miga-base 0.4.3.0 → 0.5.0.0
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- checksums.yaml +4 -4
- data/README.md +1 -1
- data/lib/miga/cli.rb +43 -223
- data/lib/miga/cli/action/add.rb +91 -62
- data/lib/miga/cli/action/classify_wf.rb +97 -0
- data/lib/miga/cli/action/daemon.rb +14 -10
- data/lib/miga/cli/action/derep_wf.rb +95 -0
- data/lib/miga/cli/action/doctor.rb +83 -55
- data/lib/miga/cli/action/get.rb +68 -52
- data/lib/miga/cli/action/get_db.rb +206 -0
- data/lib/miga/cli/action/index_wf.rb +31 -0
- data/lib/miga/cli/action/init.rb +115 -190
- data/lib/miga/cli/action/init/daemon_helper.rb +124 -0
- data/lib/miga/cli/action/ls.rb +20 -11
- data/lib/miga/cli/action/ncbi_get.rb +199 -157
- data/lib/miga/cli/action/preproc_wf.rb +46 -0
- data/lib/miga/cli/action/quality_wf.rb +45 -0
- data/lib/miga/cli/action/stats.rb +147 -99
- data/lib/miga/cli/action/summary.rb +10 -4
- data/lib/miga/cli/action/tax_dist.rb +61 -46
- data/lib/miga/cli/action/tax_test.rb +46 -39
- data/lib/miga/cli/action/wf.rb +178 -0
- data/lib/miga/cli/base.rb +11 -0
- data/lib/miga/cli/objects_helper.rb +88 -0
- data/lib/miga/cli/opt_helper.rb +160 -0
- data/lib/miga/daemon.rb +7 -4
- data/lib/miga/dataset/base.rb +5 -5
- data/lib/miga/project/base.rb +4 -4
- data/lib/miga/project/result.rb +2 -1
- data/lib/miga/remote_dataset/base.rb +5 -5
- data/lib/miga/remote_dataset/download.rb +1 -1
- data/lib/miga/version.rb +3 -3
- data/scripts/cds.bash +3 -1
- data/scripts/essential_genes.bash +1 -0
- data/scripts/stats.bash +1 -1
- data/scripts/trimmed_fasta.bash +5 -3
- data/utils/distance/runner.rb +3 -0
- data/utils/distance/temporal.rb +10 -1
- data/utils/enveomics/Manifest/Tasks/fasta.json +5 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +7 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +33 -31
- data/utils/enveomics/Scripts/FastA.tag.rb +42 -41
- data/utils/enveomics/Scripts/HMM.essential.rb +85 -55
- data/utils/enveomics/Scripts/HMM.haai.rb +29 -20
- data/utils/enveomics/Scripts/SRA.download.bash +1 -1
- data/utils/enveomics/Scripts/aai.rb +163 -128
- data/utils/enveomics/build_enveomics_r.bash +11 -10
- data/utils/enveomics/enveomics.R/DESCRIPTION +3 -2
- data/utils/enveomics/enveomics.R/R/autoprune.R +141 -107
- data/utils/enveomics/enveomics.R/R/barplot.R +105 -86
- data/utils/enveomics/enveomics.R/R/cliopts.R +131 -115
- data/utils/enveomics/enveomics.R/R/df2dist.R +144 -106
- data/utils/enveomics/enveomics.R/R/growthcurve.R +201 -133
- data/utils/enveomics/enveomics.R/R/recplot.R +350 -315
- data/utils/enveomics/enveomics.R/R/recplot2.R +1334 -914
- data/utils/enveomics/enveomics.R/R/tribs.R +521 -361
- data/utils/enveomics/enveomics.R/R/utils.R +31 -15
- data/utils/enveomics/enveomics.R/README.md +7 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +16 -21
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +31 -28
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -19
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +36 -26
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -24
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -24
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +32 -33
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +91 -64
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +57 -37
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -19
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +39 -26
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +38 -25
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +40 -26
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +67 -49
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +37 -28
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +122 -97
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +35 -31
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -23
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +68 -51
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -22
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +41 -32
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +40 -34
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -29
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +41 -42
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +43 -33
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +36 -28
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +74 -56
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +44 -31
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -22
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +32 -26
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +59 -44
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -21
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -22
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +63 -43
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +38 -29
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +38 -30
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +111 -83
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -18
- data/utils/find-medoid.R +3 -2
- data/utils/representatives.rb +5 -3
- data/utils/subclade/pipeline.rb +22 -11
- data/utils/subclade/runner.rb +5 -1
- data/utils/subclades-compile.rb +1 -1
- data/utils/subclades.R +9 -3
- metadata +15 -4
- data/utils/enveomics/enveomics.R/man/enveomics.R-package.Rd +0 -15
- data/utils/enveomics/enveomics.R/man/z$-methods.Rd +0 -26
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#==============> Define S4 classes
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#' Enveomics: Growth Curve S4 Class
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#'
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#' Enve-omics representation of fitted growth curves.
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#'
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#' @slot design \code{(array)} Experimental design of the experiment.
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#' @slot models \code{(list)} Fitted growth curve models.
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#' @slot predict \code{(list)} Fitted growth curve values.
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#' @slot call \code{(call)} Call producing this object.
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#'
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#' @author Luis M. Rodriguez-R [aut, cre]
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#'
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#' @exportClass
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enve.GrowthCurve <- setClass("enve.GrowthCurve",
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representation(
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design = "array",
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models = "list",
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predict = "list",
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call='call')
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,package='enveomics.R');
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#' Attribute accessor
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#'
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#' @param x Object
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#' @param name Attribute name
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setMethod("$", "enve.GrowthCurve", function(x, name) attr(x, name))
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#' Enveomics: Plot of Growth Curve
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#'
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#' Plots an \code{\link{enve.GrowthCurve}} object.
