- do.call(mlv, o)$M;
-  if(verbose) cat('Anchoring at mode =',mode1,'\n')
-  param.hat <- fitdist.opts$start; last.hat <- param.hat;
-  lim <- NA;
-  if(with.skewness){ param.hat$xi <- mode1 }else{ param.hat$mean <- mode1 }
-
-  # Refine peak parameters
-  for(round in 1:optim.rounds){
-    param.hat[[ 1 ]] <- param.hat[[ 1 ]]/diff(quant.est)# <- expand dispersion
-    lim.o <- param.hat
-    lim.o$p <- quant.est; lim <- do.call(paste('q',dist,sep=''), lim.o)
-    lsd1.pop <- lsd1[(lsd1>lim[1]) & (lsd1<lim[2])];
-    if(verbose) cat(' Round', round, 'with n =',length(lsd1.pop),
-                    'and params =',as.numeric(param.hat),' \r')
-    if(length(lsd1.pop) < min.points) break;
-    o <- fitdist.opts; o$data = lsd1.pop; o$start = param.hat;
-    last.last.hat <- last.hat
-    last.hat <- param.hat
-    param.hat <- as.list(do.call(fitdist, o)$estimate);
-    if(any(is.na(param.hat))){
-      if(round>1) param.hat <- last.hat;
-      break;
-    }
-    if(round > 1){
-      epsilon1 <- sum((as.numeric(last.hat)-as.numeric(param.hat))^2)
-      if(epsilon1 < optim.epsilon) break;
-      if(round > 2){
-        epsilon2 <- sum((as.numeric(last.last.hat)-as.numeric(param.hat))^2)
-        if(epsilon2 < optim.epsilon) break;
-      }
-    }
-  }
-  if(verbose) cat('\n')
-  if(is.na(param.hat[1]) | is.na(lim[1])) return(NULL);
-
-  # Mow distribution
-  lsd2 <- c();
-  lsd.pop <- c();
-  n.hat <- length(lsd1.pop)/diff(quant.est)
-  peak <- new('enve.RecPlot2.Peak', dist=dist, values=as.numeric(), mode=mode1,
-              param.hat=param.hat, n.hat=n.hat, n.total=n.total,
-              merge.logdist=merge.logdist, log=log)
-  peak.breaks <- seq(min(lsd1), max(lsd1), length=20)
-  peak.cnt <- enve.recplot2.__peakHist(peak,
-                                       (peak.breaks[-length(peak.breaks)]+peak.breaks[-1])/2)
-  for(i in 2:length(peak.breaks)){
-    values <- lsd1[ (lsd1 >= peak.breaks[i-1]) & (lsd1 < peak.breaks[i]) ]
-    n.exp <- peak.cnt[i-1]
-    if(is.na(n.exp) | n.exp==0) n.exp <- 0.1
-    if(length(values)==0) next
-    in.peak <- runif(length(values)) <= n.exp/length(values)
-    lsd2 <- c(lsd2, values[!in.peak])
-    lsd.pop <- c(lsd.pop, values[in.peak])
-  }
-  if(length(lsd.pop) < min.points) return(NULL)
-
-  # Return peak
-  attr(peak, 'values') <- lsd.pop
-  attr(peak, 'values.res') <- lsd2
-  attr(peak, 'err.res') <- 1-(cor(hist(lsd.pop, breaks=peak.breaks,
-                                       plot=FALSE)$counts, hist(lsd1, breaks=peak.breaks,
-                                                                plot=FALSE)$counts)+1)/2
-  mu <- tail(param.hat, n=1)
-  attr(peak, 'seq.depth') <- ifelse(log, exp(mu), mu)
-  if(verbose) cat(' Extracted peak with n =',length(lsd.pop),
-                  'with expected n =',n.hat,'\n')
-  return(peak)
-}
-
-#' Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
-#'
-#' @param peaks.opts List of options for \code{\link{enve.recplot2.findPeaks.__mow_one}}
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.findPeaks.__mower <- function
-(peaks.opts){
-  peaks <- list()
-  while(length(peaks.opts$lsd1) > peaks.opts$min.points){
-    peak <- do.call(enve.recplot2.findPeaks.__mow_one, peaks.opts)
-    if(is.null(peak)) break
-    peaks[[ length(peaks)+1 ]] <- peak
-    peaks.opts$lsd1 <- peak$values.res
-  }
-  return(peaks)
-}
-
-#' Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Function
-#'
-#' Internal ancillary function (see \code{\link{enve.recplot2.findPeaks}}).
-#'
-#' @param peak Query \code{\link{enve.RecPlot2.Peak}} object
-#' @param peaks list of \code{\link{enve.RecPlot2.Peak}} objects
-#'
-#' @author Luis M. Rodriguez-R [aut, cre]
-#'
-#' @export
-
-enve.recplot2.__whichClosestPeak <- function
-(peak, peaks){
-  dist <- as.numeric(lapply(peaks,
-                            function(x)
-                              abs(log(x$param.hat[[ length(x$param.hat) ]] /
-                                        peak$param.hat[[ length(peak$param.hat) ]] ))))
-  dist[ dist==0 ] <- Inf
-  return(which.min(dist))
-}