miga-base 0.7.26.3 → 1.0.0.sr1
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- checksums.yaml +4 -4
- data/lib/miga/_data/aai-intax.blast.tsv.gz +0 -0
- data/lib/miga/_data/aai-intax.diamond.tsv.gz +0 -0
- data/lib/miga/_data/aai-novel.blast.tsv.gz +0 -0
- data/lib/miga/_data/aai-novel.diamond.tsv.gz +0 -0
- data/lib/miga/cli/action/doctor.rb +50 -19
- data/lib/miga/cli/action/doctor/base.rb +20 -18
- data/lib/miga/cli/action/init.rb +11 -7
- data/lib/miga/cli/action/init/files_helper.rb +1 -0
- data/lib/miga/cli/action/ncbi_get.rb +3 -3
- data/lib/miga/cli/action/tax_dist.rb +2 -2
- data/lib/miga/cli/action/wf.rb +5 -4
- data/lib/miga/daemon.rb +11 -4
- data/lib/miga/dataset/result.rb +10 -6
- data/lib/miga/json.rb +1 -2
- data/lib/miga/metadata.rb +5 -1
- data/lib/miga/parallel.rb +11 -6
- data/lib/miga/project.rb +8 -8
- data/lib/miga/project/base.rb +4 -4
- data/lib/miga/project/result.rb +2 -2
- data/lib/miga/sqlite.rb +7 -0
- data/lib/miga/version.rb +23 -9
- data/scripts/aai_distances.bash +16 -18
- data/scripts/ani_distances.bash +16 -17
- data/scripts/assembly.bash +31 -16
- data/scripts/haai_distances.bash +3 -27
- data/scripts/miga.bash +6 -4
- data/scripts/p.bash +1 -1
- data/scripts/read_quality.bash +9 -18
- data/scripts/trimmed_fasta.bash +14 -30
- data/scripts/trimmed_reads.bash +36 -36
- data/test/parallel_test.rb +31 -0
- data/test/project_test.rb +2 -1
- data/utils/distance/commands.rb +1 -0
- data/utils/distance/runner.rb +2 -4
- data/utils/enveomics/Manifest/Tasks/fasta.json +39 -3
- data/utils/enveomics/Manifest/Tasks/fastq.json +50 -2
- data/utils/enveomics/Manifest/Tasks/mapping.json +70 -0
- data/utils/enveomics/Manifest/Tasks/other.json +77 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +138 -1
- data/utils/enveomics/Manifest/categories.json +13 -4
- data/utils/enveomics/Scripts/Aln.cat.rb +206 -148
- data/utils/enveomics/Scripts/FastA.N50.pl +33 -29
- data/utils/enveomics/Scripts/FastA.fragment.rb +69 -61
- data/utils/enveomics/Scripts/FastA.sample.rb +61 -46
- data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
- data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +59 -52
- data/utils/enveomics/Scripts/SRA.download.bash +6 -8
- data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
- data/utils/enveomics/Scripts/aai.rb +3 -2
- data/utils/enveomics/Scripts/anir.rb +137 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +17 -17
- data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +63 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +73 -0
- data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
- data/utils/enveomics/Scripts/rbm.rb +87 -133
- data/utils/enveomics/Scripts/sam.filter.rb +148 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +2 -2
- data/utils/enveomics/enveomics.R/NAMESPACE +1 -1
- data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
- data/utils/enveomics/enveomics.R/R/utils.R +30 -0
- data/utils/enveomics/enveomics.R/README.md +1 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -1
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +10 -2
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +16 -4
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +13 -3
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +9 -2
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +13 -5
- data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +9 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +23 -6
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +13 -4
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +7 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +14 -3
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +10 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +8 -2
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +17 -9
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +6 -2
- data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +14 -5
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +19 -4
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +11 -3
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +11 -4
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +26 -12
- data/utils/multitrim/Multitrim How-To.pdf +0 -0
- data/utils/multitrim/README.md +67 -0
- data/utils/multitrim/multitrim.py +1555 -0
- data/utils/multitrim/multitrim.yml +13 -0
- data/utils/requirements.txt +4 -3
- metadata +33 -6
- data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +0 -30
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/prefscore.R
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\name{enve.prefscore}
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\alias{enve.prefscore}
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\title{Enveomics: Pref Score}
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\usage{
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enve.prefscore(
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x,
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set,
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ignore = NULL,
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signif.thr,
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plot = TRUE,
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col.above = rgb(148, 17, 0, maxColorValue = 255),
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col.equal = rgb(189, 189, 189, maxColorValue = 255),
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col.below = rgb(47, 84, 150, maxColorValue = 255),
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...
