miga-base 0.7.25.2 → 0.7.25.3

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

@@ -1,27 +0,0 @@
-% 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

@@ -1,14 +0,0 @@
-
-\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

@@ -1,13 +0,0 @@
-
-\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

@@ -1,63 +0,0 @@
-% 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

@@ -1,38 +0,0 @@
-% 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

@@ -1,38 +0,0 @@
-% 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]
-}

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

@@ -1,111 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/recplot2.R
-\name{plot.enve.RecPlot2}
-\alias{plot.enve.RecPlot2}
-\title{Enveomics: Recruitment Plot (2)}
-\usage{
-\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow
-  = 2), panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2),
-  palette = grey((100:0)/100), underlay.group = TRUE,
-  peaks.col = "darkred", use.peaks, id.lim = range(x$id.breaks),
-  pos.lim = range(x$pos.breaks), pos.units = c("Mbp", "Kbp", "bp"),
-  mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1),
-  1, 5), 4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) +
-  0.1, `4` = c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1,
-  4), 4, 2) + 0.1, `5` = c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
-  pos.splines = 0, id.splines = 1/2,
-  in.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
-  out.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
-  id.lwd = ifelse(is.null(id.splines) || id.splines > 0, 1/2, 2),
-  in.col = "darkblue", out.col = "lightblue", id.col = "black",
-  breaks.col = "#AAAAAA40", peaks.opts = list(), ...)
-}
-\arguments{
-\item{x}{\code{\link{enve.RecPlot2}} object to plot.}
-
-\item{layout}{Matrix indicating the position of the different panels in the layout,
-where:
-\itemize{
-  \item 0: Empty space
-  \item 1: Counts matrix
-  \item 2: position histogram (sequencing depth)
-  \item 3: identity histogram
-  \item 4: Populations histogram (histogram of sequencing depths)
-  \item 5: Color scale for the counts matrix (vertical)
-  \item 6: Color scale of the counts matrix (horizontal)
-}
-Only panels indicated here will be plotted. To plot only one panel
-simply set this to the number of the panel you want to plot.}
-
-\item{panel.fun}{List of functions to be executed after drawing each panel. Use the
-indices in \code{layout} (as characters) as keys. Functions for indices
-missing in \code{layout} are ignored. For example, to add a vertical line
-at the 3Mbp mark in both the position histogram and the counts matrix:
-\code{list('1'=function() abline(v=3), '2'=function() abline(v=3))}.
-Note that the X-axis in both panels is in Mbp by default. To change
-this behavior, set \code{pos.units} accordingly.}
-
-\item{widths}{Relative widths of the columns of \code{layout}.}
-
-\item{heights}{Relative heights of the rows of \code{layout}.}
-
-\item{palette}{Colors to be used to represent the counts matrix, sorted from no hits
-to the maximum sequencing depth.}
-
-\item{underlay.group}{If TRUE, it indicates the in-group and out-group areas couloured based
-on \code{in.col} and \code{out.col}. Requires support for semi-transparency.}
-
-\item{peaks.col}{If not \code{NA}, it attempts to represent peaks in the population histogram
-in the specified color. Set to \code{NA} to avoid peak-finding.}
-
-\item{use.peaks}{A list of \code{\link{enve.RecPlot2.Peak}} objects, as returned by
-\code{\link{enve.recplot2.findPeaks}}. If passed, \code{peaks.opts} is ignored.}
-
-\item{id.lim}{Limits of identities to represent.}
-
-\item{pos.lim}{Limits of positions to represent (in bp, regardless of \code{pos.units}).}
-
-\item{pos.units}{Units in which the positions should be represented (powers of 1,000
-base pairs).}
-
-\item{mar}{Margins of the panels as a list, with the character representation of
-the number of the panel as index (see \code{layout}).}
-
-\item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero
-(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
-cross-validation.}
-
-\item{id.splines}{Smoothing parameter for the splines in the identity histogram. Zero
-(0) for no splines. Use \code{NULL} to automatically detect by leave-one-out
-cross-validation.}
-
-\item{in.lwd}{Line width for the sequencing depth of in-group matches.}
-
-\item{out.lwd}{Line width for the sequencing depth of out-group matches.}
-
-\item{id.lwd}{Line width for the identity histogram.}
-
-\item{in.col}{Color associated to in-group matches.}
-
-\item{out.col}{Color associated to out-group matches.}
-
-\item{id.col}{Color for the identity histogram.}
-
-\item{breaks.col}{Color of the vertical lines indicating sequence breaks.}
-
-\item{peaks.opts}{Options passed to \code{\link{enve.recplot2.findPeaks}},
-if \code{peaks.col} is not \code{NA}.}
-
-\item{...}{Any other graphic parameters (currently ignored).}
-}
-\value{
-Returns a list of \code{\link{enve.RecPlot2.Peak}} objects (see
-\code{\link{enve.recplot2.findPeaks}}). If \code{peaks.col=NA} or
-\code{layout} doesn't include 4, returns \code{NA}.
-}
-\description{
-Plots an \code{\link{enve.RecPlot2}} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/growthcurve.R
-\name{summary.enve.GrowthCurve}
-\alias{summary.enve.GrowthCurve}
-\title{Enveomics: Summary of Growth Curve}
-\usage{
-\method{summary}{enve.GrowthCurve}(object, ...)
-}
-\arguments{
-\item{object}{An \code{\link{enve.GrowthCurve}} object.}
-
-\item{...}{No additional parameters are currently supported.}
-}
-\description{
-Summary of an \code{\link{enve.GrowthCurve}} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tribs.R
-\name{summary.enve.TRIBS}
-\alias{summary.enve.TRIBS}
-\title{Enveomics: TRIBS Summary}
-\usage{
-\method{summary}{enve.TRIBS}(object, ...)
-}
-\arguments{
-\item{object}{\code{\link{enve.TRIBS}} object.}
-
-\item{...}{No additional parameters are currently supported.}
-}
-\description{
-Summary of an \code{\link{enve.TRIBS}} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

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

@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tribs.R
-\name{summary.enve.TRIBStest}
-\alias{summary.enve.TRIBStest}
-\title{Enveomics: TRIBS Summary Test}
-\usage{
-\method{summary}{enve.TRIBStest}(object, ...)
-}
-\arguments{
-\item{object}{\code{\link{enve.TRIBStest}} object.}
-
-\item{...}{No additional parameters are currently supported.}
-}
-\description{
-Summary of an \code{\link{enve.TRIBStest}} object.
-}
-\author{
-Luis M. Rodriguez-R [aut, cre]
-}

data/utils/enveomics/globals.mk

@@ -1,8 +0,0 @@
-# Global variables for the Enve-omics collection
-
-R=R
-prefix=/usr/local
-bindir=$(prefix)/bin
-mandir=$(prefix)/man/man1
-SCRIPTS := $(wildcard Scripts/*.*)
-

data/utils/enveomics/manifest.json

@@ -1,9 +0,0 @@
-{
-  "_": ["This is not standard JSON, to parse use EnveJSON, available at:",
-    "https://github.com/lmrodriguezr/enveomics-gui/."],
-  "_include": [
-    "Manifest/categories.json",
-    "Manifest/examples.json",
-    "Manifest/tasks.json"
-  ]
-}