miga-base 0.7.26.0 → 1.0.0.1

data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\docType{class}
+\name{enve.RecPlot2.Peak-class}
+\alias{enve.RecPlot2.Peak-class}
+\alias{enve.RecPlot2.Peak}
+\title{Enveomics: Recruitment Plot (2) Peak - S4 Class}
+\description{
+Enve-omics representation of a peak in the sequencing depth histogram
+of a Recruitment plot (see \code{\link{enve.recplot2.findPeaks}}).
+}
+\section{Slots}{
+
+\describe{
+\item{\code{dist}}{\code{(character)}
+Distribution of the peak. Currently supported: \code{norm} (normal) and \code{sn}
+(skew-normal).}
+
+\item{\code{values}}{\code{(numeric)}
+Sequencing depth values predicted to conform the peak.}
+
+\item{\code{values.res}}{\code{(numeric)}
+Sequencing depth values not explained by this or previously identified
+peaks.}
+
+\item{\code{mode}}{\code{(numeric)}
+Seed-value of mode anchoring the peak.}
+
+\item{\code{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.}
+
+\item{\code{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.}
+
+\item{\code{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).}
+
+\item{\code{err.res}}{\code{(numeric)}
+Error left after adding the peak (mower) or log-likelihood (em or emauto).}
+
+\item{\code{merge.logdist}}{\code{(numeric)}
+Attempted \code{merge.logdist} parameter.}
+
+\item{\code{seq.depth}}{\code{(numeric)}
+Best estimate available for the sequencing depth of the peak (centrality).}
+
+\item{\code{log}}{\code{(logical)}
+Indicates if the estimation was performed in natural logarithm space.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.seqdepth}
+\alias{enve.recplot2.seqdepth}
+\title{Enveomics: Recruitment Plot (2) Sequencing Depth}
+\usage{
+enve.recplot2.seqdepth(x, sel, low.identity = FALSE)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object.}
+
+\item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
+passed, it returns the sequencing depth of all windows.}
+
+\item{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.}
+}
+\value{
+Returns a numeric vector of sequencing depths (in bp/bp).
+}
+\description{
+Calculate the sequencing depth of the given window(s).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.windowDepthThreshold}
+\alias{enve.recplot2.windowDepthThreshold}
+\title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
+\usage{
+enve.recplot2.windowDepthThreshold(
+  rp,
+  peak,
+  lower.tail = TRUE,
+  significance = 0.05
+)
+}
+\arguments{
+\item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}
+
+\item{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}}).}
+
+\item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
+sequencing depth.}
+
+\item{significance}{Significance threshold (alpha) to select windows.}
+}
+\value{
+Returns a float. The units are depth if the peaks were estimated in
+linear scale, or log-depth otherwise (\code{peak$log}).
+}
+\description{
+Identifies the threshold below which windows should be identified as
+variable or absent.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.selvector}
+\alias{enve.selvector}
+\title{Enveomics: Selection vector}
+\usage{
+enve.selvector(sel, dim.names)
+}
+\arguments{
+\item{sel}{A vector of numbers, characters, or booleans.}
+
+\item{dim.names}{A vector of names from which to select.}
+}
+\value{
+Returns a logical vector with the same length as \code{dim.name}.
+}
+\description{