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#'
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#' @param x An \code{\link{enve.GrowthCurve}} object to plot.
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#' @param col Base colors to use for the different samples. Can be recycled.
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#' By default, grey for one sample or rainbow colors for more than one.
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#' @param pt.alpha Color alpha for the observed data points, using \code{col}
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#' as a base.
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#' @param ln.alpha Color alpha for the fitted growth curve, using \code{col}
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#' as a base.
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#' @param ln.lwd Line width for the fitted curve.
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#' @param ln.lty Line type for the fitted curve.
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#' @param band.alpha Color alpha for the confidence interval band of the
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#' fitted growth curve, using \code{col} as a base.
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#' @param band.density Density of the filling pattern in the interval band.
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#' If \code{NULL}, a solid color is used.
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#' @param band.angle Angle of the density filling pattern in the interval
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#' band. Ignored if \code{band.density} is \code{NULL}.
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#' @param xp.alpha Color alpha for the line connecting individual experiments,
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#' using \code{col} as a base.
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#' @param xp.lwd Width of line for the experiments.
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#' @param xp.lty Type of line for the experiments.
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#' @param pch Point character for observed data points.
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#' @param new Should a new plot be generated? If \code{FALSE}, the existing
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#' canvas is used.
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#' @param legend Should the plot include a legend? If \code{FALSE}, no legend
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#' is added. If \code{TRUE}, a legend is added in the bottom-right corner.
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#' Otherwise, a legend is added in the position specified as \code{xy.coords}.
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#' @param add.params Should the legend include the parameters of the fitted
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#' model?
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#' @param ... Any other graphic parameters.
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#'
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#' @author Luis M. Rodriguez-R [aut, cre]
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#'
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#' @method plot enve.GrowthCurve
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#' @export
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#==============> Define S4 methods
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plot.enve.GrowthCurve <- function
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### Density of the filling pattern in the interval band. If NULL, a solid
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### color is used.
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band.angle=45,
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### Angle of the density filling pattern in the interval band. Ignored if
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### as a base.
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### Width of line for the experiments.
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### Type of line for the experiments.
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pch=19,
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### Point character for observed data points.
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### Should a new plot be generated? If FALSE, the existing canvas is used.
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legend=new,
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### Should the plot include a legend? If FALSE, no legend is added. If TRUE,
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### added in the position specified as `xy.coords`.
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add.params=FALSE,
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### Should the legend include the parameters of the fitted model?
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...
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(x,
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col,
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ln.alpha=1.0,
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band.alpha=0.4,
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band.density=NULL,
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band.angle=45,
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xp.alpha=0.5,
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xp.lwd=1,
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pch=19,
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new=TRUE,
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legend=new,
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add.params=FALSE,
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...
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){
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# Arguments
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col <-
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# Initiate canvas
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od.obs.max <- max(sapply(x$models, function(x) max(x$data[,"od"])))
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opts <- list(...)
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if(is.null(opts[[i]])) opts[[i]] <- plot.defaults[[i]]
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}
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opts[["type"]] <- "n"
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do.call(plot, opts)
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}
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# Graphic default
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pch <- rep(pch, length.out=length(x$design))
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col <- rep(col, length.out=length(x$design))
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d <- x$predict[[i]]
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lines(d[,"t"], d[,"fit"], col=ln.col[i], lwd=ln.lwd, lty=ln.lty)
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polygon(c(d[,"t"], rev(d[,"t"])), c(d[,"lwr"], rev(d[,"upr"])),
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}
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if(add.params){
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for(p in names(coef(x$models[[1]]))){
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legend.txt <- paste(legend.txt, ", ", p, "=",
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legend(legend, legend=legend.txt, pch=pch, col=ln.col)
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#' Enveomics: Summary of Growth Curve
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#'
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#' Summary of an \code{\link{enve.GrowthCurve}} object.
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#'
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#' @param object An \code{\link{enve.GrowthCurve}} object.
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#' @param ... No additional parameters are currently supported.
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#'
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#' @author Luis M. Rodriguez-R [aut, cre]
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#'
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#' @method summary enve.GrowthCurve
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#' @export
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summary.enve.GrowthCurve <- function(
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object,
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...
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){
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x <- object
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cat('===[ enve.GrowthCurves ]------------------\n')
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for(i in names(x$design)){
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if(x$models[[i]]$convInfo$isConv){
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for(j in names(coef(x$models[[i]]))){
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cat(' - ', j, ' = ', coef(x$models[[i]])[j], '\n', sep='')
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}
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}else{
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cat(' Model didn\'t converge:\n ',
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x$models[[i]]$convInfo$stopMessage, '\n', sep='')
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}
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cat(' ', nrow(x$models[[i]]$data), ' observations, ',
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length(unique(x$models[[i]]$data[,"replicate"])), ' replicates.\n',
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sep='')
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}
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cat('------------------------------------------\n')
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cat('call:',as.character(attr(x,'call')),'\n')
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cat('------------------------------------------\n')
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}
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#' Enveomics: Growth Curve
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#'
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#' Calculates growth curves using the logistic growth function.
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#'
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#' @param x Data frame (or coercible) containing the observed growth data
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#' (e.g., O.D. values). Each column is an independent growth curve and each
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#' row is a time point. \code{NA}'s are allowed.
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#' @param times Vector with the times at which each row was taken. By default,
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#' all rows are assumed to be part of constantly periodic measurements.
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#' @param triplicates If \code{TRUE}, the columns are assumed to be sorted by
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#' sample with three replicates by sample. It requires a number of columns
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#' multiple of 3.
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#' @param design Experimental design of the data. An \strong{array} of mode list
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#' with sample names as index and the list of column names in each sample as
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#' the values. By default, each column is assumed to be an independent sample
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#' if \code{triplicates} is \code{FALSE}, or every three columns are assumed
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#' to be a sample if \code{triplicates} is \code{TRUE}. In the latter case,
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#' samples are simply numbered.
