miga-base 0.3.0.0 → 0.3.0.1

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

@@ -0,0 +1,30 @@
+\name{enve.GrowthCurve-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{enve.GrowthCurve-class}
+\alias{enve.GrowthCurve}
+%% \alias{$}
+
+\title{enve.GrowthCurve S4 class}
+\description{Enve-omics representation of fitted growth curves.}
+\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.GrowthCurve ...)}}
+\section{Slots}{
+  \describe{
+    \item{\code{design}:}{(\code{array}) Experimental design of the experiment.}
+    \item{\code{models}:}{(\code{list}) Fitted growth curve models.}
+    \item{\code{predict}:}{(\code{list}) Fitted growth curve values.}
+    \item{\code{call}:}{(\code{call}) Call producing this object.}
+  }
+}
+\section{Methods}{
+  \describe{
+    \item{$}{\code{signature(x = "enve.GrowthCurve")}: ... }
+	 }
+}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,43 @@
+\name{enve.TRIBS-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{enve.TRIBS-class}
+\alias{enve.TRIBS}
+
+\title{enve.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
+`enve.TRIBStest`) of a subset against the entire collection of objects
+with minimum impact of sampling biases. This object can be produced by
+`enve.tribs` and supports S4 methods `plot` and `summary`.}
+\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.TRIBS ...)}}
+\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.}
+  }
+}
+\section{Methods}{
+No methods defined with class "enve.TRIBS" in the signature.
+}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,19 @@
+\name{enve.TRIBS.merge}
+\alias{enve.TRIBS.merge}
+\title{enve TRIBS merge}
+\description{Merges two `enve.TRIBS` objects generated from the same objects at
+different subsampling levels.}
+\usage{enve.TRIBS.merge(x, y)}
+\arguments{
+  \item{x}{First `enve.TRIBS` object.}
+  \item{y}{Second `enve.TRIBS` object.}
+}
+
+\value{Returns an `enve.TRIBS` object.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,37 @@
+\name{enve.TRIBStest-class}
+\Rdversion{1.1}
+\docType{class}
+\alias{enve.TRIBStest-class}
+\alias{enve.TRIBStest}
+
+\title{enve.TRIBStest S4 class}
+\description{Test of significance of overclustering or overdispersion in a selected
+set of objects with respect to the entire set (see `enve.TRIBS`). This
+object can be produced by `enve.tribs.test` and supports S4 methods
+`plot` and `summary`.}
+\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.TRIBStest ...)}}
+\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 `all.dist` and `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.}
+  }
+}
+\section{Methods}{
+No methods defined with class "enve.TRIBStest" in the signature.
+}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,24 @@
+\name{enve.__prune.iter}
+\alias{enve.__prune.iter}
+\title{enve   prune iter}
+\description{Internal function for enve.prune.dist}
+\usage{enve.__prune.iter(t, dist, min_dist, quiet)}
+\arguments{
+  \item{t}{
+}
+  \item{dist}{
+}
+  \item{min_dist}{
+}
+  \item{quiet}{
+}
+}
+
+
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,24 @@
+\name{enve.__prune.reduce}
+\alias{enve.__prune.reduce}
+\title{enve   prune reduce}
+\description{Internal function for enve.prune.dist}
+\usage{enve.__prune.reduce(t, nodes, min_dist, quiet)}
+\arguments{
+  \item{t}{
+}
+  \item{nodes}{
+}
+  \item{min_dist}{
+}
+  \item{quiet}{
+}
+}
+
+
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,33 @@
+\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]}
+
+
+
+
+

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

@@ -0,0 +1,64 @@
+\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
+)
+}

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

@@ -0,0 +1,37 @@
+\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]}
+
+
+
+
+

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

@@ -0,0 +1,19 @@
+\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]}
+
+
+
+
+

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

@@ -0,0 +1,18 @@
+\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]}
+
+
+
+
+

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

@@ -0,0 +1,26 @@
+\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]}
+
+
+
+
+

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

@@ -0,0 +1,25 @@
+\name{enve.df2dist.group}
+\alias{enve.df2dist.group}
+\title{enve df2dist group}
+\description{Transform a dataframe (or coercible object, like a table) into a `dist` object, where
+there are 1 or more distances between each pair of objects.}
+\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: (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{summary}{Function summarizing the different distances between the two objects.}
+  \item{empty.rm}{Remove rows with empty or NA groups}
+}
+
+\value{Returns a `dist` object.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,26 @@
+\name{enve.df2dist.list}
+\alias{enve.df2dist.list}
+\title{enve df2dist list}
+\description{Transform a dataframe (or coercible object, like a table) into a `dist` object.}
+\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: (1) ID of the object 1,
+(2) ID of the object 2, and (3) 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{\dots}{Any other parameters supported by `enve.df2dist.group`.}
+}
+
+\value{Returns a `list` of `dist` object.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+