miga-base 0.3.1.7 → 0.3.2.0

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

@@ -0,0 +1,28 @@
+\name{enve.recplot2.findPeaks.emauto}
+\alias{enve.recplot2.findPeaks.emauto}
+\title{enve recplot2 findPeaks emauto}
+\description{Identifies peaks in the population histogram using a Gaussian Mixture
+Model Expectation Maximization (GMM-EM) method with number of components
+automatically detected.}
+\usage{enve.recplot2.findPeaks.emauto(x, components = seq(1, 10), criterion = "aic", 
+    merge.tol = 2L, verbose = FALSE, ...)}
+\arguments{
+  \item{x}{An `enve.RecPlot2` object.}
+  \item{components}{A vector of number of components to evaluate.}
+  \item{criterion}{Criterion to use for components selection. Must be one of:
+'aic' (Akaike Information Criterion),
+'bic' or 'sbc' (Bayesian Information Criterion or Schwarz Criterion).}
+  \item{merge.tol}{When attempting to merge peaks with very similar sequencing depth, use
+this number of significant digits (in log-scale).}
+  \item{verbose}{Display (mostly debugging) information.}
+  \item{\dots}{Any additional parameters supported by `enve.recplot2.findPeaks.em`.}
+}
+
+\value{Returns a list of `enve.RecPlot2.Peak` objects.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -0,0 +1,56 @@
+\name{enve.recplot2.findPeaks.mower}
+\alias{enve.recplot2.findPeaks.mower}
+\title{enve recplot2 findPeaks mower}
+\description{Identifies peaks in the population histogram potentially indicating
+sub-population mixtures, using a custom distribution-mowing method.}
+\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)}
+\arguments{
+  \item{x}{An `enve.RecPlot2` object.}
+  \item{min.points}{Minimum number of points in the quantile-estimation-range
+(`quant.est`) to estimate a peak.}
+  \item{quant.est}{Range of quantiles to be used in the estimation of a peak's
+parameters.}
+  \item{mlv.opts}{Options passed to `mlv` to estimate the mode.}
+  \item{fitdist.opts.sn}{
+}
+  \item{fitdist.opts.norm}{
+}
+  \item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
+This step is useful to remove highly conserved regions, but can be
+turned off by setting rm.top=0. The quantile is determined *after*
+removing zero-coverage windows.}
+  \item{with.skewness}{Allow skewness correction of the peaks. Typically, the
+sequencing-depth distribution for a single peak is left-skewed, due
+partly (but not exclusively) to fragmentation and mapping sensitivity.
+See Lindner et al 2013, Bioinformatics 29(10):1260-7 for an
+alternative solution for the first problem (fragmentation) called
+"tail distribution".}
+  \item{optim.rounds}{Maximum rounds of peak optimization.}
+  \item{optim.epsilon}{Trace change at which optimization stops (unless `optim.rounds` is
+reached first). The trace change is estimated as the sum of square
+differences between parameters in one round and those from two rounds
+earlier (to avoid infinite loops from approximation).}
+  \item{merge.logdist}{Maximum value of |log-ratio| between centrality parameters in peaks to
+attempt merging. The default of ~0.22 corresponds to a maximum
+difference of 25\%.}
+  \item{verbose}{Display (mostly debugging) information.}
+  \item{log}{Logical value indicating if the estimations should be performed in
+natural logarithm units. Do not change unless you know what you're
+doing.}
+}
+
+\value{Returns a list of `enve.RecPlot2.Peak` objects.}
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -26,8 +26,10 @@ ideally be equal to the length of `values`, but it's not and integer.}
     \item{\code{n.total}:}{(\code{numeric}) Total number of bins from which the peak was extracted. I.e., total
 number of position bins with non-zero sequencing depth in the recruitment
 plot (regardless of peak count).}
-    \item{\code{err.res}:}{(\code{numeric}) Error left after adding the peak.}
+    \item{\code{err.res}:}{(\code{numeric}) Error left after adding the peak (mower) or log-likelihood (em or emauto).}
     \item{\code{merge.logdist}:}{(\code{numeric}) Attempted `merge.logdist` parameter.}
+    \item{\code{seq.depth}:}{(\code{numeric}) Best estimate available for the sequencing depth of the peak (centrality).}
+    \item{\code{log}:}{(\code{logical}) Indicates if the estimation was performed in natural logarithm space}
   }
 }
 \section{Methods}{

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

@@ -0,0 +1,22 @@
+\name{enve.recplot2.seqdepth}
+\alias{enve.recplot2.seqdepth}
+\title{enve recplot2 seqdepth}
+\description{Calculate the sequencing depth of the given window(s)}
+\usage{enve.recplot2.seqdepth(x, sel, low.identity = FALSE)}
+\arguments{
+  \item{x}{`enve.RecPlot2` object.}
+  \item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
+passed, it returns the sequencing depth of all windows}
+  \item{low.identity}{A logical indicating if the sequencing depth is to be estimated only
+with low-identity matches. By default, only high-identity matches are
+used.}
+}
+
+\value{Returns a numeric vector of sequencing depths (in bp/bp). }
+
+\author{Luis M. Rodriguez-R [aut, cre]}
+
+
+
+
+

