miga-base 1.2.17.0 → 1.2.17.1

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Files changed (299) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/version.rb +1 -1
  3. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
  4. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
  5. data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
  6. data/utils/FastAAI/FastAAI +3659 -0
  7. data/utils/FastAAI/FastAAI-legacy/FastAAI +1336 -0
  8. data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +1296 -0
  9. data/utils/FastAAI/README.md +84 -0
  10. data/utils/enveomics/Docs/recplot2.md +244 -0
  11. data/utils/enveomics/Examples/aai-matrix.bash +66 -0
  12. data/utils/enveomics/Examples/ani-matrix.bash +66 -0
  13. data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
  14. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
  15. data/utils/enveomics/LICENSE.txt +73 -0
  16. data/utils/enveomics/Makefile +52 -0
  17. data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
  18. data/utils/enveomics/Manifest/Tasks/blasttab.json +790 -0
  19. data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
  20. data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
  21. data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
  22. data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
  23. data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
  24. data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
  25. data/utils/enveomics/Manifest/Tasks/other.json +906 -0
  26. data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
  27. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +650 -0
  28. data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
  29. data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
  30. data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
  31. data/utils/enveomics/Manifest/categories.json +165 -0
  32. data/utils/enveomics/Manifest/examples.json +162 -0
  33. data/utils/enveomics/Manifest/tasks.json +4 -0
  34. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
  35. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
  36. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
  37. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
  38. data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
  39. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
  40. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
  41. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
  42. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
  43. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
  44. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
  45. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
  46. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
  47. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
  48. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
  49. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
  50. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
  51. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
  52. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
  53. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
  54. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
  55. data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
  56. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
  57. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
  58. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
  59. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
  60. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
  61. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
  62. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
  63. data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
  64. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
  65. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
  66. data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
  67. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
  68. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
  69. data/utils/enveomics/README.md +42 -0
  70. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
  71. data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
  72. data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
  73. data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
  74. data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
  75. data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
  76. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
  77. data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
  78. data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
  79. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
  80. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
  81. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
  82. data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
  83. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
  84. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
  85. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
  86. data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
  87. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
  88. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
  89. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
  90. data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
  91. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
  92. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
  93. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
  94. data/utils/enveomics/Scripts/Chao1.pl +97 -0
  95. data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
  96. data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
  97. data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
  98. data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
  99. data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
  100. data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
  101. data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
  102. data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
  103. data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
  104. data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
  105. data/utils/enveomics/Scripts/FastA.length.pl +38 -0
  106. data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
  107. data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
  108. data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
  109. data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
  110. data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
  111. data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
  112. data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
  113. data/utils/enveomics/Scripts/FastA.split.pl +55 -0
  114. data/utils/enveomics/Scripts/FastA.split.rb +79 -0
  115. data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
  116. data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
  117. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  118. data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
  119. data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
  120. data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
  121. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  122. data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
  123. data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
  124. data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
  125. data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
  126. data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
  127. data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
  128. data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
  129. data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
  130. data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
  131. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
  132. data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
  133. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
  134. data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
  135. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
  136. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
  137. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
  138. data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
  139. data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
  140. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
  141. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
  142. data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
  143. data/utils/enveomics/Scripts/SRA.download.bash +55 -0
  144. data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
  145. data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
  146. data/utils/enveomics/Scripts/Table.barplot.R +31 -0
  147. data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
  148. data/utils/enveomics/Scripts/Table.filter.pl +61 -0
  149. data/utils/enveomics/Scripts/Table.merge.pl +77 -0
  150. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  151. data/utils/enveomics/Scripts/Table.replace.rb +69 -0
  152. data/utils/enveomics/Scripts/Table.round.rb +63 -0
  153. data/utils/enveomics/Scripts/Table.split.pl +57 -0
  154. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
  155. data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
  156. data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
  157. data/utils/enveomics/Scripts/aai.rb +421 -0