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#' @param new.times Values of time for the fitted curve.
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#' @param level Confidence (or prediction) interval in the fitted curve.
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#' @param interval Type of interval to be calculated for the fitted curve.
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#' @param plot Should the growth curve be plotted?
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#' @param FUN Function to fit. By default: logistic growth with paramenters
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#' \code{K}: carrying capacity,
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#' \code{r}: intrinsic growth rate, and
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#' \code{P0}: Initial population.
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#' @param nls.opt Any additional options passed to \code{nls}.
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#' @param ... Any additional parameters to be passed to
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#' \code{plot.enve.GrowthCurve}.
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#'
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#' @return Returns an \code{\link{enve.GrowthCurve}} object.
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#'
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#' @author Luis M. Rodriguez-R [aut, cre]
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#'
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#' @examples
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#' # Load data
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#' data("growth.curves", package="enveomics.R", envir=environment())
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#' # Generate growth curves with different colors
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#' g <- enve.growthcurve(growth.curves[,-1], growth.curves[,1], triplicates=TRUE)
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#' # Generate black-and-white growth curves with different symbols
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#' plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))
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#'
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#' @export
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#==============> Core functions
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enve.growthcurve <- structure(function(
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### Experimental design of the data. An `array` of mode list with sample
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### names as index and the list of column names in each sample as the
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### values. By default, each column is assumed to be an independent sample
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### if `triplicates` is FALSE, or every three columns are assumed to be a
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### sample if `triplicates` is TRUE. In the latter case, samples are
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### simply numbered.
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new.times=seq(min(times), max(times), length.out=length(times)*10),
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### Values of time for the fitted curve.
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level=0.95,
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interval=c("confidence","prediction"),
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plot=TRUE,
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### Should the growth curve be plotted?
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FUN=function(t,K,r,P0) K*P0*exp(r*t)/(K+P0*(exp(r*t)-1)),
|
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### Function to fit. By default: logistic growth with paramenters `K`:
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### carrying capacity, `r`: intrinsic growth rate, and `P0`: Initial
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### population.
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nls.opt=list(),
|
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### Any additional options passed to `nls`.
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...
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### Any additional parameters to be passed to `plot.enve.GrowthCurve`.
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){
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x,
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times=1:nrow(x),
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triplicates=FALSE,
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design,
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new.times=seq(min(times), max(times), length.out=length(times)*10),
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level=0.95,
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interval=c("confidence","prediction"),
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plot=TRUE,
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FUN=function(t,K,r,P0) K*P0*exp(r*t)/(K+P0*(exp(r*t)-1)),
|
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nls.opt=list(),
|
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...
|
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){
|
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# Arguments
|
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if(missing(design)){
|
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design <-
|
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if(triplicates)
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tapply(colnames(x), colnames(x)[rep(1:(ncol(x)/3)*3-2, each=3)], c,
|
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simplify=FALSE)
|
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else tapply(colnames(x), colnames(x), c, simplify=FALSE)
|
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|
}
|
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mod <- list()
|
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fit <- list()
|
@@ -207,18 +268,18 @@ enve.growthcurve <- structure(function(
|
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od <- c(od, x[,col])
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}
|
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|
data <- data.frame(t=rep(times, length(design[[sample]])), od=od,
|
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replicate=rep(1:length(design[[sample]]), each=length(times)))
|
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|
data <- data[!is.na(data$od),]
|
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|
opts <- nls.opt
|
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opts[["data"]] <- data
|
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opt.defaults <- list(formula = od ~ enve._growth.fx(t, K, r, P0),
|
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algorithm="port", lower=list(P0=1e-16),
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control=nls.control(warnOnly=TRUE),
|
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start=list(
|
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K = 2*max(data$od),
|
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r = length(times)/max(data$t),
|
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P0 = min(data$od[data$od>0])
|
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))
|
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for(i in names(opt.defaults)){
|
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if(is.null(opts[[i]])){
|
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opts[[i]] <- opt.defaults[[i]]
|
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|
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}
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mod[[sample]] <- do.call(nls, opts)
|
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|
fit[[sample]] <- cbind(t=new.times,
|
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predFit(mod[[sample]], level=level, interval=interval,
|
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newdata=data.frame(t=new.times)))
|
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}
|
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enve._growth.fx <<- NULL
|
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|
gc <- new("enve.GrowthCurve",
|
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|
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|
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|
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design=design, models=mod, predict=fit,
|
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call=match.call());
|
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|
if(plot) plot(gc, ...);
|
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|
return(gc)
|
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|
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### Returns an `enve.GrowthCurve` object.
|
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|
}, ex=function(){
|
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|
# Load data
|
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data("growth.curves", package="enveomics.R", envir=environment())
|
@@ -245,13 +305,21 @@ enve.growthcurve <- structure(function(
|
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plot(g, pch=15:17, col="black", band.density=45, band.angle=c(-45,45,0))
|
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});
|
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#' Enveomics: Color to Alpha
|
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#'
|
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#' Takes a vector of colors and sets the alpha.
|
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#'
|
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#' @param x A vector of any value base colors.
|
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#' @param alpha Alpha level to set (in the 0-1 range).
|
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#'
|
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#' @author Luis M. Rodriguez-R [aut, cre]
|
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#'
|
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#' @export
|
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|
enve.col2alpha <- function(
|
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alpha
|
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### Alpha level to set (in the 0-1 range).
|
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){
|
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x,
|
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alpha
|
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){
|
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|
out <- c()
|
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|
for(i in x){
|
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|
opt <- as.list(col2rgb(i)[,1]/256)
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|
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|
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|
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|
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|
116
|
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|
117
|
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|
118
|
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|
119
|
-
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|
120
|
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|
121
|
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|
122
|
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|
123
|
-
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|
124
|
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|
125
|
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}else if(id.metric==2){
|
126
|
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if(ncol(rec)<6) stop("Requesting corrected identity, but .rec file doesn't have 6th column")
|
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|
-
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|
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|
-
id.shortname <- 'cId.'
