miga-base 0.4.3.0 → 0.5.0.0

data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd

@@ -1,41 +1,45 @@
-\name{enve.RecPlot2-class}
-\Rdversion{1.1}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
 \docType{class}
+\name{enve.RecPlot2-class}
 \alias{enve.RecPlot2-class}
 \alias{enve.RecPlot2}
-%% \alias{$}
-
-\title{enve.RecPlot2 S4 class}
-\description{Enve-omics representation of Recruitment plots. This object can
-be produced by `enve.recplot2` and supports S4 method plot.}
-\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.RecPlot2 ...)}}
-\section{Slots}{
-  \describe{
-    \item{\code{counts}:}{(\code{matrix}) Counts as a two-dimensional histogram.}
-    \item{\code{pos.counts.in}:}{(\code{numeric}) Counts of in-group hits per position bin.}
-    \item{\code{pos.counts.out}:}{(\code{numeric}) Counts of out-group hits per position bin.}
-    \item{\code{id.counts}:}{(\code{numeric}) Counts per ID bin.}
-    \item{\code{id.breaks}:}{(\code{numeric}) Breaks of identity bins.}
-    \item{\code{pos.breaks}:}{(\code{numeric}) Breaks of position bins.}
-    \item{\code{pos.names}:}{(\code{character}) Names of the position bins.}
-    \item{\code{seq.breaks}:}{(\code{numeric}) Breaks of input sequences.}
-    \item{\code{peaks}:}{(\code{list}) Peaks identified in the recplot.
-Limits of the subject sequences after concatenation.}
-    \item{\code{seq.names}:}{(\code{character}) Names of the subject sequences.}
-    \item{\code{id.metric}:}{(\code{character}) Metric used as 'identity'.}
-    \item{\code{id.ingroup}:}{(\code{logical}) Identity bins considered in-group.}
-    \item{\code{call}:}{(\code{call}) Call producing this object.}
-  }
-}
-\section{Methods}{
-  \describe{
-    \item{$}{\code{signature(x = "enve.RecPlot2")}: ... }
-	 }
+\title{Enveomics: Recruitment Plot (2) - S4 Class}
+\description{
+Enve-omics representation of Recruitment plots. This object can
+be produced by \code{\link{enve.recplot2}} and supports S4 method plot.
 }
+\section{Slots}{
+
+\describe{
+\item{\code{counts}}{\code{(matrix)} Counts as a two-dimensional histogram.}
+
+\item{\code{pos.counts.in}}{\code{(numeric)} Counts of in-group hits per position bin.}
 
-\author{Luis M. Rodriguez-R [aut, cre]}
+\item{\code{pos.counts.out}}{\code{(numeric)} Counts of out-group hits per position bin.}
 
