miga-base 0.7.26.0 → 0.7.26.1

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

@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cliopts.R
+\name{enve.cliopts}
+\alias{enve.cliopts}
+\title{Enveomics: Cliopts}
+\usage{
+enve.cliopts(fx, rd_file, positional_arguments, usage, mandatory = c(),
+  vectorize = c(), ignore = c(), number = c(), defaults = list(),
+  o_desc = list(), p_desc = "")
+}
+\arguments{
+\item{fx}{Function for which the interface should be generated.}
+
+\item{rd_file}{(Optional) .Rd file with the standard documentation of 
+the function.}
+
+\item{positional_arguments}{(Optional) Number of \strong{positional} 
+arguments passed to \code{\link[optparse]{parse_args}} 
+(package: \pkg{optparse}).}
+
+\item{usage}{(Optional) Usage passed to \code{\link[optparse]{OptionParser}} 
+(package: \pkg{optparse}).}
+
+\item{mandatory}{Mandatory arguments.}
+
+\item{vectorize}{Arguments of the function to vectorize (comma-delimited).
+If numeric, use also \code{number}.}
+
+\item{ignore}{Arguments of the function to ignore.}
+
+\item{number}{Force these arguments as numerics. Useful for numeric
+vectors (see \code{vectorize}) or arguments with no defaults.}
+
+\item{defaults}{Defaults to use instead of the ones provided by the 
+formals.}
+
+\item{o_desc}{Descriptions of the options. Help from \code{rd} is ignored
+for arguments present in this list.}
+
+\item{p_desc}{Description Description of the function. Help from \code{rd} 
+is ignored for the function description unless this value is an empty string.}
+}
+\value{
+Returns a list with keys: 
+\itemize{
+   \item{\code{options}, a named list with the values for the function's 
+   arguments} 
+   \item{\code{args}, a vector with zero or more strings containing the
+   positional arguments}}
+}
+\description{
+Generates nicely formatted command-line interfaces for functions 
+(\strong{closures} only).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.col.alpha}
+\alias{enve.col.alpha}
+\title{Enveomics: Color Alpha}
+\usage{
+enve.col.alpha(col, alpha = 1/2)
+}
+\arguments{
+\item{col}{Color or vector of colors. It can be any value supported by 
+\code{\link[grDevices]{col2rgb}}, such as \code{darkred} or \code{#009988}.}
+
+\item{alpha}{Alpha value to add to the color, from 0 to 1.}
+}
+\value{
+Returns a color or a vector of colors in \emph{hex} notation, 
+including \code{alpha}.
+}
+\description{
+Modify alpha in a color (or vector of colors).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{enve.col2alpha}
+\alias{enve.col2alpha}
+\title{Enveomics: Color to Alpha}
+\usage{
+enve.col2alpha(x, alpha)
+}
+\arguments{
+\item{x}{A vector of any value base colors.}
+
+\item{alpha}{Alpha level to set (in the 0-1 range).}
+}
+\description{
+Takes a vector of colors and sets the alpha.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd

