miga-base 0.7.26.0 → 0.7.26.1
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- checksums.yaml +4 -4
- data/lib/miga/version.rb +1 -1
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
- data/utils/FastAAI/FastAAI/FastAAI +1336 -0
- data/utils/FastAAI/README.md +84 -0
- data/utils/FastAAI/kAAI_v1.0_virus.py +1296 -0
- data/utils/enveomics/Docs/recplot2.md +244 -0
- data/utils/enveomics/Examples/aai-matrix.bash +66 -0
- data/utils/enveomics/Examples/ani-matrix.bash +66 -0
- data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
- data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
- data/utils/enveomics/LICENSE.txt +73 -0
- data/utils/enveomics/Makefile +52 -0
- data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
- data/utils/enveomics/Manifest/Tasks/blasttab.json +786 -0
- data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
- data/utils/enveomics/Manifest/Tasks/fasta.json +766 -0
- data/utils/enveomics/Manifest/Tasks/fastq.json +243 -0
- data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
- data/utils/enveomics/Manifest/Tasks/mapping.json +67 -0
- data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
- data/utils/enveomics/Manifest/Tasks/other.json +829 -0
- data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +501 -0
- data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
- data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
- data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
- data/utils/enveomics/Manifest/categories.json +156 -0
- data/utils/enveomics/Manifest/examples.json +154 -0
- data/utils/enveomics/Manifest/tasks.json +4 -0
- data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
- data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
- data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
- data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
- data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
- data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
- data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
- data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
- data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
- data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
- data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
- data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
- data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
- data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
- data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
- data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
- data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
- data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
- data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
- data/utils/enveomics/README.md +42 -0
- data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
- data/utils/enveomics/Scripts/Aln.cat.rb +163 -0
- data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
- data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
- data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
- data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
- data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
- data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
- data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
- data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
- data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
- data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
- data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
- data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
- data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +101 -0
- data/utils/enveomics/Scripts/Chao1.pl +97 -0
- data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
- data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
- data/utils/enveomics/Scripts/FastA.N50.pl +56 -0
- data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
- data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
- data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
- data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
- data/utils/enveomics/Scripts/FastA.fragment.rb +92 -0
- data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
- data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
- data/utils/enveomics/Scripts/FastA.length.pl +38 -0
- data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
- data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
- data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
- data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
- data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
- data/utils/enveomics/Scripts/FastA.sample.rb +83 -0
- data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
- data/utils/enveomics/Scripts/FastA.split.pl +55 -0
- data/utils/enveomics/Scripts/FastA.split.rb +79 -0
- data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
- data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
- data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
- data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
- data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +63 -0
- data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
- data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
- data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
- data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
- data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
- data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
- data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
- data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
- data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
- data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
- data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
- data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
- data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
- data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
- data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
- data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
- data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
- data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
- data/utils/enveomics/Scripts/SRA.download.bash +57 -0
- data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
- data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
- data/utils/enveomics/Scripts/Table.barplot.R +31 -0
- data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
- data/utils/enveomics/Scripts/Table.filter.pl +61 -0
- data/utils/enveomics/Scripts/Table.merge.pl +77 -0
- data/utils/enveomics/Scripts/Table.replace.rb +69 -0
- data/utils/enveomics/Scripts/Table.round.rb +63 -0
- data/utils/enveomics/Scripts/Table.split.pl +57 -0
- data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
- data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
- data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
- data/utils/enveomics/Scripts/aai.rb +418 -0