|
129
|
-
id.fullname <- 'Corrected identity'
|
130
|
-
id.units <- '%'
|
131
|
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|
132
|
-
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|
133
|
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|
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|
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|
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|
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}else if(id.metric==3){
|
136
|
-
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|
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|
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|
138
|
-
id.fullname <- 'Bit score'
|
139
|
-
id.units <- 'bits'
|
140
|
-
max.bs <- max(rec[, id.reccol])
|
141
|
-
id.hallmarks <- seq(0, max.bs*1.2, by=50)
|
142
|
-
if(is.null(id.max)) id.max <- max.bs
|
143
|
-
if(is.null(id.cutoff)) id.cutoff <- 0.95 * max.bs
|
144
|
-
if(is.null(id.binsize)) id.binsize <- 5
|
145
|
-
}
|
146
|
-
if(is.null(id.min)) id.min <- min(rec[, id.reccol]);
|
147
|
-
if(is.null(pos.max)) pos.max <- max(lim[, 3]);
|
148
|
-
id.lim <- c(id.min, id.max);
|
149
|
-
pos.lim <- c(pos.min, pos.max)/1e6;
|
150
|
-
id.breaks <- round((id.max-id.min)/id.binsize);
|
151
|
-
pos.breaks <- round((pos.max-pos.min)/pos.binsize);
|
152
|
-
if(is.null(main)) main <- paste('Recruitment plot of ', prefix, sep='');
|
153
|
-
pos.marks=seq(pos.min, pos.max, length.out=pos.breaks+1)/1e6;
|
154
|
-
id.marks=seq(id.min, id.max, length.out=id.breaks+1);
|
155
|
-
id.topclasses <- 0;
|
156
|
-
for(i in length(id.marks):1) if(id.marks[i]>id.cutoff) id.topclasses <- id.topclasses + 1;
|
157
|
-
|
158
|
-
# Set-up image
|
159
|
-
layout(matrix(c(3,4,1,2), nrow=2, byrow=TRUE), widths=c(2,1), heights=c(1,2));
|
160
|
-
out <- list();
|
161
|
-
|
162
|
-
# Recruitment plot
|
163
|
-
if(verbose) cat("Rec. plot.\n")
|
164
|
-
par(mar=c(5,4,0,0)+0.1);
|
165
|
-
rec.hist <- matrix(0, nrow=pos.breaks, ncol=id.breaks);
|
166
|
-
for(i in 1:nrow(rec)){
|
167
|
-
id.class <- ceiling((id.breaks)*((rec[i, id.reccol]-id.min)/(id.max-id.min)));
|
168
|
-
if(id.class<=id.breaks & id.class>0){
|
169
|
-
for(pos in rec[i, 1]:rec[i, 2]){
|
170
|
-
pos.class <- ceiling((pos.breaks)*((pos-pos.min)/(pos.max-pos.min)));
|
171
|
-
if(pos.class<=pos.breaks & pos.class>0) rec.hist[pos.class, id.class] <- rec.hist[pos.class, id.class]+1;
|
172
|
-
}
|
173
|
-
}
|
174
|
-
}
|
175
|
-
id.top <- c((1-id.topclasses):0) + id.breaks;
|
176
|
-
rec.col=gplots::colorpanel(256, rec.col1, rec.col2);
|
177
|
-
image(x=pos.marks, y=id.marks, z=log10(rec.hist),
|
178
|
-
breaks=seq(0, log10(max(rec.hist)), length.out=1+length(rec.col)), col=rec.col,
|
179
|
-
xlim=pos.lim, ylim=id.lim, xlab='Position in genome (Mbp)',
|
180
|
-
ylab=paste(id.fullname, ' (',id.units,')', sep=''), xaxs='i', yaxs='r');
|
181
|
-
if(!is.na(contig.col)) abline(v=c(lim$V2, lim$V3)/1e6, lty=1, col=contig.col);
|
182
|
-
abline(h=id.hallmarks, lty=2, col=grey(0.7));
|
183
|
-
abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
|
184
|
-
legend('bottomleft', 'Rec. plot', bg=rgb(1,1,1,2/3));
|
185
|
-
out <- c(out, list(pos.marks=pos.marks, id.marks=id.marks));
|
186
|
-
if(ret.recplot) out <- c(out, list(recplot=rec.hist));
|
187
|
-
|
188
|
-
# Identity histogram
|
189
|
-
if(verbose) cat(id.shortname, " hist.\n", sep='')
|
190
|
-
par(mar=c(5,0,0,2)+0.1);
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id.hist <- id.summary.func(rec.hist);
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plot(1, t='n', xlim=c(1, max(id.hist)), ylim=id.lim, ylab='', yaxt='n', xlab=paste('Sequences (bp),', id.summary.name), log='x', ...);
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id.x <- rep(id.marks, each=2)[2:(id.breaks*2+1)]
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id.f <- rep(id.hist, each=2)[1:(id.breaks*2)]
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if(sum(id.f)>0){
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lines(id.f, id.x, lwd=ifelse(id.splines>0, 1/2, 2), type='o', pch='.');
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if(id.splines>0){
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id.spline <- smooth.spline(id.x[id.f>0], log(id.f[id.f>0]), spar=id.splines)
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lines(exp(id.spline$y), id.spline$x, lwd=2)
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}
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}
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abline(h=id.hallmarks, lty=2, col=grey(0.7));
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abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
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legend('bottomright', paste(id.shortname, 'histogram'), bg=rgb(1,1,1,2/3));
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out <- c(out, list(id.mean=mean(rec[, id.reccol])));
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out <- c(out, list(id.median=median(rec[, id.reccol])));
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if(ret.hist) out <- c(out, list(id.hist=id.hist));
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#' Enveomics: Recruitment Plots
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#'
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#' @description
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#' Produces recruitment plots provided that BlastTab.catsbj.pl has
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#' been previously executed. Requires the \pkg{gplots} library.
