miga-base 0.7.26.0 → 1.0.0.1

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

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+#' Enveomics: Color Alpha
+#' 
+#' Modify alpha in a color (or vector of colors).
+#'
+#' @param col Color or vector of colors. It can be any value supported by 
+#' \code{\link[grDevices]{col2rgb}}, such as \code{darkred} or \code{#009988}.
+#' @param alpha Alpha value to add to the color, from 0 to 1.
+#'
+#' @return Returns a color or a vector of colors in \emph{hex} notation, 
+#' including \code{alpha}.
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.col.alpha <- function
+    (col,
+    alpha=1/2
+    ){
+  return(
+    apply(col2rgb(col), 2,
+      function(x) do.call(rgb, as.list(c(x[1:3]/256, alpha))) ) )
+}
+
+#' Enveomics: Truncate
+#' 
+#' Removes the \code{n} highest and lowest values from a vector, and applies
+#' summary function. The value of \code{n} is determined such that the central
+#' range is used, corresponding to the \code{f} fraction of values.
+#'
+#' @param x A vector of numbers.
+#' @param f The fraction of values to retain.
+#' @param FUN Summary function to apply to the vectors. To obtain the 
+#' truncated vector itself, use \code{c}.
+#' 
+#' @return Returns the summary \code{(FUN)} of the truncated vector.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.truncate <- function
+    (x,
+    f=0.95,
+    FUN=mean
+    ){
+  n <- round(length(x)*(1-f)/2)
+  y <- sort(x)[ -c(seq(1, n), seq(length(x)+1-n, length(x))) ]
+  return(FUN(y))
+}
+
+#' Enveomics: Selection vector
+#' 
+#' Normalizes a selection vector \code{sel} to a logical vector with indexes
+#' from \code{dim.names}.
+#'
+#' @param sel A vector of numbers, characters, or booleans.
+#' @param dim.names A vector of names from which to select.
+#' 
+#' @return Returns a logical vector with the same length as \code{dim.name}.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.selvector <- function(sel, dim.names) {
+  if(is.logical(sel)) {
+    if(length(sel) != length(dim.names))
+      stop('sel is logical but differs in length from dim.names')
+    sel
+  } else if(is.numeric(sel)) {
+    if(max(sel) > length(dim.names))
+      stop('sel includes numeric index beyond the length of dim.names')
+    1:length(dim.names) %in% sel
+  } else {
+    if(any(!sel %in% dim.names))
+      stop('sel includes character index missing from dim.names')
+    dim.names %in% sel
+  }
+}

