miga-base 0.7.26.3 → 1.0.0.sr1

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]
+}

data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd

@@ -4,8 +4,15 @@
 \alias{enve.prune.dist}
 \title{Enveomics: Prune Dist}
 \usage{
-enve.prune.dist(t, dist.quantile = 0.25, min_dist, quiet = FALSE,
-  max_iters = 100, min_nodes_random = 40000, random_nodes_frx = 1)
+enve.prune.dist(
+  t,
+  dist.quantile = 0.25,
+  min_dist,
+  quiet = FALSE,
+  max_iters = 100,
+  min_nodes_random = 40000,
+  random_nodes_frx = 1
+)
 }
 \arguments{
 \item{t}{A \strong{phylo} object or a path to the Newick file.}

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

@@ -4,12 +4,29 @@
 \alias{enve.recplot}
 \title{Enveomics: Recruitment Plots}
 \usage{
-enve.recplot(prefix, id.min = NULL, id.max = NULL, id.binsize = NULL,
-  id.splines = 0, id.metric = "id", id.summary = "sum",
-  pos.min = 1, pos.max = NULL, pos.binsize = 1000, pos.splines = 0,
-  rec.col1 = "white", rec.col2 = "black", main = NULL,
-  contig.col = grey(0.85), ret.recplot = FALSE, ret.hist = FALSE,
-  ret.mode = FALSE, id.cutoff = NULL, verbose = TRUE, ...)
+enve.recplot(
+  prefix,
+  id.min = NULL,
+  id.max = NULL,
+  id.binsize = NULL,
+  id.splines = 0,
+  id.metric = "id",
+  id.summary = "sum",
+  pos.min = 1,
+  pos.max = NULL,
+  pos.binsize = 1000,
+  pos.splines = 0,
+  rec.col1 = "white",
+  rec.col2 = "black",
+  main = NULL,
+  contig.col = grey(0.85),
+  ret.recplot = FALSE,
+  ret.hist = FALSE,
+  ret.mode = FALSE,
+  id.cutoff = NULL,
+  verbose = TRUE,
+  ...
+)
 }
 \arguments{
 \item{prefix}{Path to the prefix of the BlastTab.catsbj.pl output files. At

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

@@ -4,11 +4,20 @@
 \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,
+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,
-  ...)
+  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

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

@@ -4,8 +4,14 @@
 \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)
+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.}

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

@@ -4,8 +4,13 @@
 \alias{enve.recplot2.extractWindows}
 \title{Enveomics: Recruitment Plot (2) Extract Windows}
 \usage{
-enve.recplot2.extractWindows(rp, peak, lower.tail = TRUE,
-  significance = 0.05, seq.names = FALSE)
+enve.recplot2.extractWindows(
+  rp,
+  peak,
+  lower.tail = TRUE,
+  significance = 0.05,
+  seq.names = FALSE
+)
 }
 \arguments{
 \item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}

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

@@ -4,9 +4,20 @@
 \alias{enve.recplot2.findPeaks.__mow_one}
 \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1}
 \usage{
-enve.recplot2.findPeaks.__mow_one(lsd1, min.points, quant.est, mlv.opts,
-  fitdist.opts, with.skewness, optim.rounds, optim.epsilon, n.total,
-  merge.logdist, verbose, log)
+enve.recplot2.findPeaks.__mow_one(
+  lsd1,
+  min.points,
+  quant.est,
+  mlv.opts,
+  fitdist.opts,
+  with.skewness,
+  optim.rounds,
+  optim.epsilon,
+  n.total,
+  merge.logdist,
+  verbose,
+  log
+)
 }
 \arguments{
 \item{lsd1}{Vector of log-transformed sequencing depths}

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

@@ -4,8 +4,16 @@
 \alias{enve.recplot2.findPeaks.em}
 \title{Enveomics: Recruitment Plot (2) Em Peak Finder}
 \usage{
-enve.recplot2.findPeaks.em(x, max.iter = 1000, ll.diff.res = 1e-08,
-  components = 2, rm.top = 0.05, verbose = FALSE, init, log = TRUE)
+enve.recplot2.findPeaks.em(
+  x,
+  max.iter = 1000,
+  ll.diff.res = 1e-08,
+  components = 2,
+  rm.top = 0.05,
+  verbose = FALSE,
+  init,
+  log = TRUE
+)
 }
 \arguments{
 \item{x}{An \code{\link{enve.RecPlot2}} object.}