- data/utils/enveomics/Scripts/ani.rb +362 -0
- data/utils/enveomics/Scripts/clust.rand.rb +102 -0
- data/utils/enveomics/Scripts/gi2tax.rb +103 -0
- data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
- data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +30 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
- data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
- data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
- data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
- data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
- data/utils/enveomics/Scripts/ogs.rb +104 -0
- data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
- data/utils/enveomics/Scripts/rbm.rb +146 -0
- data/utils/enveomics/Tests/Makefile +10 -0
- data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
- data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
- data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
- data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
- data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
- data/utils/enveomics/Tests/alkB.nwk +1 -0
- data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
- data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
- data/utils/enveomics/Tests/hiv1.faa +59 -0
- data/utils/enveomics/Tests/hiv1.fna +134 -0
- data/utils/enveomics/Tests/hiv2.faa +70 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
- data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
- data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
- data/utils/enveomics/build_enveomics_r.bash +45 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
- data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
- data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
- data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
- data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
- data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
- data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
- data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
- data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
- data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
- data/utils/enveomics/enveomics.R/R/utils.R +50 -0
- data/utils/enveomics/enveomics.R/README.md +80 -0
- data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
- data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -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 +25 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +32 -0
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +91 -0
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +57 -0
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +39 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +38 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +40 -0
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +67 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +37 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +122 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +68 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +41 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +40 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +41 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +43 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +37 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +74 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +32 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +59 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
- data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +63 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +38 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +38 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +111 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
- data/utils/enveomics/globals.mk +8 -0
- data/utils/enveomics/manifest.json +9 -0
- metadata +277 -4
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/recplot2.R
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\docType{class}
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\name{enve.RecPlot2-class}
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\alias{enve.RecPlot2-class}
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\alias{enve.RecPlot2}
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\title{Enveomics: Recruitment Plot (2) - S4 Class}
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\description{
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Enve-omics representation of Recruitment plots. This object can
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be produced by \code{\link{enve.recplot2}} and supports S4 method plot.
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\describe{
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\item{\code{counts}}{\code{(matrix)} Counts as a two-dimensional histogram.}
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|
17
|
+
\item{\code{pos.counts.in}}{\code{(numeric)} Counts of in-group hits per position bin.}
|
18
|
+
|
19
|
+
\item{\code{pos.counts.out}}{\code{(numeric)} Counts of out-group hits per position bin.}
|
20
|
+
|
21
|
+
\item{\code{id.counts}}{\code{(numeric)} Counts per ID bin.}
|
22
|
+
|
23
|
+
\item{\code{id.breaks}}{\code{(numeric)} Breaks of identity bins.}
|
24
|
+
|
25
|
+
\item{\code{pos.breaks}}{\code{(numeric)} Breaks of position bins.}
|
26
|
+
|
27
|
+
\item{\code{pos.names}}{\code{(character)} Names of the position bins.}
|
28
|
+
|
29
|
+
\item{\code{seq.breaks}}{\code{(numeric)} Breaks of input sequences.}
|
30
|
+
|
31
|
+
\item{\code{peaks}}{\code{(list)} Peaks identified in the recplot.
|
32
|
+
Limits of the subject sequences after concatenation.}
|
33
|
+
|
34
|
+
\item{\code{seq.names}}{\code{(character}) Names of the subject sequences.}
|
35
|
+
|
36
|
+
\item{\code{id.metric}}{\code{(character}) Metric used as 'identity'.}
|
37
|
+
|
38
|
+
\item{\code{id.ingroup}}{\code{(logical}) Identity bins considered in-group.}
|
39
|
+
|
40
|
+
\item{\code{call}}{\code{(call)} Call producing this object.}
|
41
|
+
}}
|
42
|
+
|
43
|
+
\author{
|
44
|
+
Luis M. Rodriguez-R [aut, cre]
|
45
|
+
}
|
@@ -0,0 +1,24 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.ANIr}
|
4
|
+
\alias{enve.recplot2.ANIr}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) ANI Estimate}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.ANIr(x, range = c(0, Inf))
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{x}{\code{\link{enve.RecPlot2}} object.}
|
11
|
+
|
12
|
+
\item{range}{Range of identities to be considered. By default, the full range
|
13
|
+
is used (note that the upper boundary is \code{Inf} and not 100 because
|
14
|
+
recruitment plots can also be built with bit-scores). To use only
|
15
|
+
intra-population matches (with identities), use c(95,100). To use only
|
16
|
+
inter-population values, use c(0,95).}
|
17
|
+
}
|
18
|
+
\description{
|
19
|
+
Estimate the Average Nucleotide Identity from reads (ANIr) from a
|
20
|
+
recruitment plot.