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)
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}
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\arguments{
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\item{x}{Occupancy matrix (logical or numeric binary) with species as rows and samples
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as columns}
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\item{set}{Vector indicating samples in the test set. It can be any selection vector:
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boolean (same length as the number of columns in \code{x}), or numeric or
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character vector with indexes of the \code{x} columns.}
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\item{ignore}{Vector indicating species to ignore. It can be any selection vector with
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respect to the rows in \code{x} (see \code{set}).}
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\item{signif.thr}{Absolute value of the significance threshold}
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\item{plot}{Indicates if a plot should be generated}
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\item{col.above}{Color for points significantly above zero}
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\item{col.equal}{Color for points not significantly different from zero}
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\item{col.below}{Color for points significantly below zero}
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\item{...}{Any additional parameters supported by \code{plot}}
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}
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\value{
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Returns a named vector of preference scores.
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}
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\description{
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Estimate preference score of species based on occupancy in biased sample sets
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}
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\author{
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Luis M. Rodriguez-R [aut, cre]
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}
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\alias{enve.prune.dist}
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\title{Enveomics: Prune Dist}
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\usage{
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enve.prune.dist(
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enve.prune.dist(
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t,
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dist.quantile = 0.25,
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min_dist,
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quiet = FALSE,
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max_iters = 100,
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min_nodes_random = 40000,
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random_nodes_frx = 1
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)
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}
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\arguments{
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\item{t}{A \strong{phylo} object or a path to the Newick file.}
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\alias{enve.recplot}
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\title{Enveomics: Recruitment Plots}
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\usage{
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enve.recplot(
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enve.recplot(
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prefix,
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id.min = NULL,
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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",
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id.summary = "sum",
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pos.min = 1,
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pos.max = NULL,
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pos.binsize = 1000,
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pos.splines = 0,
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rec.col1 = "white",
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rec.col2 = "black",
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main = NULL,
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contig.col = grey(0.85),
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ret.recplot = FALSE,
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ret.hist = FALSE,
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ret.mode = FALSE,
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id.cutoff = NULL,
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verbose = TRUE,
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...
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)
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\arguments{
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\item{prefix}{Path to the prefix of the BlastTab.catsbj.pl output files. At
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\alias{enve.recplot2}
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\title{Enveomics: Recruitment Plot (2)}
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\usage{
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enve.recplot2(
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enve.recplot2(
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prefix,
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plot = TRUE,
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pos.breaks = 1000,
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pos.breaks.tsv = NA,
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id.breaks = 60,
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id.free.range = FALSE,
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id.metric = c("identity", "corrected identity", "bit score"),
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id.summary = sum,
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id.summary = sum,
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id.cutoff = 95,
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threads = 2,
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verbose = TRUE,
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...
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)
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\arguments{
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\item{prefix}{Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
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\alias{enve.recplot2.compareIdentities}
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\title{Enveomics: Recruitment Plot (2) Compare Identities}
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\usage{
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enve.recplot2.compareIdentities(
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enve.recplot2.compareIdentities(
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x,
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y,
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method = "hellinger",
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smooth.par = NULL,
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pseudocounts = 0,
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max.deviation = 0.75
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)
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\item{x}{First \code{\link{enve.RecPlot2}} object.}
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\alias{enve.recplot2.extractWindows}
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\title{Enveomics: Recruitment Plot (2) Extract Windows}
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\usage{
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enve.recplot2.extractWindows(
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enve.recplot2.extractWindows(
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rp,