+Normalizes a selection vector \code{sel} to a logical vector with indexes
+from \code{dim.names}.
+}
+\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}
+\usage{
+enve.tribs(
+  dist,
+  selection = labels(dist),
+  replicates = 1000,
+  summary.fx = median,
+  dist.method = "euclidean",
+  subsamples = seq(0, 1, by = 0.01),
+  dimensions = ceiling(length(selection) * 0.05),
+  metaMDS.opts = list(),
+  threads = 2,
+  verbosity = 1,
+  points,
+  pre.tribs
+)
+}
+\arguments{
+\item{dist}{Distances as a \code{dist} object.}
+
+\item{selection}{Objects to include in the subsample. By default, all objects are
+selected.}
+
+\item{replicates}{Number of replications per point.}
+
+\item{summary.fx}{Function to summarize the distance distributions in a given replicate. By
+default, the median distance is estimated.}
+
+\item{dist.method}{Distance method between random points and samples in the transformed
+space. See \code{dist}.}
+
+\item{subsamples}{Subsampling fractions.}
+
+\item{dimensions}{Dimensions to use in the NMDS. By default, 5\% of the selection length.}
+
+\item{metaMDS.opts}{Any additional options to pass to metaMDS, as \code{list}.}
+
+\item{threads}{Number of threads to use.}
+
+\item{verbosity}{Verbosity. Use 0 to run quietly, increase for additional information.}
+
+\item{points}{Optional. If passed, the MDS step is skipped and this object is used
+instead.  It can be the \code{$points} slot of class \code{metaMDS} 
+(from \code{vegan}).
+It must be a matrix or matrix-coercible object, with samples as rows and
+dimensions as columns.}
+
+\item{pre.tribs}{Optional. If passed, the points are recovered from this object (except if
+\code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object 
+estimated on the same objects (the selection is unimportant).}
+}
+\value{
+Returns an \code{\link{enve.TRIBS}} object.
+}
+\description{
+Subsample any objects in "distance space" to reduce the effect of
+sample-clustering. This function was originally designed to subsample
+genomes in "phylogenetic distance space", a clear case of strong
+clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
+Weigand.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{enve.tribs.test}
+\alias{enve.tribs.test}
+\title{Enveomics: TRIBS Test}
+\usage{
+enve.tribs.test(dist, selection, bins = 50, ...)
+}
+\arguments{
+\item{dist}{Distances as \code{dist} object.}
+
+\item{selection}{Selection defining the subset.}
+
+\item{bins}{Number of bins to evaluate in the range of distances.}
+
+\item{...}{Any other parameters supported by \code{\link{enve.tribs}}, 
+except \code{subsamples}.}
+}
+\value{
+Returns an \code{\link{enve.TRIBStest}} object.
+}
+\description{
+Estimates the empirical difference between all the distances in a set of
+objects and a subset, together with its statistical significance.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.truncate}
+\alias{enve.truncate}
+\title{Enveomics: Truncate}
+\usage{
+enve.truncate(x, f = 0.95, FUN = mean)
+}
+\arguments{
+\item{x}{A vector of numbers.}
+
+\item{f}{The fraction of values to retain.}
+
+\item{FUN}{Summary function to apply to the vectors. To obtain the 
+truncated vector itself, use \code{c}.}
+}
+\value{
+Returns the summary \code{(FUN)} of the truncated vector.
+}
+\description{
+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.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/growth.curves.Rd