|
21
|
+
}
|
22
|
+
\author{
|
23
|
+
Luis M. Rodriguez-R [aut, cre]
|
24
|
+
}
|
@@ -0,0 +1,68 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2}
|
4
|
+
\alias{enve.recplot2}
|
5
|
+
\title{Enveomics: Recruitment Plot (2)}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2(prefix, plot = TRUE, pos.breaks = 1000,
|
8
|
+
pos.breaks.tsv = NA, id.breaks = 60, id.free.range = FALSE,
|
9
|
+
id.metric = c("identity", "corrected identity", "bit score"),
|
10
|
+
id.summary = sum, id.cutoff = 95, threads = 2, verbose = TRUE,
|
11
|
+
...)
|
12
|
+
}
|
13
|
+
\arguments{
|
14
|
+
\item{prefix}{Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
|
15
|
+
least the files .rec and .lim must exist with this prefix.}
|
16
|
+
|
17
|
+
\item{plot}{Should the object be plotted?}
|
18
|
+
|
19
|
+
\item{pos.breaks}{Breaks in the positions histogram. It can also be a vector of break
|
20
|
+
points, and values outside the range are ignored. If zero (0), it
|
21
|
+
uses the sequence breaks as defined in the .lim file, which means
|
22
|
+
one bin per contig (or gene, if the mapping is agains genes). Ignored
|
23
|
+
if `pos.breaks.tsv` is passed.}
|
24
|
+
|
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|
+
\item{pos.breaks.tsv}{Path to a list of (absolute) coordinates to use as position breaks.
|
26
|
+
This tab-delimited file can be produced by \code{GFF.catsbj.pl}, and it
|
27
|
+
must contain at least one column: coordinates of the break positions of
|
28
|
+
each position bin. If it has a second column, this is used as the name
|
29
|
+
of the position bin that ends at the given coordinate (the first row is
|
30
|
+
ignored). Any additional columns are currently ignored. If \code{NA},
|
31
|
+
position bins are determined by \code{pos.breaks}.}
|
32
|
+
|
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|
+
\item{id.breaks}{Breaks in the identity histogram. It can also be a vector of break
|
34
|
+
points, and values outside the range are ignored.}
|
35
|
+
|
36
|
+
\item{id.free.range}{Indicates that the range should be freely set from the observed
|
37
|
+
values. Otherwise, 70-100\% is included in the identity histogram
|
38
|
+
(default).}
|
39
|
+
|
40
|
+
\item{id.metric}{Metric of identity to be used (Y-axis). Corrected identity is only
|
41
|
+
supported if the original BLAST file included sequence lengths.}
|
42
|
+
|
43
|
+
\item{id.summary}{Function summarizing the identity bins. Other recommended options
|
44
|
+
include: \code{median} to estimate the median instead of total bins, and
|
45
|
+
\code{function(x) mlv(x,method='parzen')$M} to estimate the mode.}
|
46
|
+
|
47
|
+
\item{id.cutoff}{Cutoff of identity metric above which the hits are considered
|
48
|
+
\code{in-group}. The 95\% identity corresponds to the expectation of
|
49
|
+
ANI<95\% within species.}
|
50
|
+
|
51
|
+
\item{threads}{Number of threads to use.}
|
52
|
+
|
53
|
+
\item{verbose}{Indicates if the function should report the advance.}
|
54
|
+
|
55
|
+
\item{...}{Any additional parameters supported by \code{\link{plot.enve.RecPlot2}}.}
|
56
|
+
}
|
57
|
+
\value{
|
58
|
+
Returns an object of class \code{\link{enve.RecPlot2}}.
|
59
|
+
}
|
60
|
+
\description{
|
61
|
+
Produces recruitment plots provided that \code{BlastTab.catsbj.pl} has
|
62
|
+
been previously executed.
