miga-base 1.2.17.1 → 1.2.17.2

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

@@ -16,29 +16,31 @@
 #' 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.
+#' 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:
+#' Metric of identity to be used (Y-axis). It can be any unambiguous prefix of:
 #' \itemize{
-#' \item "identity"
-#' \item "corrected identity" 
-#' \item "bit score"}
+#'   \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: 
+#' 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" }
+#'   \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.
+#' 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
@@ -47,8 +49,8 @@
 #' @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.
+#' 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
@@ -65,13 +67,14 @@
 #' 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.
+#' 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).
+#' Any additional graphic parameters to be passed to plot for all panels except
+#' the recruitment plot (lower-left).
 #' 
 #' @return 
 #' 
@@ -81,83 +84,92 @@
 #' \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}).}
+#'       (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.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.}
+#'       \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.}
+#'       This is returned because \code{id.cutoff=NULL} may vary.}
 #' \item{\code{seqdepth.mean.top}}{Average sequencing depth with identity above 
-#'      \code{id.cutoff}.}
+#'       \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.}
+#'       \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.}}
+#' \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(
+enve.recplot <- function(
   prefix,
-  
+
   # Id. hist.
-  id.min=NULL,
-  id.max=NULL,
-  id.binsize=NULL,
-  id.splines=0,
-  id.metric='id',
-  id.summary='sum',
-  
+  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,
-  
+  pos.min     = 1,
+  pos.max     = NULL,
+  pos.binsize = 1e3,
+  pos.splines = 0,
+
   # Rec. plot
-  rec.col1='white',
-  rec.col2='black',
-  
+  rec.col1    = "white",
+  rec.col2    = "black",
+
   # General
-  main=NULL,
-  contig.col=grey(0.85),
-  
+  main        = NULL,
+  contig.col  = grey(0.85),
+
   # Return
-  ret.recplot=FALSE,
-  ret.hist=FALSE,
-  ret.mode=FALSE,
-  
+  ret.recplot = FALSE,
+  ret.hist    = FALSE,
+  ret.mode    = FALSE,
+
   # General
-  id.cutoff=NULL,
-  verbose=TRUE,
+  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.');
+  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='');
-  
+  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.');
@@ -184,7 +196,7 @@ enve.recplot <- structure(function(
     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.');
@@ -229,32 +241,43 @@ enve.recplot <- structure(function(
   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;
+  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();
+  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;
+  mar <- par(mar=c(5, 4, 0, 0) + 0.1)
+  on.exit(par(mar))
+  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);
+  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));
@@ -262,16 +285,21 @@ enve.recplot <- structure(function(
   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', ...);
+  if(verbose) cat(id.shortname, " hist.\n", sep = "")
+  par(mar=c(5,0,0,2)+0.1) # par(mar) already being watched by on.exit
+  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='.');
+    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)
+      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)
     }
   }
@@ -285,27 +313,36 @@ enve.recplot <- structure(function(
   
   # 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;
+  par(mar = c(0, 4, 4, 0) + 0.1) # par(mar) already being watched by on.exit
+  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);
+  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)
+      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));
@@ -315,40 +352,68 @@ enve.recplot <- structure(function(
     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)
+      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));
+    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("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);
+  par(mar=c(0, 0, 4, 2) + 0.1) # par(mar) already being watched by on.exit
+  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]);
+      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);
+    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);
-});
+  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)
+}