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peak,
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lower.tail = TRUE,
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significance = 0.05,
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seq.names = FALSE
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)
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\arguments{
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\item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}
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\alias{enve.recplot2.findPeaks.__mow_one}
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\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1}
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\usage{
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enve.recplot2.findPeaks.__mow_one(
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enve.recplot2.findPeaks.__mow_one(
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lsd1,
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min.points,
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quant.est,
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mlv.opts,
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fitdist.opts,
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with.skewness,
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optim.rounds,
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optim.epsilon,
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n.total,
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merge.logdist,
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verbose,
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log
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)
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\arguments{
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\item{lsd1}{Vector of log-transformed sequencing depths}
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\alias{enve.recplot2.findPeaks.em}
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\title{Enveomics: Recruitment Plot (2) Em Peak Finder}
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\usage{
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enve.recplot2.findPeaks.em(
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enve.recplot2.findPeaks.em(
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x,
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max.iter = 1000,
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ll.diff.res = 1e-08,
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components = 2,
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rm.top = 0.05,
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verbose = FALSE,
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init,
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log = TRUE
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)
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\arguments{
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\item{x}{An \code{\link{enve.RecPlot2}} object.}
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\alias{enve.recplot2.findPeaks.emauto}
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\title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
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\usage{
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enve.recplot2.findPeaks.emauto(
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enve.recplot2.findPeaks.emauto(
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x,
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components = seq(1, 5),
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criterion = "aic",
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merge.tol = 2L,
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verbose = FALSE,
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\item{x}{An \code{\link{enve.RecPlot2}} object.}
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\alias{enve.recplot2.findPeaks.mower}
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\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
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\usage{
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enve.recplot2.findPeaks.mower(
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x,
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min.points = 10,
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quant.est = c(0.002, 0.998),
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mlv.opts = list(method = "parzen"),
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fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start =
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list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
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fitdist.opts.norm = list(distr = "norm", method = "qme", probs = c(0.4, 0.6), start =
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list(sd = 1), lower = c(0, -Inf)),
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rm.top = 0.05,
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with.skewness = TRUE,
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optim.rounds = 200,
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optim.epsilon = 1e-04,
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merge.logdist = log(1.75),
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verbose = FALSE,
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log = TRUE
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\arguments{
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\item{x}{An \code{\link{enve.RecPlot2}} object.}
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\alias{enve.recplot2.windowDepthThreshold}
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\title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
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\usage{
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enve.recplot2.windowDepthThreshold(
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enve.recplot2.windowDepthThreshold(
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rp,
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9
|
+
peak,
|
10
|
+
lower.tail = TRUE,
|
11
|
+
significance = 0.05
|
12
|
+
)
|
9
13
|
}
|
10
14
|
\arguments{
|
11
15
|
\item{rp}{Recruitment plot, an \code{\link{enve.RecPlot2}} object.}
|
@@ -0,0 +1,23 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/utils.R
|
3
|
+
\name{enve.selvector}
|
4
|
+
\alias{enve.selvector}
|
5
|
+
\title{Enveomics: Selection vector}
|
6
|
+
\usage{
|
7
|
+
enve.selvector(sel, dim.names)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{sel}{A vector of numbers, characters, or booleans.}
|
11
|
+
|
12
|
+
\item{dim.names}{A vector of names from which to select.}
|
13
|
+
}
|
14
|
+
\value{
|
15
|
+
Returns a logical vector with the same length as \code{dim.name}.
|
16
|
+
}
|
17
|
+
\description{
|
18
|
+
Normalizes a selection vector \code{sel} to a logical vector with indexes
|
19
|
+
from \code{dim.names}.
|
20
|
+
}
|
21
|
+
\author{
|
22
|
+
Luis M. Rodriguez-R [aut, cre]
|
23
|
+
}
|
@@ -4,11 +4,20 @@
|
|
4
4
|
\alias{enve.tribs}
|
5
5
|
\title{Enveomics: TRIBS}
|
6
6
|
\usage{
|
7
|
-
enve.tribs(
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
7
|
+
enve.tribs(
|
8
|
+
dist,
|
9
|
+
selection = labels(dist),
|
10
|
+
replicates = 1000,
|
11
|
+
summary.fx = median,
|
12
|
+
dist.method = "euclidean",
|
13
|
+
subsamples = seq(0, 1, by = 0.01),
|
14
|
+
dimensions = ceiling(length(selection) * 0.05),
|
15
|
+
metaMDS.opts = list(),
|
16
|
+
threads = 2,
|
17
|
+
verbosity = 1,
|
18
|
+
points,
|
19
|
+
pre.tribs
|
20
|
+
)
|
12
21
|
}
|
13
22
|
\arguments{
|
14
23
|
\item{dist}{Distances as a \code{dist} object.}
|
@@ -4,10 +4,25 @@
|
|
4
4
|
\alias{plot.enve.GrowthCurve}
|
5
5
|
\title{Enveomics: Plot of Growth Curve}
|
6
6
|
\usage{
|
7
|
-
\method{plot}{enve.GrowthCurve}(
|
8
|
-
|
9
|
-
|
10
|
-
|
7
|
+
\method{plot}{enve.GrowthCurve}(
|
8
|
+
x,
|
9
|
+
col,
|
10
|
+
pt.alpha = 0.9,
|
11
|
+
ln.alpha = 1,
|
12
|
+
ln.lwd = 1,
|
13
|
+
ln.lty = 1,
|
14
|
+
band.alpha = 0.4,
|
15
|
+
band.density = NULL,
|
16
|
+
band.angle = 45,
|
17
|
+
xp.alpha = 0.5,
|
18
|
+
xp.lwd = 1,
|
19
|
+
xp.lty = 1,
|
20
|
+
pch = 19,
|
21
|
+
new = TRUE,
|
22
|
+
legend = new,
|
23
|
+
add.params = FALSE,
|
24
|
+
...