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+
+\name{growth.curves}
+\docType{data}
+\alias{growth.curves}
+\title{Bacterial growth curves for three Escherichia coli mutants}
+\description{
+  This data set provides time (first column) and three triplicated growth
+  curves as optical density at 600nm (OD_600nm) for different mutants of E.
+  coli.
+}
+\usage{growth.curves}
+\format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
+\keyword{datasets}
+

data/utils/enveomics/enveomics.R/man/phyla.counts.Rd

@@ -0,0 +1,13 @@
+
+\name{phyla.counts}
+\docType{data}
+\alias{phyla.counts}
+\title{Counts of microbial phyla in four sites}
+\description{
+  This data set gives the counts of phyla in three different
+  sites.
+}
+\usage{phyla.counts}
+\format{A data frame with 9 rows (phyla) and 4 rows (sites).}
+\keyword{datasets}
+

data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd

@@ -0,0 +1,78 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{plot.enve.GrowthCurve}
+\alias{plot.enve.GrowthCurve}
+\title{Enveomics: Plot of Growth Curve}
+\usage{
+\method{plot}{enve.GrowthCurve}(
+  x,
+  col,
+  pt.alpha = 0.9,
+  ln.alpha = 1,
+  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{
+\item{x}{An \code{\link{enve.GrowthCurve}} object to plot.}
+
+\item{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.}
+
+\item{pt.alpha}{Color alpha for the observed data points, using \code{col}
+as a base.}
+
+\item{ln.alpha}{Color alpha for the fitted growth curve, using \code{col}
+as a base.}
+
+\item{ln.lwd}{Line width for the fitted curve.}
+
+\item{ln.lty}{Line type for the fitted curve.}
+
+\item{band.alpha}{Color alpha for the confidence interval band of the 
+fitted growth curve, using \code{col} as a base.}
+
+\item{band.density}{Density of the filling pattern in the interval band.
+If \code{NULL}, a solid color is used.}
+
+\item{band.angle}{Angle of the density filling pattern in the interval 
+band. Ignored if \code{band.density} is \code{NULL}.}
+
+\item{xp.alpha}{Color alpha for the line connecting individual experiments,
+using \code{col} as a base.}
+
+\item{xp.lwd}{Width of line for the experiments.}
+
+\item{xp.lty}{Type of line for the experiments.}
+
+\item{pch}{Point character for observed data points.}
+
+\item{new}{Should a new plot be generated? If \code{FALSE}, the existing
+canvas is used.}
+
+\item{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}.}
+
+\item{add.params}{Should the legend include the parameters of the fitted 
+model?}
+
+\item{...}{Any other graphic parameters.}
+}
+\description{
+Plots an \code{\link{enve.GrowthCurve}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBS}
+\alias{plot.enve.TRIBS}
+\title{Enveomics: TRIBS Plot}
+\usage{
+\method{plot}{enve.TRIBS}(
+  x,
+  new = TRUE,
+  type = c("boxplot", "points"),
+  col = "#00000044",
+  pt.cex = 1/2,
+  pt.pch = 19,
+  pt.col = col,
+  ln.col = col,
+  ...
+)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBS}} object to plot.}
+
+\item{new}{Should a new canvas be drawn?}
+
+\item{type}{Type of plot. The \strong{points} plot shows all the replicates, the 
+\strong{boxplot} plot represents the values found by
+\code{\link[grDevices]{boxplot.stats}}.
+as areas, and plots the outliers as points.}
+
+\item{col}{Color of the areas and/or the points.}
+
+\item{pt.cex}{Size of the points.}
+
+\item{pt.pch}{Points character.}
+
+\item{pt.col}{Color of the points.}
+
+\item{ln.col}{Color of the lines.}
+
+\item{...}{Any additional parameters supported by \code{plot}.}
+}
+\description{
+Plot an \code{\link{enve.TRIBS}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tribs.R
+\name{plot.enve.TRIBStest}
+\alias{plot.enve.TRIBStest}
+\title{Enveomics: TRIBS Plot Test}
+\usage{
+\method{plot}{enve.TRIBStest}(
+  x,
+  type = c("overlap", "difference"),
+  col = "#00000044",
+  col1 = col,
+  col2 = "#44001144",
+  ylab = "Probability",
+  xlim = range(attr(x, "dist.mids")),
+  ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))),
+  ...
+)
+}
+\arguments{
+\item{x}{\code{\link{enve.TRIBStest}} object to plot.}
+
+\item{type}{What to plot. \code{overlap} generates a plot of the two contrasting empirical
+PDFs (to compare against each other), \code{difference} produces a plot of the
+differences between the empirical PDFs (to compare against zero).}
+
+\item{col}{Main color of the plot if type=\code{difference}.}
+
+\item{col1}{First color of the plot if type=\code{overlap}.}
+
+\item{col2}{Second color of the plot if type=\code{overlap}.}
+
+\item{ylab}{Y-axis label.}
+
+\item{xlim}{X-axis limits.}
+
+\item{ylim}{Y-axis limits.}
+
+\item{...}{Any other graphical arguments.}
+}
+\description{
+Plots an \code{\link{enve.TRIBStest}} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}