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#'
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#' @param prefix
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#' Path to the prefix of the BlastTab.catsbj.pl output files. At
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#' least the files \strong{.rec} and \strong{.lim} must exist with this prefix.
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#' @param id.min
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#' Minimum identity to be considered. By default, the minimum detected
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#' identity. This value is a percentage.
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#' @param id.max
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#' Maximum identity to be considered. By default, 100\%.
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#' @param id.binsize
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#' Size of the identity bins (vertical histograms). By default, 0.1 for
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#' identity metrics and 5 for bit score.
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#' @param id.splines
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#' Smoothing parameter for the splines in the identity histogram. Zero (0) for no
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#' splines. A generally good value is 1/2. If non-zero, requires the \pkg{stats} package.
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#' @param id.metric
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#' Metric of identity to be used (Y-axis).
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#' It can be any unambiguous prefix of:
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#' \itemize{
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#' \item "identity"
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#' \item "corrected identity"
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#' \item "bit score"}
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#' @param id.summary
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#' Method used to build the identity histogram (Horizontal axis of the right panel).
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#' It can be any unambiguous prefix of:
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#' \itemize{
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#' \item "sum"
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#' \item "average"
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#' \item "median"
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#' \item "90\% lower bound"
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#' \item "90\% upper bound"
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#' \item "95\% lower bound"
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#' \item "95\% upper bound" }
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#' The last four options
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#' correspond to the upper and lower boundaries of the 90\% and 95\% empirical confidence
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#' intervals.
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#' @param pos.min
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#' Minimum (leftmost) position in the reference (concatenated) genome (in bp).
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#' @param pos.max
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#' Maximum (rightmost) position in the reference (concatenated) genome (in bp).
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#' By default: Length of the genome.
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#' @param pos.binsize
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#' Size of the position bins (horizontal histograms) in bp.
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#' @param pos.splines
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#' Smoothing parameter for the splines in the position histogram. Zero (0) for no splines.
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#' If non-zero, requires the stats package.
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#' @param rec.col1
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#' Lightest color in the recruitment plot.
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#' @param rec.col2
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#' Darkest color in the recruitment plot.
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#' @param main
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#' Title of the plot.
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#' @param contig.col
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#' Color of the Contig boundaries. Set to \code{NA} to ignore Contig boundaries.
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#' @param ret.recplot
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#' Indicates if the matrix of the recruitment plot is to be returned.
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#' @param ret.hist
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#' Ignored, for backwards compatibility.
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#' @param ret.mode
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#' Indicates if the mode of the identity is to be computed. It requires the
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#' \pkg{modeest} package.
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#' @param id.cutoff
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#' Minimum identity to consider an alignment as "top". By default, it is 0.95 for the
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#' identity metrics and 95\% of the best scoring alignment for bit score.
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#' @param verbose
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#' Indicates if the function should report the advance.
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#' @param ...
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#' Any additional graphic parameters to be passed to plot for all panels except the
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#' recruitment plot (lower-left).
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#'
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#' @return
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#'
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#' Returns a list with the following elements:
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#'
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#' \describe{
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#' \item{\code{pos.marks}}{Midpoints of the position histogram.}
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#' \item{\code{id.matrix}}{Midpoints of the identity histogram.}
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#' \item{\code{recplot}}{Matrix containing the recruitment plot values
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#' (if \code{ret.recplot=TRUE}).}
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#' \item{\code{id.mean}}{Mean identity.}
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#' \item{\code{id.median}}{Median identity.}
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#' \item{\code{id.mode}}{Mode of the identity (if \code{ret.mode=TRUE}). Deprecated.}
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#' \item{\code{id.hist}}{Values of the identity histogram (if \code{ret.hist=TRUE}).}
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#' \item{\code{pos.hist.low}}{Values of the position histogram (depth) with "low"
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#' identity (i.e., below id.cutoff) (if \code{ret.hist=TRUE}).}
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#' \item{\code{pos.hist.top}}{Values of the position histogram (depth) with "top"
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#' identity (i.e., above id.cutoff) (if \code{ret.hist=TRUE}).}
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#' \item{\code{id.max}}{Value of \code{id.max}. This is returned because
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#' \code{id.max=NULL} may vary.}
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#' \item{\code{id.cutoff}}{Value of \code{id.cutoff}.
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#' This is returned because \code{id.cutoff=NULL} may vary.}
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#' \item{\code{seqdepth.mean.top}}{Average sequencing depth with identity above
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#' \code{id.cutoff}.}
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#' \item{\code{seqdepth.mean.low}}{Average sequencing depth with identity below
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#' \code{id.cutoff}.}
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#' \item{\code{seqdepth.mean.all}}{Average sequencing depth without identity filtering.}
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#' \item{\code{seqdepth.median.top}}{Median sequencing depth with identity above
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#' \code{id.cutoff}.}
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#' \item{\code{seqdepth.median.low}}{Median sequencing depth with identity below
|
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#' \code{id.cutoff}.}
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#' \item{\code{seqdepth.median.all}}{Median sequencing depth without identity filtering.}
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#' \item{\code{id.metric}}{Full name of the used identity metric.}
|
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#' \item{\code{id.summary}}{Full name of the summary method used to build the identity plot.}}
|
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#'
|
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#' @author Luis M. Rodriguez-R [aut, cre]
|
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#'
|
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#' @export
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114
|
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enve.recplot <- structure(function(