data/utils/enveomics/enveomics.R/README.md

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+# enveomics.R
+
+## Installing `enveomics.R`
+To install the latest version of `enveomics.R` uploaded to CRAN, execute in R:
+
+```R
+install.packages('enveomics.R')
+```
+
+To install the current developer version of `enveomics.R`, execute in R:
+
+```R
+install.packages('devtools')
+library('devtools')
+install_github('lmrodriguezr/enveomics', subdir='enveomics.R')
+```
+
+## Using `enveomics.R`
+To load enveomics.R, simply execute:
+
+```R
+library(enveomics.R);
+```
+
+And open help messages using any of the following commands:
+
+```R
+?enveomics.R
+?enve.barplot
+?enve.recplot2
+?enve.recplot2.compareIdentities
+?enve.recplot2.changeCutoff
+?enve.recplot2.findPeaks
+?enve.recplot2.corePeak
+?enve.recplot2.windowDepthThreshold
+?enve.recplot2.extractWindows
+?enve.recplot2.coordinates
+?enve.recplot2.seqdepth
+?enve.recplot2.ANIr
+?enve.prune.dist
+?enve.tribs
+?enve.tribs.test
+?enve.growthcurve
+?enve.col.alpha
+?enve.truncate
+```
+
+You can run some examples using these libraries in the
+[enveomics-GUI](https://github.com/lmrodriguezr/enveomics-gui).
+
+For additional information on recruitment plots, see the
+[Recruitment plots working document](https://github.com/lmrodriguezr/enveomics/blob/master/Docs/recplot2.md).
+
+## Changelog
+* 1.8.0: New functions `enve.selvector` and `enve.prefscore`.
+* 1.7.1: Improved efficiency of `enve.df2dist` about five-fold.
+* 1.7.0: Uniformized output for `enve.recplot2.extractWindows` and
+  `enve.recplot2.coordinates` to ease automation. Thanks to Tomeu Viver and
+  Roth Conrad for troubleshooting.
+* 1.6.0: Speed up in recplot2 with proper structure manipulation
+  (by: Kenji Gerhardt). Also, default value for `id.breaks` was changed from
+  300 to 60.
+* 1.5.0: Modernized documentation, now in ROxygen2 (by: Tatyana Kiryutina)
+* 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder
+  initialization to median (instead of mode).
+* 1.4.2: Solved bug #36.
+* 1.4.0: New option `pos.breaks.tsv` for `enve.recplot2`.
+* 1.3.4: Gracefully handles and plots recruitment plots with insufficient data
+  to find peaks.
+* 1.3.3: New function `enve.recplot2.windowDepthThreshold`.
+* 1.3.2: New option `panel.fun` for `plot.enve.RecPlot2`.
+* 1.3.1: New function enve.truncate.
+* 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
+* 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve
+  with S3 methods plot and summary.
+* 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and
+  solved a minor bug in enve.recplot2 that caused failures in low-coverage
+  datasets when using too many threads.
+* 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a
+  bin per subject sequence.
+

data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{$,enve.GrowthCurve-method}
+\alias{$,enve.GrowthCurve-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.GrowthCurve}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{$,enve.RecPlot2-method}
+\alias{$,enve.RecPlot2-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.RecPlot2}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{$,enve.RecPlot2.Peak-method}
+\alias{$,enve.RecPlot2.Peak-method}
+\title{Attribute accessor}
+\usage{
+\S4method{$}{enve.RecPlot2.Peak}(x, name)
+}
+\arguments{
+\item{x}{Object}
+
+\item{name}{Attribute name}
+}
+\description{
+Attribute accessor
+}