@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/df2dist.R
+\name{enve.df2dist}
+\alias{enve.df2dist}
+\title{Enveomics: Data Frame to Dist}
+\usage{
+enve.df2dist(x, obj1.index = 1, obj2.index = 2, dist.index = 3,
+  default.d = NA, max.sim = 0)
+}
+\arguments{
+\item{x}{A dataframe (or coercible object) with at least three columns:
+\enumerate{
+   \item ID of the object 1, 
+   \item ID of the object 2, and 
+   \item distance between the two objects.}}
+
+\item{obj1.index}{Index of the column containing the ID of the object 1.}
+
+\item{obj2.index}{Index of the column containing the ID of the object 2.}
+
+\item{dist.index}{Index of the column containing the distance.}
+
+\item{default.d}{Default value (for missing values).}
+
+\item{max.sim}{If not zero, assumes that the values are similarity
+(not distance) and this is the maximum similarity (corresponding to 
+distance 0). Applies transformation: 
+\eqn{distance = (max.sim - values)/max.sim.}}
+}
+\value{
+Returns a \strong{dist} object.
+}
+\description{
+Transform a dataframe (or coercible object, like a table) into a
+\strong{dist} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/df2dist.R
+\name{enve.df2dist.group}
+\alias{enve.df2dist.group}
+\title{Enveomics: Data Frame to Dist (Group)}
+\usage{
+enve.df2dist.group(x, obj1.index = 1, obj2.index = 2, dist.index = 3,
+  summary = median, empty.rm = TRUE)
+}
+\arguments{
+\item{x}{A dataframe (or coercible object) with at least three columns:
+\enumerate{
+   \item ID of the object 1, 
+   \item ID of the object 2, and 
+   \item distance between the two objects.}}
+
+\item{obj1.index}{Index of the column containing the ID of the object 1.}
+
+\item{obj2.index}{Index of the column containing the ID of the object 2.}
+
+\item{dist.index}{Index of the column containing the distance.}
+
+\item{summary}{Function summarizing the different distances between the 
+two objects.}
+
+\item{empty.rm}{Remove rows with empty or \code{NA} groups.}
+}
+\value{
+Returns a \strong{dist} object.
+}
+\description{
+Transform a dataframe (or coercible object, like a table) into a 
+\strong{dist} object, where there are 1 or more distances between each pair 
+of objects.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd

@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/df2dist.R
+\name{enve.df2dist.list}
+\alias{enve.df2dist.list}
+\title{Enveomics: Data Frame to Dist (List)}
+\usage{
+enve.df2dist.list(x, groups, obj1.index = 1, obj2.index = 2,
+  dist.index = 3, empty.rm = TRUE, ...)
+}
+\arguments{
+\item{x}{A dataframe (or coercible object) with at least three columns:
+\enumerate{
+   \item ID of the object 1, 
+   \item ID of the object 2, and 
+   \item distance between the two objects.}}
+
+\item{groups}{Named array where the IDs correspond to the object IDs,
+and the values correspond to the group.}
+
+\item{obj1.index}{Index of the column containing the ID of the object 1.}
+
+\item{obj2.index}{Index of the column containing the ID of the object 2.}
+
+\item{dist.index}{Index of the column containing the distance.}
+
+\item{empty.rm}{Remove incomplete matrices.}
+
+\item{...}{Any other parameters supported by
+\code{\link{enve.df2dist.group}}.}
+}
+\value{
+Returns a \strong{list} of \strong{dist} objects.
+}
+\description{
+Transform a dataframe (or coercible object, like a table)
+into a \strong{dist} object.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/growthcurve.R
+\name{enve.growthcurve}
+\alias{enve.growthcurve}
+\title{Enveomics: Growth Curve}
+\usage{
+enve.growthcurve(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{
+\item{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.}
+
+\item{times}{Vector with the times at which each row was taken. By default,
+all rows are assumed to be part of constantly periodic measurements.}
+
+\item{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.}
+
+\item{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.}
+
+\item{new.times}{Values of time for the fitted curve.}
+
+\item{level}{Confidence (or prediction) interval in the fitted curve.}
+
+\item{interval}{Type of interval to be calculated for the fitted curve.}
+
+\item{plot}{Should the growth curve be plotted?}
+
+\item{FUN}{Function to fit. By default: logistic growth with paramenters
+\code{K}: carrying capacity, 
+\code{r}: intrinsic growth rate, and
+\code{P0}: Initial population.}
+
+\item{nls.opt}{Any additional options passed to \code{nls}.}
+
+\item{...}{Any additional parameters to be passed to 
+\code{plot.enve.GrowthCurve}.}
+}
+\value{
+Returns an \code{\link{enve.GrowthCurve}} object.
+}
+\description{
+Calculates growth curves using the logistic growth function.
+}
+\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))
+
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd

@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/autoprune.R
+\name{enve.prune.dist}
+\alias{enve.prune.dist}
+\title{Enveomics: Prune Dist}
+\usage{
+enve.prune.dist(t, dist.quantile = 0.25, min_dist, quiet = FALSE,
+  max_iters = 100, min_nodes_random = 40000, random_nodes_frx = 1)
+}
+\arguments{
+\item{t}{A \strong{phylo} object or a path to the Newick file.}
+
+\item{dist.quantile}{The quantile of edge lengths.}
+
+\item{min_dist}{The minimum distance to allow between two tips.
+If not set, \code{dist.quantile} is used instead to calculate it.}
+
+\item{quiet}{Boolean indicating if the function must run without output.}
+
+\item{max_iters}{Maximum number of iterations.}
+
+\item{min_nodes_random}{Minimum number of nodes to trigger \emph{tip-pairs} nodes sampling. 
+This sampling is less reproducible and more computationally expensive,
+but it's the only solution if the cophenetic matrix exceeds \code{2^31-1} 
+entries; above that, it cannot be represented in R.}
+
+\item{random_nodes_frx}{Fraction of the nodes to be sampled if more than \code{min_nodes_random}.}
+}
+\value{
+Returns a pruned \strong{phylo} object.
+}
+\description{
+Automatically prunes a tree, to keep representatives of each clade.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -0,0 +1,122 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot.R
+\name{enve.recplot}
+\alias{enve.recplot}
+\title{Enveomics: Recruitment Plots}
+\usage{
+enve.recplot(prefix, id.min = NULL, id.max = NULL, id.binsize = NULL,
+  id.splines = 0, id.metric = "id", id.summary = "sum",
+  pos.min = 1, pos.max = NULL, pos.binsize = 1000, pos.splines = 0,
+  rec.col1 = "white", rec.col2 = "black", main = NULL,
+  contig.col = grey(0.85), ret.recplot = FALSE, ret.hist = FALSE,
+  ret.mode = FALSE, id.cutoff = NULL, verbose = TRUE, ...)
+}
+\arguments{
+\item{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.}
+
+\item{id.min}{Minimum identity to be considered. By default, the minimum detected
+identity. This value is a percentage.}
+
+\item{id.max}{Maximum identity to be considered. By default, 100\%.}
+
+\item{id.binsize}{Size of the identity bins (vertical histograms). By default, 0.1 for
+identity metrics and 5 for bit score.}
+
+\item{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.}
+
+\item{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"}}
+
+\item{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.}
+
+\item{pos.min}{Minimum (leftmost) position in the reference (concatenated) genome (in bp).}
+
+\item{pos.max}{Maximum (rightmost) position in the reference (concatenated) genome (in bp).
+By default: Length of the genome.}
+
+\item{pos.binsize}{Size of the position bins (horizontal histograms) in bp.}
+
+\item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero (0) for no splines.
+If non-zero, requires the stats package.}
+
+\item{rec.col1}{Lightest color in the recruitment plot.}
+
+\item{rec.col2}{Darkest color in the recruitment plot.}
+
+\item{main}{Title of the plot.}
+
+\item{contig.col}{Color of the Contig boundaries. Set to \code{NA} to ignore Contig boundaries.}
+
+\item{ret.recplot}{Indicates if the matrix of the recruitment plot is to be returned.}
+
+\item{ret.hist}{Ignored, for backwards compatibility.}
+
+\item{ret.mode}{Indicates if the mode of the identity is to be computed. It requires the 
+\pkg{modeest} package.}
+
+\item{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.}
+
+\item{verbose}{Indicates if the function should report the advance.}
+
+\item{...}{Any additional graphic parameters to be passed to plot for all panels except the
+recruitment plot (lower-left).}
+}
+\value{
+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.}}
+}
+\description{
+Produces recruitment plots provided that BlastTab.catsbj.pl has
+been previously executed. Requires the \pkg{gplots} library.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}