|
115
|
+
prefix,
|
116
|
+
|
117
|
+
# Id. hist.
|
118
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+
id.min=NULL,
|
119
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+
id.max=NULL,
|
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+
id.binsize=NULL,
|
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+
id.splines=0,
|
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+
id.metric='id',
|
123
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+
id.summary='sum',
|
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+
|
125
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+
# Pos. hist.
|
126
|
+
pos.min=1,
|
127
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+
pos.max=NULL,
|
128
|
+
pos.binsize=1e3,
|
129
|
+
pos.splines=0,
|
130
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+
|
131
|
+
# Rec. plot
|
132
|
+
rec.col1='white',
|
133
|
+
rec.col2='black',
|
134
|
+
|
135
|
+
# General
|
136
|
+
main=NULL,
|
137
|
+
contig.col=grey(0.85),
|
138
|
+
|
139
|
+
# Return
|
140
|
+
ret.recplot=FALSE,
|
141
|
+
ret.hist=FALSE,
|
142
|
+
ret.mode=FALSE,
|
143
|
+
|
144
|
+
# General
|
145
|
+
id.cutoff=NULL,
|
146
|
+
verbose=TRUE,
|
147
|
+
...
|
148
|
+
){
|
149
|
+
|
150
|
+
# Settings
|
151
|
+
METRICS <- c('identity', 'corrected identity', 'bit score');
|
152
|
+
SUMMARY <- c('sum', 'average', 'median', '');
|
153
|
+
if(is.null(prefix)) stop('Parameter prefix is mandatory.');
|
154
|
+
if(!requireNamespace("gplots", quietly=TRUE)) stop('Unavailable gplots library.');
|
155
|
+
|
156
|
+
# Read files
|
157
|
+
if(verbose) cat("Reading files.\n")
|
158
|
+
rec <- read.table(paste(prefix, '.rec', sep=''), sep="\t", comment.char='', quote='');
|
159
|
+
lim <- read.table(paste(prefix, '.lim', sep=''), sep="\t", comment.char='', quote='');
|
160
|
+
|
161
|
+
# Configure ID summary
|
162
|
+
id.summary <- pmatch(id.summary, SUMMARY);
|
163
|
+
if(is.na(id.summary)) stop('Invalid identity summary.');
|
164
|
+
if(id.summary == -1) stop('Ambiguous identity summary.');
|
165
|
+
if(id.summary==1){
|
166
|
+
id.summary.func <- function(x) colSums(x);
|
167
|
+
id.summary.name <- 'sum'
|
168
|
+
}else if(id.summary==2){
|
169
|
+
id.summary.func <- function(x) colMeans(x);
|
170
|
+
id.summary.name <- 'mean'
|
171
|
+
}else if(id.summary==3){
|
172
|
+
id.summary.func <- function(x) apply(x,2,median);
|
173
|
+
id.summary.name <- 'median'
|
174
|
+
}else if(id.summary==4){
|
175
|
+
id.summary.func <- function(x) apply(x,2,quantile,probs=0.05,names=FALSE);
|
176
|
+
id.summary.name <- '90% LB'
|
177
|
+
}else if(id.summary==5){
|
178
|
+
id.summary.func <- function(x) apply(x,2,quantile,probs=0.95,names=FALSE);
|
179
|
+
id.summary.name <- '90% UB'
|
180
|
+
}else if(id.summary==6){
|
181
|
+
id.summary.func <- function(x) apply(x,2,quantile,probs=0.025,names=FALSE);
|
182
|
+
id.summary.name <- '95% LB'
|
183
|
+
}else if(id.summary==7){
|
184
|
+
id.summary.func <- function(x) apply(x,2,quantile,probs=0.975,names=FALSE);
|
185
|
+
id.summary.name <- '95% UB'
|
186
|
+
}
|
187
|
+
|
188
|
+
# Configure metrics
|
189
|
+
id.metric <- pmatch(id.metric, METRICS);
|
190
|
+
if(is.na(id.metric)) stop('Invalid identity metric.');
|
191
|
+
if(id.metric == -1) stop('Ambiguous identity metric.');
|
192
|
+
if(id.metric==1){
|
193
|
+
id.reccol <- 3
|
194
|
+
id.shortname <- 'Id.'
|
195
|
+
id.fullname <- 'Identity'
|
196
|
+
id.units <- '%'
|
197
|
+
id.hallmarks <- seq(0, 100, by=5)
|
198
|
+
if(is.null(id.max)) id.max <- 100
|
199
|
+
if(is.null(id.cutoff)) id.cutoff <- 95
|
200
|
+
if(is.null(id.binsize)) id.binsize <- 0.1
|
201
|
+
}else if(id.metric==2){
|
202
|
+
if(ncol(rec)<6) stop("Requesting corrected identity, but .rec file doesn't have 6th column")
|
203
|
+
id.reccol <- 6
|
204
|
+
id.shortname <- 'cId.'
|
205
|
+
id.fullname <- 'Corrected identity'
|
206
|
+
id.units <- '%'
|
207
|
+
id.hallmarks <- seq(0, 100, by=5)
|
208
|
+
if(is.null(id.max)) id.max <- 100
|
209
|
+
if(is.null(id.cutoff)) id.cutoff <- 95
|
210
|
+
if(is.null(id.binsize)) id.binsize <- 0.1
|
211
|
+
}else if(id.metric==3){
|
212
|
+
id.reccol <- 4
|
213
|
+
id.shortname <- 'BSc.'
