miga-base 0.7.26.0 → 1.0.0.1

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

@@ -0,0 +1,103 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/barplot.R
+\name{enve.barplot}
+\alias{enve.barplot}
+\title{Enveomics: Barplot}
+\usage{
+enve.barplot(
+  x,
+  sizes,
+  top = 25,
+  colors.per.group = 9,
+  bars.width = 4,
+  legend.ncol = 1,
+  other.col = "#000000",
+  add.trend = FALSE,
+  organic.trend = FALSE,
+  sort.by = median,
+  min.report = 101,
+  order = NULL,
+  col,
+  ...
+)
+}
+\arguments{
+\item{x}{Can be either the input data or the path to the file containing 
+the table. 
+\itemize{
+   \item{If it contains the data, it must be a data frame or an
+   object coercible to a data frame.} 
+   \item{If it is a path, it must point to a
+   tab-delimited file containing a header (first row) and row names 
+   (first column).}
+   }}
+
+\item{sizes}{A numeric vector containing the real size of the samples
+(columns) in the same order of the input table. If set, the values are
+assumed to be 100\%. Otherwise, the sum of the columns is used.}
+
+\item{top}{Maximum number of categories to display. Any additional
+categories will be listed as "Others".}
+
+\item{colors.per.group}{Number of categories in the first two saturation 
+groups of colors. The third group contains the remaining categories if 
+needed.}
+
+\item{bars.width}{Width of the barplot with respect to the legend.}
+
+\item{legend.ncol}{Number of columns in the legend.}
+
+\item{other.col}{Color of the "Others" category.}
+
+\item{add.trend}{Controls if semi-transparent areas are to be plotted
+between the bars to connect the regions (trend regions).}
+
+\item{organic.trend}{Controls if the trend regions are to be smoothed 
+(curves). By default, trend regions have straight edges. If \code{TRUE}, 
+forces \code{add.trend=TRUE}.}
+
+\item{sort.by}{Any function that takes a numeric vector and returns a
+numeric scalar. This function is applied to each row, and the resulting
+values are used to sort the rows (decreasingly). Good options include: 
+\code{sd, min, max, mean, median}.}
+
+\item{min.report}{Minimum percentage to report the value in the plot.
+Any value above 100 indicates that no values are to be reported.}
+
+\item{order}{Controls how the rows should be ordered. 
+\itemize{
+   \item{If \code{NULL} 
+   (default), \code{sort.by} is applied per row and the results are 
+   sorted decreasingly.}
+   \item{If \code{NA}, no sorting is performed, i.e., the original
+   order is respected.}
+   \item{If a vector is provided, it is assumed to be the 
+   custom order to be used (either by numeric index or by row names).}
+   }}
+
+\item{col}{Colors to use. If provided, overrides the variables \code{top}
+and \code{colors.per.group}, but \code{other.col} is still used if the 
+vector is insufficient for all the rows. An additional palette is available with
+\code{col='coto'} (contributed by Luis (Coto) Orellana).}
+
+\item{...}{Any additional parameters to be passed to barplot.}
+}
+\description{
+Creates nice barplots from tab-delimited tables.
+}
+\examples{
+# Load data
+data("phyla.counts", package="enveomics.R", envir=environment())
+# Create a barplot sorted by variance with organic trends
+enve.barplot(
+    phyla.counts, # Counts of phyla in four sites
+    sizes=c(250,100,75,200), # Total sizes of the datasets of each site
+    bars.width=2, # Decrease from default, so the names are fully displayed
+    organic.trend=TRUE, # Nice curvy background
+    sort.by=var # Sort by variance across sites
+    )
+
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

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+% 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

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+% 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 +1,45 @@
+% 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 +1,44 @@
+% 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 +1,47 @@
+% 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 +1,75 @@
+% 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.prefscore.Rd

@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prefscore.R
+\name{enve.prefscore}
+\alias{enve.prefscore}
+\title{Enveomics: Pref Score}
+\usage{
+enve.prefscore(
+  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),
+  ...
+)
+}
+\arguments{
+\item{x}{Occupancy matrix (logical or numeric binary) with species as rows and samples
+as columns}
+
+\item{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.}
+
+\item{ignore}{Vector indicating species to ignore. It can be any selection vector with
+respect to the rows in \code{x} (see \code{set}).}
+
+\item{signif.thr}{Absolute value of the significance threshold}
+
+\item{plot}{Indicates if a plot should be generated}
+
+\item{col.above}{Color for points significantly above zero}
+
+\item{col.equal}{Color for points not significantly different from zero}
+
+\item{col.below}{Color for points significantly below zero}
+
+\item{...}{Any additional parameters supported by \code{plot}}
+}
+\value{
+Returns a named vector of preference scores.
+}
+\description{
+Estimate preference score of species based on occupancy in biased sample sets
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}