data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\docType{class}
+\name{enve.GrowthCurve-class}
+\alias{enve.GrowthCurve-class}
+\alias{enve.GrowthCurve}
+\title{Enveomics: Growth Curve S4 Class}
+\description{
+Enve-omics representation of fitted growth curves.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{design}}{\code{(array)} Experimental design of the experiment.}
+
+\item{\code{models}}{\code{(list)} Fitted growth curve models.}
+
+\item{\code{predict}}{\code{(list)} Fitted growth curve values.}
+
+\item{\code{call}}{\code{(call)} Call producing this object.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\docType{class}
+\name{enve.TRIBS-class}
+\alias{enve.TRIBS-class}
+\alias{enve.TRIBS}
+\title{Enveomics: TRIBS S4 Class}
+\description{
+Enve-omics representation of "Transformed-space Resampling In Biased Sets
+(TRIBS)". This object represents sets of distances between objects,
+sampled nearly-uniformly at random in "distance space". Subsampling
+without selection is trivial, since both the distances space and the
+selection occur in the same transformed space. However, it's useful to
+compare randomly subsampled sets against a selected set of objects. This
+is intended to identify overdispersion or overclustering (see
+\code{\link{enve.TRIBStest}}) of a subset against the entire collection of objects
+with minimum impact of sampling biases. This object can be produced by
+\code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{distance}}{\code{(numeric)} Centrality measurement of the distances 
+between the selected objects (without subsampling).}
+
+\item{\code{points}}{\code{(matrix)}    Position of the different objects in distance
+space.}
+
+\item{\code{distances}}{\code{(matrix)} Subsampled distances, where the rows are 
+replicates and the columns are subsampling levels.}
+
+\item{\code{spaceSize}}{\code{(numeric)} Number of objects.}
+
+\item{\code{selSize}}{\code{(numeric)} Number of selected objects.}
+
+\item{\code{dimensions}}{\code{(numeric)} Number of dimensions in the distance space.}
+
+\item{\code{subsamples}}{\code{(numeric)} Subsampling levels (as fractions, from 
+0 to 1).}
+
+\item{\code{call}}{\code{(call)} Call producing this object.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{enve.TRIBS.merge}
+\alias{enve.TRIBS.merge}
+\title{Enveomics: TRIBS Merge}
+\usage{
+enve.TRIBS.merge(x, y)
+}
+\arguments{
+\item{x}{First \code{\link{enve.TRIBS}} object.}
+
+\item{y}{Second \code{\link{enve.TRIBS}} object.}
+}
+\value{
+Returns an \code{\link{enve.TRIBS}} object.
+}
+\description{
+Merges two \code{\link{enve.TRIBS}} objects generated from the same objects at
+different subsampling levels.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\docType{class}
+\name{enve.TRIBStest-class}
+\alias{enve.TRIBStest-class}
+\alias{enve.TRIBStest}
+\title{Enveomics: TRIBS Test S4 Class}
+\description{
+Test of significance of overclustering or overdispersion in a selected
+set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}). This
+object can be produced by \code{\link{enve.tribs.test}} and supports S4 methods
+\code{plot} and \code{summary}.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{pval.gt}}{\code{(numeric)}
+P-value for the overdispersion test.}
+
+\item{\code{pval.lt}}{\code{(numeric)}
+P-value for the overclustering test.}
+
+\item{\code{all.dist}}{\code{(numeric)}
+Empiric PDF of distances for the entire dataset (subsampled at selection
+size).}
+
+\item{\code{sel.dist}}{\code{(numeric)}
+Empiric PDF of distances for the selected objects (without subsampling).}
+
+\item{\code{diff.dist}}{\code{(numeric)}
+Empiric PDF of the difference between \code{all.dist} and \code{sel.dist}. 
+The p-values are estimating by comparing areas in this PDF greater than and
+lesser than zero.}
+
+\item{\code{dist.mids}}{\code{(numeric)}
+Midpoints of the empiric PDFs of distances.}
+
+\item{\code{diff.mids}}{\code{(numeric)}
+Midpoints of the empiric PDF of difference of distances.}
+
+\item{\code{call}}{\code{(call)}
+Call producing this object.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoprune.R
+\name{enve.__prune.iter}
+\alias{enve.__prune.iter}
+\title{Enveomics: Prune Iter (Internal Function)}
+\usage{
+enve.__prune.iter(t, dist, min_dist, quiet)
+}
+\arguments{
+\item{t}{A \strong{phylo} object}
+
+\item{dist}{Cophenetic distance matrix}
+
+\item{min_dist}{Minimum distance}
+
+\item{quiet}{If running quietly}
+}
+\description{
+Internal function for \code{\link{enve.prune.dist}}.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoprune.R
+\name{enve.__prune.reduce}
+\alias{enve.__prune.reduce}
+\title{Enveomics: Prune Reduce (Internal Function)}
+\usage{
+enve.__prune.reduce(t, nodes, min_dist, quiet)
+}
+\arguments{
+\item{t}{A \strong{phylo} object}
+
+\item{nodes}{Vector of nodes}
+
+\item{min_dist}{Minimum distance}
+
+\item{quiet}{If running quietly}
+}
+\description{
+Internal function for \code{\link{enve.prune.dist}}.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{enve.__tribs}
+\alias{enve.__tribs}
+\title{Enveomics: TRIBS - Internal Ancillary Function}
+\usage{
+enve.__tribs(
+  rep,
+  frx,
+  selection,
+  dimensions,
+  dots,
+  dist.method,
+  summary.fx,
+  dist
+)
+}
+\arguments{
+\item{rep}{Replicates}
+
+\item{frx}{Fraction}
+
+\item{selection}{Selection}
+
+\item{dimensions}{Dimensions}
+
+\item{dots}{Sampling points}
+
+\item{dist.method}{Distance method}
+
+\item{summary.fx}{Summary function}
+
+\item{dist}{Distance}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.tribs}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}