|
214
|
+
id.fullname <- 'Bit score'
|
215
|
+
id.units <- 'bits'
|
216
|
+
max.bs <- max(rec[, id.reccol])
|
217
|
+
id.hallmarks <- seq(0, max.bs*1.2, by=50)
|
218
|
+
if(is.null(id.max)) id.max <- max.bs
|
219
|
+
if(is.null(id.cutoff)) id.cutoff <- 0.95 * max.bs
|
220
|
+
if(is.null(id.binsize)) id.binsize <- 5
|
221
|
+
}
|
222
|
+
if(is.null(id.min)) id.min <- min(rec[, id.reccol]);
|
223
|
+
if(is.null(pos.max)) pos.max <- max(lim[, 3]);
|
224
|
+
id.lim <- c(id.min, id.max);
|
225
|
+
pos.lim <- c(pos.min, pos.max)/1e6;
|
226
|
+
id.breaks <- round((id.max-id.min)/id.binsize);
|
227
|
+
pos.breaks <- round((pos.max-pos.min)/pos.binsize);
|
228
|
+
if(is.null(main)) main <- paste('Recruitment plot of ', prefix, sep='');
|
229
|
+
pos.marks=seq(pos.min, pos.max, length.out=pos.breaks+1)/1e6;
|
230
|
+
id.marks=seq(id.min, id.max, length.out=id.breaks+1);
|
231
|
+
id.topclasses <- 0;
|
232
|
+
for(i in length(id.marks):1) if(id.marks[i]>id.cutoff) id.topclasses <- id.topclasses + 1;
|
233
|
+
|
234
|
+
# Set-up image
|
235
|
+
layout(matrix(c(3,4,1,2), nrow=2, byrow=TRUE), widths=c(2,1), heights=c(1,2));
|
236
|
+
out <- list();
|
237
|
+
|
238
|
+
# Recruitment plot
|
239
|
+
if(verbose) cat("Rec. plot.\n")
|
240
|
+
par(mar=c(5,4,0,0)+0.1);
|
241
|
+
rec.hist <- matrix(0, nrow=pos.breaks, ncol=id.breaks);
|
242
|
+
for(i in 1:nrow(rec)){
|
243
|
+
id.class <- ceiling((id.breaks)*((rec[i, id.reccol]-id.min)/(id.max-id.min)));
|
244
|
+
if(id.class<=id.breaks & id.class>0){
|
245
|
+
for(pos in rec[i, 1]:rec[i, 2]){
|
246
|
+
pos.class <- ceiling((pos.breaks)*((pos-pos.min)/(pos.max-pos.min)));
|
247
|
+
if(pos.class<=pos.breaks & pos.class>0) rec.hist[pos.class, id.class] <- rec.hist[pos.class, id.class]+1;
|
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|
}
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-
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311
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-
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312
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-
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313
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-
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314
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-
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315
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-
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316
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-
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317
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-
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249
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+
}
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250
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+
}
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251
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+
id.top <- c((1-id.topclasses):0) + id.breaks;
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252
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+
rec.col=gplots::colorpanel(256, rec.col1, rec.col2);
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253
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+
image(x=pos.marks, y=id.marks, z=log10(rec.hist),
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254
|
+
breaks=seq(0, log10(max(rec.hist)), length.out=1+length(rec.col)), col=rec.col,
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255
|
+
xlim=pos.lim, ylim=id.lim, xlab='Position in genome (Mbp)',
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256
|
+
ylab=paste(id.fullname, ' (',id.units,')', sep=''), xaxs='i', yaxs='r');
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257
|
+
if(!is.na(contig.col)) abline(v=c(lim$V2, lim$V3)/1e6, lty=1, col=contig.col);
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258
|
+
abline(h=id.hallmarks, lty=2, col=grey(0.7));
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259
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+
abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
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260
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+
legend('bottomleft', 'Rec. plot', bg=rgb(1,1,1,2/3));
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261
|
+
out <- c(out, list(pos.marks=pos.marks, id.marks=id.marks));
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262
|
+
if(ret.recplot) out <- c(out, list(recplot=rec.hist));
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263
|
+
|
264
|
+
# Identity histogram
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265
|
+
if(verbose) cat(id.shortname, " hist.\n", sep='')
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266
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+
par(mar=c(5,0,0,2)+0.1);
