miga-base 1.2.15.1 → 1.2.15.3

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

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

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

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