|
63
|
+
}
|
64
|
+
\author{
|
65
|
+
Luis M. Rodriguez-R [aut, cre]
|
66
|
+
|
67
|
+
Kenji Gerhardt [aut]
|
68
|
+
}
|
@@ -0,0 +1,25 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.__counts}
|
4
|
+
\alias{enve.recplot2.__counts}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Internal Ancillary Function}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.__counts(x, pos.breaks, id.breaks, rec.idcol)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{x}{\code{\link{enve.RecPlot2}} object}
|
11
|
+
|
12
|
+
\item{pos.breaks}{Position breaks}
|
13
|
+
|
14
|
+
\item{id.breaks}{Identity breaks}
|
15
|
+
|
16
|
+
\item{rec.idcol}{Identity column to use}
|
17
|
+
}
|
18
|
+
\description{
|
19
|
+
Internal ancillary function (see \code{\link{enve.recplot2}}).
|
20
|
+
}
|
21
|
+
\author{
|
22
|
+
Luis M. Rodriguez-R [aut, cre]
|
23
|
+
|
24
|
+
Kenji Gerhardt [aut]
|
25
|
+
}
|
@@ -0,0 +1,21 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.__peakHist}
|
4
|
+
\alias{enve.recplot2.__peakHist}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Function}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.__peakHist(x, mids, counts = TRUE)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{x}{\code{\link{enve.RecPlot2.Peak}} object}
|
11
|
+
|
12
|
+
\item{mids}{Midpoints}
|
13
|
+
|
14
|
+
\item{counts}{Counts}
|
15
|
+
}
|
16
|
+
\description{
|
17
|
+
Internal ancillary function (see \code{\link{enve.RecPlot2.Peak}}).
|
18
|
+
}
|
19
|
+
\author{
|
20
|
+
Luis M. Rodriguez-R [aut, cre]
|
21
|
+
}
|
@@ -0,0 +1,19 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.__whichClosestPeak}
|
4
|
+
\alias{enve.recplot2.__whichClosestPeak}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Function}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.__whichClosestPeak(peak, peaks)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{peak}{Query \code{\link{enve.RecPlot2.Peak}} object}
|
11
|
+
|
12
|
+
\item{peaks}{list of \code{\link{enve.RecPlot2.Peak}} objects}
|
13
|
+
}
|
14
|
+
\description{
|
15
|
+
Internal ancillary function (see \code{\link{enve.recplot2.findPeaks}}).
|
16
|
+
}
|
17
|
+
\author{
|
18
|
+
Luis M. Rodriguez-R [aut, cre]
|
19
|
+
}
|
@@ -0,0 +1,19 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.changeCutoff}
|
4
|
+
\alias{enve.recplot2.changeCutoff}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Change Cutoff}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.changeCutoff(rp, new.cutoff = 98)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{rp}{\code{\link{enve.RecPlot2}} object.}
|
11
|
+
|
12
|
+
\item{new.cutoff}{New cutoff to use.}
|
13
|
+
}
|
14
|
+
\description{
|
15
|
+
Change the intra-species cutoff of an existing recruitment plot.