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267
|
+
id.hist <- id.summary.func(rec.hist);
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268
|
+
plot(1, t='n', xlim=c(1, max(id.hist)), ylim=id.lim, ylab='', yaxt='n', xlab=paste('Sequences (bp),', id.summary.name), log='x', ...);
|
269
|
+
id.x <- rep(id.marks, each=2)[2:(id.breaks*2+1)]
|
270
|
+
id.f <- rep(id.hist, each=2)[1:(id.breaks*2)]
|
271
|
+
if(sum(id.f)>0){
|
272
|
+
lines(id.f, id.x, lwd=ifelse(id.splines>0, 1/2, 2), type='o', pch='.');
|
273
|
+
if(id.splines>0){
|
274
|
+
id.spline <- smooth.spline(id.x[id.f>0], log(id.f[id.f>0]), spar=id.splines)
|
275
|
+
lines(exp(id.spline$y), id.spline$x, lwd=2)
|
276
|
+
}
|
277
|
+
}
|
278
|
+
|
279
|
+
abline(h=id.hallmarks, lty=2, col=grey(0.7));
|
280
|
+
abline(h=id.marks[id.top[1]], lty=3, col=grey(0.5))
|
281
|
+
legend('bottomright', paste(id.shortname, 'histogram'), bg=rgb(1,1,1,2/3));
|
282
|
+
out <- c(out, list(id.mean=mean(rec[, id.reccol])));
|
283
|
+
out <- c(out, list(id.median=median(rec[, id.reccol])));
|
284
|
+
if(ret.hist) out <- c(out, list(id.hist=id.hist));
|
285
|
+
|
286
|
+
# Position histogram
|
287
|
+
if(verbose) cat("Pos. hist.\n")
|
288
|
+
par(mar=c(0,4,4,0)+0.1);
|
289
|
+
h1<-rep(0,nrow(rec.hist)) ;
|
290
|
+
h2<-rep(0,nrow(rec.hist)) ;
|
291
|
+
pos.winsize <- (pos.max-pos.min+1)/pos.breaks;
|
292
|
+
if(sum(rec.hist[, id.top])>0) h1 <- rowSums(matrix(rec.hist[, id.top], nrow=nrow(rec.hist)))/pos.winsize;
|
293
|
+
if(sum(rec.hist[,-id.top])>0) h2 <- rowSums(matrix(rec.hist[,-id.top], nrow=nrow(rec.hist)))/pos.winsize;
|
294
|
+
|
295
|
+
ymin <- min(1, h1[h1>0], h2[h2>0]);
|
296
|
+
ymax <- max(10, h1, h2);
|
297
|
+
if(is.na(ymin) || ymin<=0) ymin <- 1e-10;
|
298
|
+
if(is.na(ymax) || ymax<=0) ymax <- 1;
|
299
|
+
plot(1, t='n', xlab='', xaxt='n', ylab='Sequencing depth (X)', log='y', xlim=pos.lim,
|
300
|
+
ylim=c(ymin, ymax), xaxs='i', main=main, ...);
|
301
|
+
if(!is.na(contig.col)) abline(v=c(lim[,2], lim[,3])/1e6, lty=1, col=contig.col);
|
302
|
+
abline(h=10^c(0:5), lty=2, col=grey(0.7));
|
303
|
+
if(sum(h2)>0){
|
304
|
+
h2.x <- rep(pos.marks, each=2)[2:(pos.breaks*2+1)]
|
305
|
+
h2.y <- rep(h2, each=2)[1:(pos.breaks*2)]
|
306
|
+
lines(h2.x, h2.y, lwd=ifelse(pos.splines>0, 1/2, 2), col=grey(0.5));
|
307
|
+
if(pos.splines>0){
|
308
|
+
h2.spline <- smooth.spline(h2.x[h2.y>0], log(h2.y[h2.y>0]), spar=pos.splines)
|
309
|
+
lines(h2.spline$x, exp(h2.spline$y), lwd=2, col=grey(0.5))
|
310
|
+
}
|
311
|
+
if(ret.hist) out <- c(out, list(pos.hist.low=h2.y));
|
312
|
+
}
|
313
|
+
if(sum(h1)>0){
|
314
|
+
h1.x <- rep(pos.marks, each=2)[2:(pos.breaks*2+1)]
|
315
|
+
h1.y <- rep(h1, each=2)[1:(pos.breaks*2)]
|
316
|
+
lines(h1.x, h1.y, lwd=ifelse(pos.splines>0, 1/2, 2), col=grey(0));
|
317
|
+
if(pos.splines>0){
|
318
|
+
h1.spline <- smooth.spline(h1.x[h1.y>0], log(h1.y[h1.y>0]), spar=pos.splines)
|
319
|
+
lines(h1.spline$x, exp(h1.spline$y), lwd=2, col=grey(0))
|
320
|
+
}
|
321
|
+
if(ret.hist) out <- c(out, list(pos.hist.top=h1.y));
|
322
|
+
}
|
323
|
+
legend('topleft', 'Pos. histogram', bg=rgb(1,1,1,2/3));
|
324
|
+
out <- c(out, list(id.max=id.max, id.cutoff=id.marks[id.top[1]]));
|
325
|
+
out <- c(out, list(seqdepth.mean.top=mean(h1)));
|
326
|
+
out <- c(out, list(seqdepth.mean.low=mean(h2)));
|
327
|
+
out <- c(out, list(seqdepth.mean=mean(h1+h2)));
|
328
|
+
out <- c(out, list(seqdepth.median.top=median(h1)));
|
329
|
+
out <- c(out, list(seqdepth.median.low=median(h2)));
|
330
|
+
out <- c(out, list(seqdepth.median=median(h1+h2)));
|
331
|
+
out <- c(out, list(id.metric=id.fullname));
|
332
|
+
out <- c(out, list(id.summary=id.summary.name));
|
333
|
+
|
334
|
+
# Legend
|
335
|
+
par(mar=c(0,0,4,2)+0.1);
|
336
|
+
plot(1, t='n', xlab='', xaxt='n', ylab='', yaxt='n', xlim=c(0,1), ylim=c(0,1), xaxs='r', yaxs='i', ...);
|
337
|
+
text(1/2, 5/6, labels=paste('Reads per ', signif((pos.max-pos.min)/pos.breaks, 2), ' bp (rec. plot)', sep=''), pos=3);
|
338
|
+
leg.col <- gplots::colorpanel(100, rec.col1, rec.col2);
|
339
|
+
leg.lab <- signif(10^seq(0, log10(max(rec.hist)), length.out=10), 2);
|
340
|
+
for(i in 1:10){
|
341
|
+
for(j in 1:10){
|
342
|
+
k <- (i-1)*10 + j;
|
343
|
+
polygon(c(k-1, k, k, k-1)/100, c(2/3, 2/3, 5/6, 5/6), border=leg.col[k], col=leg.col[k]);
|
344
|
+
}
|
345
|
+
text((i-0.5)/10, 2/3, labels=paste(leg.lab[i], ''), srt=90, pos=2, offset=0, cex=3/4);
|
346
|
+
}
|
347
|
+
legend('bottom',
|
348
|
+
legend=c('Contig boundary', 'Hallmark', paste(id.fullname, 'cutoff'),
|
349
|
+
paste('Pos. hist.: ',id.shortname,' > ',signif(id.marks[id.top[1]],2),id.units,sep=''),
|
350
|
+
paste('Pos. hist.: ',id.shortname,' < ',signif(id.marks[id.top[1]],2),id.units,sep='')), ncol=2,
|
351
|
+
col=grey(c(0.85, 0.7, 0.5, 0, 0.5)), lty=c(1,2,3,1,1), lwd=c(1,1,1,2,2), bty='n', inset=0.05, cex=5/6);
|
352
|
+
return(out);
|
318
353
|
});
|
319
354
|
|