|
25
|
+
)
|
11
26
|
}
|
12
27
|
\arguments{
|
13
28
|
\item{x}{An \code{\link{enve.GrowthCurve}} object to plot.}
|
@@ -4,9 +4,17 @@
|
|
4
4
|
\alias{plot.enve.TRIBS}
|
5
5
|
\title{Enveomics: TRIBS Plot}
|
6
6
|
\usage{
|
7
|
-
\method{plot}{enve.TRIBS}(
|
8
|
-
|
9
|
-
|
7
|
+
\method{plot}{enve.TRIBS}(
|
8
|
+
x,
|
9
|
+
new = TRUE,
|
10
|
+
type = c("boxplot", "points"),
|
11
|
+
col = "#00000044",
|
12
|
+
pt.cex = 1/2,
|
13
|
+
pt.pch = 19,
|
14
|
+
pt.col = col,
|
15
|
+
ln.col = col,
|
16
|
+
...
|
17
|
+
)
|
10
18
|
}
|
11
19
|
\arguments{
|
12
20
|
\item{x}{\code{\link{enve.TRIBS}} object to plot.}
|
@@ -4,10 +4,17 @@
|
|
4
4
|
\alias{plot.enve.TRIBStest}
|
5
5
|
\title{Enveomics: TRIBS Plot Test}
|
6
6
|
\usage{
|
7
|
-
\method{plot}{enve.TRIBStest}(
|
8
|
-
|
9
|
-
|
10
|
-
|
7
|
+
\method{plot}{enve.TRIBStest}(
|
8
|
+
x,
|
9
|
+
type = c("overlap", "difference"),
|
10
|
+
col = "#00000044",
|
11
|
+
col1 = col,
|
12
|
+
col2 = "#44001144",
|
13
|
+
ylab = "Probability",
|
14
|
+
xlim = range(attr(x, "dist.mids")),
|
15
|
+
ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))),
|
16
|
+
...
|
17
|
+
)
|
11
18
|
}
|
12
19
|
\arguments{
|
13
20
|
\item{x}{\code{\link{enve.TRIBStest}} object to plot.}
|
@@ -4,21 +4,35 @@
|
|
4
4
|
\alias{plot.enve.RecPlot2}
|
5
5
|
\title{Enveomics: Recruitment Plot (2)}
|
6
6
|
\usage{
|
7
|
-
\method{plot}{enve.RecPlot2}(
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
|
15
|
-
|
16
|
-
|
7
|
+
\method{plot}{enve.RecPlot2}(
|
8
|
+
x,
|
9
|
+
layout = matrix(c(5, 5, 2, 1, 4, 3), nrow = 2),
|
10
|
+
panel.fun = list(),
|
11
|
+
widths = c(1, 7, 2),
|
12
|
+
heights = c(1, 2),
|
13
|
+
palette = grey((100:0)/100),
|
14
|
+
underlay.group = TRUE,
|
15
|
+
peaks.col = "darkred",
|
16
|
+
use.peaks,
|
17
|
+
id.lim = range(x$id.breaks),
|
18
|
+
pos.lim = range(x$pos.breaks),
|
19
|
+
pos.units = c("Mbp", "Kbp", "bp"),
|
20
|
+
mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1), 1, 5), 4, 4, 1)
|
21
|
+
+ 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) + 0.1, `4` =
|
22
|
+
c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1, 4), 4, 2) + 0.1, `5` =
|
23
|
+
c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
|
24
|
+
pos.splines = 0,
|
25
|
+
id.splines = 1/2,
|
17
26
|
in.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
|
18
27
|
out.lwd = ifelse(is.null(pos.splines) || pos.splines > 0, 1/2, 2),
|
19
28
|
id.lwd = ifelse(is.null(id.splines) || id.splines > 0, 1/2, 2),
|
20
|
-
in.col = "darkblue",
|
21
|
-
|
29
|
+
in.col = "darkblue",
|
30
|
+
out.col = "lightblue",
|
31
|
+
id.col = "black",
|
32
|
+
breaks.col = "#AAAAAA40",
|
33
|
+
peaks.opts = list(),
|
34
|
+
...
|
35
|
+
)
|
22
36
|
}
|
23
37
|
\arguments{
|
24
38
|
\item{x}{\code{\link{enve.RecPlot2}} object to plot.}
|