|
16
|
+
}
|
17
|
+
\author{
|
18
|
+
Luis M. Rodriguez-R [aut, cre]
|
19
|
+
}
|
@@ -0,0 +1,41 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.compareIdentities}
|
4
|
+
\alias{enve.recplot2.compareIdentities}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Compare Identities}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.compareIdentities(x, y, method = "hellinger",
|
8
|
+
smooth.par = NULL, pseudocounts = 0, max.deviation = 0.75)
|
9
|
+
}
|
10
|
+
\arguments{
|
11
|
+
\item{x}{First \code{\link{enve.RecPlot2}} object.}
|
12
|
+
|
13
|
+
\item{y}{Second \code{\link{enve.RecPlot2}} object.}
|
14
|
+
|
15
|
+
\item{method}{Distance method to use. This should be (an unambiguous abbreviation of)
|
16
|
+
one of:
|
17
|
+
\itemize{
|
18
|
+
\item{"hellinger" (\emph{Hellinger, 1090, doi:10.1515/crll.1909.136.210}),}
|
19
|
+
\item{"bhattacharyya" (\emph{Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35}),}
|
20
|
+
\item{"kl" or "kullback-leibler" (\emph{Kullback & Leibler, 1951,
|
21
|
+
doi:10.1214/aoms/1177729694}), or}
|
22
|
+
\item{"euclidean"}
|
23
|
+
}}
|
24
|
+
|
25
|
+
\item{smooth.par}{Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
|
26
|
+
Use \code{NULL} to automatically determine this value using leave-one-out
|
27
|
+
cross-validation (see \code{smooth.spline} parameter \code{spar}).}
|
28
|
+
|
29
|
+
\item{pseudocounts}{Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
|
30
|
+
1 for add-one smoothing.}
|
31
|
+
|
32
|
+
\item{max.deviation}{Maximum mean deviation between identity breaks tolerated (as percent
|
33
|
+
identity). Difference in number of \code{id.breaks} is never tolerated.}
|
34
|
+
}
|
35
|
+
\description{
|
36
|
+
Compare the distribution of identities between two
|
37
|
+
\code{\link{enve.RecPlot2}} objects.
|
38
|
+
}
|
39
|
+
\author{
|
40
|
+
Luis M. Rodriguez-R [aut, cre]
|
41
|
+
}
|
@@ -0,0 +1,29 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.coordinates}
|
4
|
+
\alias{enve.recplot2.coordinates}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Coordinates}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.coordinates(x, bins)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{x}{\code{\link{enve.RecPlot2}} object.}
|
11
|
+
|
12
|
+
\item{bins}{Vector of selected bins to return. It can be a vector of logical values
|
13
|
+
with the same length as \code{x$pos.breaks-1} or a vector of integers. If
|
14
|
+
missing, returns the coordinates of all windows.}
|
15
|
+
}
|
16
|
+
\value{
|
17
|
+
Returns a data.frame with five columns: \code{name.from} (character),
|
18
|
+
\code{pos.from} (numeric), \code{name.to} (character), \code{pos.to}
|
19
|
+
(numeric), and \code{seq.name} (character).
|
20
|
+
The first two correspond to sequence and position of the start point of the
|
21
|
+
bin. The next two correspond to the sequence and position of the end point of
|
22
|
+
the bin. The last one indicates the name of the sequence (if defined).
|
23
|
+
}
|
24
|
+
\description{
|
25
|
+
Returns the sequence name and coordinates of the requested position bins.
|
26
|
+
}
|
27
|
+
\author{
|
28
|
+
Luis M. Rodriguez-R [aut, cre]
|
29
|
+
}
|
@@ -0,0 +1,18 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.corePeak}
|
4
|
+
\alias{enve.recplot2.corePeak}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Core Peak Finder}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.corePeak(x)
|
8
|
+
}
|
9
|
+
\arguments{
|
10
|
+
\item{x}{\code{list} of \code{\link{enve.RecPlot2.Peak}} objects.}
|
11
|
+
}
|
12
|
+
\description{
|
13
|
+
Finds the peak in a list of peaks that is most likely to represent the
|
14
|
+
"core genome" of a population.
