miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,354 +0,0 @@
-#' 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);
-});
-