+\item{\code{id.counts}}{\code{(numeric)} Counts per ID bin.}
 
+\item{\code{id.breaks}}{\code{(numeric)} Breaks of identity bins.}
 
+\item{\code{pos.breaks}}{\code{(numeric)} Breaks of position bins.}
 
+\item{\code{pos.names}}{\code{(character)} Names of the position bins.}
 
+\item{\code{seq.breaks}}{\code{(numeric)} Breaks of input sequences.}
+
+\item{\code{peaks}}{\code{(list)} Peaks identified in the recplot.
+Limits of the subject sequences after concatenation.}
+
+\item{\code{seq.names}}{\code{(character}) Names of the subject sequences.}
+
+\item{\code{id.metric}}{\code{(character}) Metric used as 'identity'.}
+
+\item{\code{id.ingroup}}{\code{(logical}) Identity bins considered in-group.}
+
+\item{\code{call}}{\code{(call)} Call producing this object.}
+}}
+
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,23 +1,24 @@
-\name{enve.recplot2.ANIr}
-\alias{enve.recplot2.ANIr}
-\title{enve recplot2 ANIr}
-\description{Estimate the Average Nucleotide Identity from reads (ANIr) from a
-recruitment plot}
-\usage{enve.recplot2.ANIr(x, range = c(0, Inf))}
-\arguments{
-  \item{x}{`enve.RecPlot2` object.}
-  \item{range}{Range of identities to be considered. By default, the full range
-is used (note that the upper boundary is `Inf` and not 100 because
-recruitment plots can also be built with bit-scores). To use only
-intra-population matches (with identities), use c(95,100). To use only
-inter-population values, use c(0,95).}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.ANIr}
+\alias{enve.recplot2.ANIr}
+\title{Enveomics: Recruitment Plot (2) ANI Estimate}
+\usage{
+enve.recplot2.ANIr(x, range = c(0, Inf))
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object.}
+
+\item{range}{Range of identities to be considered. By default, the full range
+is used (note that the upper boundary is \code{Inf} and not 100 because
+recruitment plots can also be built with bit-scores). To use only
+intra-population matches (with identities), use c(95,100). To use only
+inter-population values, use c(0,95).}
+}
+\description{
+Estimate the Average Nucleotide Identity from reads (ANIr) from a
+recruitment plot.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,51 +1,68 @@
-\name{enve.recplot2}
-\alias{enve.recplot2}
-\title{enve recplot2}
-\description{Produces recruitment plots provided that BlastTab.catsbj.pl has
-been previously executed.}
-\usage{enve.recplot2(prefix, plot = TRUE, pos.breaks = 1000, pos.breaks.tsv = NA, 
-    id.breaks = 300, id.free.range = FALSE, id.metric = c("identity", 
-        "corrected identity", "bit score"), id.summary = sum, 
-    id.cutoff = 95, threads = 2, verbose = TRUE, ...)}
-\arguments{
-  \item{prefix}{Path to the prefix of the BlastTab.catsbj.pl output files. At
-least the files .rec and .lim must exist with this prefix.}
-  \item{plot}{Should the object be plotted?}
-  \item{pos.breaks}{Breaks in the positions histogram. It can also be a vector of break
-points, and values outside the range are ignored. If zero (0), it
-uses the sequence breaks as defined in the .lim file, which means
-one bin per contig (or gene, if the mapping is agains genes). Ignored
-if `pos.breaks.tsv` is passed.}
-  \item{pos.breaks.tsv}{Path to a list of (absolute) coordinates to use as position breaks.
-This tab-delimited file can be produced by `GFF.catsbj.pl`, and it
-must contain at least one column: coordinates of the break positions of
-each position bin. If it has a second column, this is used as the name
-of the position bin that ends at the given coordinate (the first row is
-ignored). Any additional columns are currently ignored. If NA,
-position bins are determined by `pos.breaks`.}
-  \item{id.breaks}{Breaks in the identity histogram. It can also be a vector of break