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

@@ -4,8 +4,14 @@
 \alias{enve.recplot2.findPeaks.emauto}
 \title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
 \usage{
-enve.recplot2.findPeaks.emauto(x, components = seq(1, 5),
-  criterion = "aic", merge.tol = 2L, verbose = FALSE, ...)
+enve.recplot2.findPeaks.emauto(
+  x,
+  components = seq(1, 5),
+  criterion = "aic",
+  merge.tol = 2L,
+  verbose = FALSE,
+  ...
+)
 }
 \arguments{
 \item{x}{An \code{\link{enve.RecPlot2}} object.}

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

@@ -4,15 +4,23 @@
 \alias{enve.recplot2.findPeaks.mower}
 \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
 \usage{
-enve.recplot2.findPeaks.mower(x, min.points = 10, quant.est = c(0.002,
-  0.998), mlv.opts = list(method = "parzen"),
-  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1,
-  0.5, 0.8), start = list(omega = 1, alpha = -1), lower = c(0, -Inf,
-  -Inf)), fitdist.opts.norm = list(distr = "norm", method = "qme", probs
-  = c(0.4, 0.6), start = list(sd = 1), lower = c(0, -Inf)),
-  rm.top = 0.05, with.skewness = TRUE, optim.rounds = 200,
-  optim.epsilon = 1e-04, merge.logdist = log(1.75), verbose = FALSE,
-  log = TRUE)
+enve.recplot2.findPeaks.mower(
+  x,
+  min.points = 10,
+  quant.est = c(0.002, 0.998),
+  mlv.opts = list(method = "parzen"),
+  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start =
+    list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
+  fitdist.opts.norm = list(distr = "norm", method = "qme", probs = c(0.4, 0.6), start =
+    list(sd = 1), lower = c(0, -Inf)),
+  rm.top = 0.05,
+  with.skewness = TRUE,
+  optim.rounds = 200,
+  optim.epsilon = 1e-04,
+  merge.logdist = log(1.75),
+  verbose = FALSE,
+  log = TRUE
+)
 }
 \arguments{
 \item{x}{An \code{\link{enve.RecPlot2}} object.}

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

@@ -4,8 +4,12 @@
 \alias{enve.recplot2.windowDepthThreshold}
 \title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
 \usage{
-enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE,
-  significance = 0.05)
+enve.recplot2.windowDepthThreshold(
+  rp,
+  peak,
+  lower.tail = TRUE,
+  significance = 0.05
+)
 }
 \arguments{
 \item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}

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

@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{enve.selvector}
+\alias{enve.selvector}
+\title{Enveomics: Selection vector}
+\usage{
+enve.selvector(sel, dim.names)
+}
+\arguments{
+\item{sel}{A vector of numbers, characters, or booleans.}
+
+\item{dim.names}{A vector of names from which to select.}
+}
+\value{
+Returns a logical vector with the same length as \code{dim.name}.
+}
+\description{
+Normalizes a selection vector \code{sel} to a logical vector with indexes
+from \code{dim.names}.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

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

@@ -4,11 +4,20 @@
 \alias{enve.tribs}
 \title{Enveomics: TRIBS}
 \usage{
-enve.tribs(dist, selection = labels(dist), replicates = 1000,
-  summary.fx = median, dist.method = "euclidean", subsamples = seq(0,
-  1, by = 0.01), dimensions = ceiling(length(selection) * 0.05),
-  metaMDS.opts = list(), threads = 2, verbosity = 1, points,
-  pre.tribs)
+enve.tribs(
+  dist,
+  selection = labels(dist),
+  replicates = 1000,
+  summary.fx = median,
+  dist.method = "euclidean",
+  subsamples = seq(0, 1, by = 0.01),
+  dimensions = ceiling(length(selection) * 0.05),
+  metaMDS.opts = list(),
+  threads = 2,
+  verbosity = 1,
+  points,
+  pre.tribs
+)
 }
 \arguments{
 \item{dist}{Distances as a \code{dist} object.}

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

@@ -4,10 +4,25 @@
 \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, ...)
+\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.}

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

@@ -4,9 +4,17 @@
 \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, ...)
+\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.}

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

@@ -4,10 +4,17 @@
 \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")))), ...)
+\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.}

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

@@ -4,21 +4,35 @@
 \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,
+\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(), ...)
+  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.}