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

@@ -4,18 +4,20 @@
 \description{Plots an `enve.RecPlot2` object.}
 \usage{\method{plot}{enve.RecPlot2}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow = 2), 
     widths = c(1, 7, 2), heights = c(1, 2), palette = grey((100:0)/100), 
-    underlay.group = TRUE, peaks.col = "darkred", 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(pos.splines > 
-        0, 1/2, 2), out.lwd = ifelse(pos.splines > 0, 1/2, 2), 
-    id.lwd = ifelse(id.splines > 0, 1/2, 2), in.col = "darkblue", 
-    out.col = "lightblue", id.col = "black", breaks.col = "#AAAAAA40", 
-    peaks.opts = list(), ...)}
+    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}{`enve.RecPlot2` object to plot.}
   \item{layout}{Matrix indicating the position of the different panels in the layout,
@@ -38,6 +40,8 @@ to the maximum sequencing depth.}
 on `in.col` and `out.col`. Requires support for semi-transparency.}
   \item{peaks.col}{If not NA, it attempts to represent peaks in the population histogram
 in the specified color. Set to NA to avoid peak-finding.}
+  \item{use.peaks}{A list of `enve.RecPlot2.Peak` objects, as returned by
+`enve.recplot2.findPeaks`. If passed, `peaks.opts` is ignored.}
   \item{id.lim}{Limits of identities to represent.}
   \item{pos.lim}{Limits of positions to represent (in bp, regardless of `pos.units`).}
   \item{pos.units}{Units in which the positions should be represented (powers of 1,000
@@ -45,9 +49,11 @@ base pairs).}
   \item{mar}{
 }
   \item{pos.splines}{Smoothing parameter for the splines in the position histogram. Zero
-(0) for no splines. If non-zero, requires the stats package.}
+(0) for no splines. Use 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. If non-zero, requires the stats package.}
+(0) for no splines. Use 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.}

data/utils/requirements.txt

@@ -14,6 +14,6 @@ Barrnap		barrnap		http://www.vicbioinformatics.com/software.barrnap.shtml
 Scythe		scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
 FastQC		fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
 SolexaQA++	SolexaQA++	http://solexaqa.sourceforge.net					Required version: v3.1.3+
-DIAMOND (opt)	diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.7.9+
+DIAMOND (opt)	diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.9.20+
 MyTaxa (opt)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa				The folder must contain the db and utils dirs, and the AllGenomes.faa.dmnd database
 Krona (opt)	ktImportText	https://github.com/marbl/Krona/wiki

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.1.7
+  version: 0.3.2.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-13 00:00:00.000000000 Z
+date: 2018-06-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -145,7 +145,11 @@ files:
 - lib/miga/_data/aai-intax.tsv.gz
 - lib/miga/_data/aai-novel.tsv.gz
 - lib/miga/common.rb
+- lib/miga/common/base.rb
+- lib/miga/common/format.rb
+- lib/miga/common/path.rb
 - lib/miga/daemon.rb
+- lib/miga/daemon/base.rb
 - lib/miga/dataset.rb
 - lib/miga/dataset/base.rb
 - lib/miga/dataset/result.rb
@@ -199,6 +203,14 @@ files:
 - utils/adapters.fa
 - utils/arch-ess-genes.rb
 - utils/core-pan-plot.R
+- utils/distance/base.rb
+- utils/distance/commands.rb
+- utils/distance/database.rb
+- utils/distance/pipeline.rb
+- utils/distance/runner.rb
+- utils/distance/temporal.rb
+- utils/distances.rb
+- utils/enveomics/Docs/recplot2.md
 - utils/enveomics/Examples/aai-matrix.bash
 - utils/enveomics/Examples/ani-matrix.bash
 - utils/enveomics/Examples/essential-phylogeny.bash
@@ -263,6 +275,7 @@ files:
 - utils/enveomics/Scripts/Aln.convert.pl
 - utils/enveomics/Scripts/AlphaDiversity.pl
 - utils/enveomics/Scripts/BedGraph.tad.rb
+- utils/enveomics/Scripts/BedGraph.window.rb
 - utils/enveomics/Scripts/BlastPairwise.AAsubs.pl
 - utils/enveomics/Scripts/BlastTab.addlen.rb
 - utils/enveomics/Scripts/BlastTab.advance.bash
@@ -321,6 +334,7 @@ files:
 - utils/enveomics/Scripts/NCBIacc2tax.rb
 - utils/enveomics/Scripts/Newick.autoprune.R
 - utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl
+- utils/enveomics/Scripts/RecPlot2.compareIdentities.R
 - utils/enveomics/Scripts/RefSeq.download.bash
 - utils/enveomics/Scripts/SRA.download.bash
 - utils/enveomics/Scripts/TRIBS.plot-test.R
@@ -418,17 +432,27 @@ files:
 - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__findPeak.Rd
-- utils/enveomics/enveomics.R/man/enve.recplot2.__findPeaks.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
+- utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
 - utils/enveomics/enveomics.R/man/enveomics.R-package.Rd

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

@@ -1,40 +0,0 @@
-\name{enve.recplot2.__findPeak}
-\alias{enve.recplot2.__findPeak}
-\title{enve recplot2   findPeak}
-\description{Internall ancilliary function (see `enve.recplot2.findPeaks`).}
-\usage{enve.recplot2.__findPeak(lsd1, min.points, quant.est, mlv.opts, 
-    fitdist.opts, with.skewness, optim.rounds, optim.epsilon, 
-    n.total, merge.logdist, verbose)}
-\arguments{
-  \item{lsd1}{
-}
-  \item{min.points}{
-}
-  \item{quant.est}{
-}
-  \item{mlv.opts}{
-}
-  \item{fitdist.opts}{
-}
-  \item{with.skewness}{
-}
-  \item{optim.rounds}{
-}
-  \item{optim.epsilon}{
-}
-  \item{n.total}{
-}
-  \item{merge.logdist}{
-}
-  \item{verbose}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-

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

@@ -1,18 +0,0 @@
-\name{enve.recplot2.__findPeaks}
-\alias{enve.recplot2.__findPeaks}
-\title{enve recplot2   findPeaks}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks`).}
-\usage{enve.recplot2.__findPeaks(peaks.opts)}
-\arguments{
-  \item{peaks.opts}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-