-points, and values outside the range are ignored.}
-  \item{id.free.range}{Indicates that the range should be freely set from the observed
-values. Otherwise, 70-100\% is included in the identity histogram
-(default).}
-  \item{id.metric}{Metric of identity to be used (Y-axis). Corrected identity is only
-supported if the original BLAST file included sequence lengths.}
-  \item{id.summary}{Function summarizing the identity bins. Other recommended options
-include: `median` to estimate the median instead of total bins, and
-`function(x) mlv(x,method='parzen')$M` to estimate the mode.}
-  \item{id.cutoff}{Cutoff of identity metric above which the hits are considered
-'in-group'. The 95\% identity corresponds to the expectation of
-ANI<95\% within species.}
-  \item{threads}{Number of threads to use.}
-  \item{verbose}{Indicates if the function should report the advance.}
-  \item{\dots}{Any additional parameters supported by `plot.enve.RecPlot2`.}
-}
-
-\value{Returns an object of class `enve.RecPlot2`.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2}
+\alias{enve.recplot2}
+\title{Enveomics: Recruitment Plot (2)}
+\usage{
+enve.recplot2(prefix, plot = TRUE, pos.breaks = 1000,
+  pos.breaks.tsv = NA, id.breaks = 60, id.free.range = FALSE,
+  id.metric = c("identity", "corrected identity", "bit score"),
+  id.summary = sum, id.cutoff = 95, threads = 2, verbose = TRUE,
+  ...)
+}
+\arguments{
+\item{prefix}{Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
+least the files .rec and .lim must exist with this prefix.}
+
+\item{plot}{Should the object be plotted?}
+
+\item{pos.breaks}{Breaks in the positions histogram. It can also be a vector of break
+points, and values outside the range are ignored. If zero (0), it
+uses the sequence breaks as defined in the .lim file, which means
+one bin per contig (or gene, if the mapping is agains genes). Ignored
+if `pos.breaks.tsv` is passed.}
+
+\item{pos.breaks.tsv}{Path to a list of (absolute) coordinates to use as position breaks.
+This tab-delimited file can be produced by \code{GFF.catsbj.pl}, and it
+must contain at least one column: coordinates of the break positions of
+each position bin. If it has a second column, this is used as the name
+of the position bin that ends at the given coordinate (the first row is
+ignored). Any additional columns are currently ignored. If \code{NA},
+position bins are determined by \code{pos.breaks}.}
+
+\item{id.breaks}{Breaks in the identity histogram. It can also be a vector of break
+points, and values outside the range are ignored.}
+
+\item{id.free.range}{Indicates that the range should be freely set from the observed
+values. Otherwise, 70-100\% is included in the identity histogram
+(default).}
+
+\item{id.metric}{Metric of identity to be used (Y-axis). Corrected identity is only
+supported if the original BLAST file included sequence lengths.}
+
+\item{id.summary}{Function summarizing the identity bins. Other recommended options
+include: \code{median} to estimate the median instead of total bins, and
+\code{function(x) mlv(x,method='parzen')$M} to estimate the mode.}
+
+\item{id.cutoff}{Cutoff of identity metric above which the hits are considered
+\code{in-group}. The 95\% identity corresponds to the expectation of
+ANI<95\% within species.}
+
+\item{threads}{Number of threads to use.}
+
+\item{verbose}{Indicates if the function should report the advance.}
+
+\item{...}{Any additional parameters supported by \code{\link{plot.enve.RecPlot2}}.}
+}
+\value{
+Returns an object of class \code{\link{enve.RecPlot2}}.
+}
+\description{
+Produces recruitment plots provided that \code{BlastTab.catsbj.pl} has
+been previously executed.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+
+Kenji Gerhardt [aut]
+}