|
15
|
+
}
|
16
|
+
\author{
|
17
|
+
Luis M. Rodriguez-R [aut, cre]
|
18
|
+
}
|
@@ -0,0 +1,40 @@
|
|
1
|
+
% Generated by roxygen2: do not edit by hand
|
2
|
+
% Please edit documentation in R/recplot2.R
|
3
|
+
\name{enve.recplot2.extractWindows}
|
4
|
+
\alias{enve.recplot2.extractWindows}
|
5
|
+
\title{Enveomics: Recruitment Plot (2) Extract Windows}
|
6
|
+
\usage{
|
7
|
+
enve.recplot2.extractWindows(rp, peak, lower.tail = TRUE,
|
8
|
+
significance = 0.05, seq.names = FALSE)
|
9
|
+
}
|
10
|
+
\arguments{
|
11
|
+
\item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}
|
12
|
+
|
13
|
+
\item{peak}{Peak, an \code{\link{enve.RecPlot2.Peak}} object. If list, it is assumed to be a
|
14
|
+
list of \code{\link{enve.RecPlot2.Peak}} objects, in which case the core peak is
|
15
|
+
used (see \code{\link{enve.recplot2.corePeak}}).}
|
16
|
+
|
17
|
+
\item{lower.tail}{If \code{FALSE}, it returns windows significantly above the peak in
|
18
|
+
sequencing depth.}
|
19
|
+
|
20
|
+
\item{significance}{Significance threshold (alpha) to select windows.}
|
21
|
+
|
22
|
+
\item{seq.names}{Returns subject sequence names instead of a vector of Booleans. If
|
23
|
+
the recruitment plot was generated with named position bins (e.g, using
|
24
|
+
\code{pos.breaks=0} or a two-column \code{pos.breaks.tsv}), it returns a
|
25
|
+
vector of characters (the sequence identifiers), otherwise it returns a
|
26
|
+
data.frame with a name column and two columns of coordinates.}
|
27
|
+
}
|
28
|
+
\value{
|
29
|
+
Returns a vector of logicals if \code{seq.names = FALSE}.
|
30
|
+
If \code{seq.names = TRUE}, it returns a data.frame with five columns:
|
31
|
+
\code{name.from}, \code{name.to}, \code{pos.from}, \code{pos.to}, and
|
32
|
+
\code{seq.name} (see \code{\link{enve.recplot2.coordinates}}).
|
33
|
+
}
|
34
|
+
\description{
|
35
|
+
Extract windows significantly below (or above) the peak in sequencing
|
36
|
+
depth.
|
37
|
+
}
|
38
|
+
\author{
|
39
|
+
Luis M. Rodriguez-R [aut, cre]
|
40
|
+
}
|
@@ -0,0 +1,36 @@
|
|
1
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/recplot2.R
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\name{enve.recplot2.findPeaks}
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\alias{enve.recplot2.findPeaks}
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\title{Enveomics: Recruitment Plot (2) Peak Finder}
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\usage{
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enve.recplot2.findPeaks(x, method = "emauto", ...)
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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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+
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\item{method}{Peak-finder method. This should be one of:
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\itemize{
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\item \strong{emauto}
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(Expectation-Maximization with auto-selection of components)
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\item \strong{em}
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(Expectation-Maximization)
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\item \strong{mower}
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(Custom distribution-mowing method)
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}}
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\item{...}{Any additional parameters supported by
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\code{\link{enve.recplot2.findPeaks}}.}
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}
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\value{
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Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
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}
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\description{
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Identifies peaks in the population histogram potentially indicating
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sub-population mixtures.
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}
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\author{
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Luis M. Rodriguez-R [aut, cre]
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export
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}
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/recplot2.R
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\name{enve.recplot2.findPeaks.__em_e}
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\alias{enve.recplot2.findPeaks.__em_e}
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\title{Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectation}
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\usage{
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enve.recplot2.findPeaks.__em_e(x, theta)
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}
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\arguments{
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\item{x}{Vector of log-transformed sequencing depths}
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+
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\item{theta}{Parameters list}
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}
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\description{
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Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
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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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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/recplot2.R
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\name{enve.recplot2.findPeaks.__em_m}
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\alias{enve.recplot2.findPeaks.__em_m}
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\title{Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximization}
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\usage{
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enve.recplot2.findPeaks.__em_m(x, posterior)
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}
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\arguments{
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\item{x}{Vector of log-transformed sequencing depths}
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+
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\item{posterior}{Posterior probability}
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}
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\description{
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Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.em}}).
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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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