miga-base 0.4.3.0 → 0.5.0.0

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

@@ -1,33 +1,32 @@
-\name{enve.__tribs}
-\alias{enve.__tribs}
-\title{enve   tribs}
-\description{Internal ancilliary function (see `enve.tribs`).}
-\usage{enve.__tribs(rep, frx, selection, dimensions, dots, dist.method, 
-    summary.fx, dist)}
-\arguments{
-  \item{rep}{
-}
-  \item{frx}{
-}
-  \item{selection}{
-}
-  \item{dimensions}{
-}
-  \item{dots}{
-}
-  \item{dist.method}{
-}
-  \item{summary.fx}{
-}
-  \item{dist}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% 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]
+}

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

@@ -1,64 +1,91 @@
-\name{enve.barplot}
-\alias{enve.barplot}
-\title{enve barplot}
-\description{Creates nice barplots from tab-delimited tables}
-\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. If it contains the data, it must be a data frame or an object
-coercible to data frame. If it is a path, it must point to a
-tab-delimited file containing 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 TRUE, forces 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: 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. If NULL (default), sort.by is
-applied per row and the results are sorted decreasingly. If NA, no
-sorting is performed, i.e., the original order is respected. 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 `top` and
-`colors.per.group`, but `other.col` is still used if the vector is
-insufficient for all the rows. An additional palette is available with
-col='coto' (contributed by Luis (Coto) Orellana).}
-  \item{\dots}{Any additional parameters to be passed to `barplot`.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-\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
-)
-}
+% 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

@@ -1,37 +1,57 @@
-\name{enve.cliopts}
-\alias{enve.cliopts}
-\title{enve cliopts}
-\description{Generates nicely formatted command-line interfaces for
-functions (_closures_ only).}
-\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 _positional_ arguments passed to parse_args
-(package:optparse).}
-  \item{usage}{(Optional) Usage passed to OptionParser (package:optparse).}
-  \item{mandatory}{Mandatory arguments.}
-  \item{vectorize}{Arguments of the function to vectorize (comma-delimited). If numeric,
-use also `number`.}
-  \item{ignore}{Arguments of the function to ignore.}
-  \item{number}{Force these arguments as numerics. Useful for numeric
-vectors (see `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 `rd` is ignored for arguments
-present in this list.}
-  \item{p_desc}{Description of the function. Help from `rd` is ignored for the
-function description unless this value is an empty string.}
-}
-
-\value{Returns a `list` with keys: `options`, a named list with the values for
-the function's arguments; and `args`, a vector with zero or more strings
-containing the positional arguments.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% 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

@@ -1,19 +1,24 @@
-\name{enve.col.alpha}
-\alias{enve.col.alpha}
-\title{enve col alpha}
-\description{Modify alpha in a color (or vector of colors).}
-\usage{enve.col.alpha(col, alpha = 1/2)}
-\arguments{
-  \item{col}{Color or vector of colors. It can be any value supported by `col2rgb`, 
-such as 'darkred' or '#009988'.}
-  \item{alpha}{Alpha value to add to the color, from 0 to 1.}
-}
-
-\value{Returns a color or a vector of colors in hex notation including alpha.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% 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

@@ -1,18 +1,19 @@
-\name{enve.col2alpha}
-\alias{enve.col2alpha}
-\title{enve col2alpha}
-\description{Takes a vector of colors and sets the 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).}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% 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

@@ -1,26 +1,39 @@
-\name{enve.df2dist}
-\alias{enve.df2dist}
-\title{enve df2dist}
-\description{Transform a dataframe (or coercible object, like a table) into a `dist` object.}
-\usage{enve.df2dist(x, obj1.index = 1, obj2.index = 2, dist.index = 3, 
-    default.d = NA, max.sim = 0)}
-\arguments{
-  \item{x}{A table (or coercible object) with at least three columns: (1) ID of the object 1,
-(2) ID of the object 2, and (3) 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: distance = (max.sim - values)/max.sim.}
-}
-
-\value{Returns a `dist` object.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% 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]
+}