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

@@ -1,24 +1,25 @@
-\name{enve.recplot2.__counts}
-\alias{enve.recplot2.__counts}
-\title{enve recplot2   counts}
-\description{Internal ancilliary function (see `enve.recplot2`).}
-\usage{enve.recplot2.__counts(x, pos.breaks, id.breaks, rec.idcol)}
-\arguments{
-  \item{x}{
-}
-  \item{pos.breaks}{
-}
-  \item{id.breaks}{
-}
-  \item{rec.idcol}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.__counts}
+\alias{enve.recplot2.__counts}
+\title{Enveomics: Recruitment Plot (2) Internal Ancillary Function}
+\usage{
+enve.recplot2.__counts(x, pos.breaks, id.breaks, rec.idcol)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object}
+
+\item{pos.breaks}{Position breaks}
+
+\item{id.breaks}{Identity breaks}
+
+\item{rec.idcol}{Identity column to use}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+
+Kenji Gerhardt [aut]
+}

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

@@ -1,22 +1,21 @@
-\name{enve.recplot2.__peakHist}
-\alias{enve.recplot2.__peakHist}
-\title{enve recplot2   peakHist}
-\description{Internal ancilliary function (see `enve.RecPlot2.Peak`).}
-\usage{enve.recplot2.__peakHist(x, mids, counts = TRUE)}
-\arguments{
-  \item{x}{
-}
-  \item{mids}{
-}
-  \item{counts}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.__peakHist}
+\alias{enve.recplot2.__peakHist}
+\title{Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Function}
+\usage{
+enve.recplot2.__peakHist(x, mids, counts = TRUE)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2.Peak}} object}
+
+\item{mids}{Midpoints}
+
+\item{counts}{Counts}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.RecPlot2.Peak}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,20 +1,19 @@
-\name{enve.recplot2.__whichClosestPeak}
-\alias{enve.recplot2.__whichClosestPeak}
-\title{enve recplot2   whichClosestPeak}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks`).}
-\usage{enve.recplot2.__whichClosestPeak(peak, peaks)}
-\arguments{
-  \item{peak}{
-}
-  \item{peaks}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.__whichClosestPeak}
+\alias{enve.recplot2.__whichClosestPeak}
+\title{Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Function}
+\usage{
+enve.recplot2.__whichClosestPeak(peak, peaks)
+}
+\arguments{
+\item{peak}{Query \code{\link{enve.RecPlot2.Peak}} object}
+
+\item{peaks}{list of \code{\link{enve.RecPlot2.Peak}} objects}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2.findPeaks}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,18 +1,19 @@
-\name{enve.recplot2.changeCutoff}
-\alias{enve.recplot2.changeCutoff}
-\title{enve recplot2 changeCutoff}
-\description{Change the intra-species cutoff of an existing recruitment plot.}
-\usage{enve.recplot2.changeCutoff(rp, new.cutoff = 98)}
-\arguments{
-  \item{rp}{enve.RecPlot2 object.}
-  \item{new.cutoff}{New cutoff to use.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.changeCutoff}
+\alias{enve.recplot2.changeCutoff}
+\title{Enveomics: Recruitment Plot (2) Change Cutoff}
+\usage{
+enve.recplot2.changeCutoff(rp, new.cutoff = 98)
+}
+\arguments{
+\item{rp}{\code{\link{enve.RecPlot2}} object.}
+
+\item{new.cutoff}{New cutoff to use.}
+}
+\description{
+Change the intra-species cutoff of an existing recruitment plot.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -1,32 +1,41 @@
-\name{enve.recplot2.compareIdentities}
-\alias{enve.recplot2.compareIdentities}
-\title{enve recplot2 compareIdentities}
-\description{Compare the distribution of identities between two enve.RecPlot2 objects.}
-\usage{enve.recplot2.compareIdentities(x, y, method = "hellinger", smooth.par = NULL, 
-    pseudocounts = 0, max.deviation = 0.75)}
-\arguments{
-  \item{x}{First enve.RecPlot2 object.}
-  \item{y}{Second enve.RecPlot2 object.}
-  \item{method}{Distance method to use. This should be (an unambiguous abbreviation of)
-one of:
-"hellinger" (Hellinger, 1090, doi:10.1515/crll.1909.136.210),
-"bhattacharyya" (Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35),
-"kl" or "kullback-leibler" (Kullback & Leibler, 1951,
-doi:10.1214/aoms/1177729694), or "euclidean".}
-  \item{smooth.par}{Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
-Use NULL to automatically determine this value using leave-one-out
-cross-validation (see `smooth.spline` parameter `spar`).}
-  \item{pseudocounts}{Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
-1 for add-one smoothing.}
-  \item{max.deviation}{Maximum mean deviation between identity breaks tolerated (as percent
-identity). Difference in number of id.breaks is never tolerated.}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.compareIdentities}
+\alias{enve.recplot2.compareIdentities}
+\title{Enveomics: Recruitment Plot (2) Compare Identities}
+\usage{
+enve.recplot2.compareIdentities(x, y, method = "hellinger",
+  smooth.par = NULL, pseudocounts = 0, max.deviation = 0.75)
+}
+\arguments{
+\item{x}{First \code{\link{enve.RecPlot2}} object.}
+
+\item{y}{Second \code{\link{enve.RecPlot2}} object.}
+
+\item{method}{Distance method to use. This should be (an unambiguous abbreviation of)
+one of:
+\itemize{
+   \item{"hellinger" (\emph{Hellinger, 1090, doi:10.1515/crll.1909.136.210}),}
+   \item{"bhattacharyya" (\emph{Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35}),}
+   \item{"kl" or "kullback-leibler" (\emph{Kullback & Leibler, 1951,
+   doi:10.1214/aoms/1177729694}), or}
+   \item{"euclidean"}
+}}
+
+\item{smooth.par}{Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
+Use \code{NULL} to automatically determine this value using leave-one-out
+cross-validation (see \code{smooth.spline} parameter \code{spar}).}
+
+\item{pseudocounts}{Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
+1 for add-one smoothing.}
+
+\item{max.deviation}{Maximum mean deviation between identity breaks tolerated (as percent
+identity). Difference in number of \code{id.breaks} is never tolerated.}
+}
+\description{
+Compare the distribution of identities between two
+\code{\link{enve.RecPlot2}} objects.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}