  158. data/utils/enveomics/Scripts/ani.rb +362 -0
  159. data/utils/enveomics/Scripts/anir.rb +137 -0
  160. data/utils/enveomics/Scripts/clust.rand.rb +102 -0
  161. data/utils/enveomics/Scripts/gi2tax.rb +103 -0
  162. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
  163. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  164. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  165. data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
  166. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  167. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  168. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
  169. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  170. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  171. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
  172. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
  173. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
  174. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  175. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
  176. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
  177. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  178. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  179. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  180. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
  182. data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
  183. data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
  184. data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
  185. data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
  186. data/utils/enveomics/Scripts/ogs.rb +104 -0
  187. data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
  188. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  189. data/utils/enveomics/Scripts/rbm.rb +108 -0
  190. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  191. data/utils/enveomics/Tests/Makefile +10 -0
  192. data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
  193. data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
  194. data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
  195. data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
  196. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  197. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
  198. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
  199. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
  200. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
  201. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
  202. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
  203. data/utils/enveomics/Tests/alkB.nwk +1 -0
  204. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
  205. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
  206. data/utils/enveomics/Tests/hiv1.faa +59 -0
  207. data/utils/enveomics/Tests/hiv1.fna +134 -0
  208. data/utils/enveomics/Tests/hiv2.faa +70 -0
  209. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
  210. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
  211. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
  212. data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
  213. data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
  214. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
  215. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
  216. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
  217. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
  218. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
  219. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
  220. data/utils/enveomics/build_enveomics_r.bash +45 -0
  221. data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
  222. data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
  223. data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
  224. data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
  225. data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
  226. data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
  227. data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
  228. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  229. data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
  230. data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
  231. data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
  232. data/utils/enveomics/enveomics.R/R/utils.R +80 -0
  233. data/utils/enveomics/enveomics.R/README.md +81 -0
  234. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  235. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  236. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
  237. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
  238. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
  239. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
  240. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
  241. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
  242. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
  243. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
  244. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
  245. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
  246. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
  247. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
  248. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
  249. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
  250. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
  251. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
  252. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
  253. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
  254. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
  255. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
  256. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
  257. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
  258. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
  259. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
  260. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
  261. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
  262. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
  263. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
  264. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
  280. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
  281. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
  282. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
  283. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
  284. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
  285. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
  286. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
  287. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
  288. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
  289. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
  290. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
  291. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
  292. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
  293. data/utils/enveomics/globals.mk +8 -0
  294. data/utils/enveomics/manifest.json +9 -0
  295. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  296. data/utils/multitrim/README.md +67 -0
  297. data/utils/multitrim/multitrim.py +1555 -0
  298. data/utils/multitrim/multitrim.yml +13 -0
  299. metadata +301 -5
@@ -0,0 +1,81 @@
1
+ # enveomics.R
2
+
3
+ ## Installing `enveomics.R`
4
+ To install the latest version of `enveomics.R` uploaded to CRAN, execute in R:
5
+
6
+ ```R
7
+ install.packages('enveomics.R')
8
+ ```
9
+
10
+ To install the current developer version of `enveomics.R`, execute in R:
11
+
12
+ ```R
13
+ install.packages('devtools')
14
+ library('devtools')
15
+ install_github('lmrodriguezr/enveomics', subdir='enveomics.R')
16
+ ```
17
+
18
+ ## Using `enveomics.R`
19
+ To load enveomics.R, simply execute:
20
+
21
+ ```R
22
+ library(enveomics.R);
23
+ ```
24
+
25
+ And open help messages using any of the following commands:
26
+
27
+ ```R
28
+ ?enveomics.R
29
+ ?enve.barplot
30
+ ?enve.recplot2
31
+ ?enve.recplot2.compareIdentities
32
+ ?enve.recplot2.changeCutoff
33
+ ?enve.recplot2.findPeaks
34
+ ?enve.recplot2.corePeak
35
+ ?enve.recplot2.windowDepthThreshold
36
+ ?enve.recplot2.extractWindows
37
+ ?enve.recplot2.coordinates
38
+ ?enve.recplot2.seqdepth
39
+ ?enve.recplot2.ANIr
40
+ ?enve.prune.dist
41
+ ?enve.tribs
42
+ ?enve.tribs.test
43
+ ?enve.growthcurve
44
+ ?enve.col.alpha
45
+ ?enve.truncate
46
+ ```
47
+
48
+ You can run some examples using these libraries in the
49
+ [enveomics-GUI](https://github.com/lmrodriguezr/enveomics-gui).
50
+
51
+ For additional information on recruitment plots, see the
52
+ [Recruitment plots working document](https://github.com/lmrodriguezr/enveomics/blob/master/Docs/recplot2.md).
53
+
54
+ ## Changelog
55
+ * 1.8.0: New functions `enve.selvector` and `enve.prefscore`.
56
+ * 1.7.1: Improved efficiency of `enve.df2dist` about five-fold.
57
+ * 1.7.0: Uniformized output for `enve.recplot2.extractWindows` and
58
+ `enve.recplot2.coordinates` to ease automation. Thanks to Tomeu Viver and
59
+ Roth Conrad for troubleshooting.
60
+ * 1.6.0: Speed up in recplot2 with proper structure manipulation
61
+ (by: Kenji Gerhardt). Also, default value for `id.breaks` was changed from
62
+ 300 to 60.
63
+ * 1.5.0: Modernized documentation, now in ROxygen2 (by: Tatyana Kiryutina)
64
+ * 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder
65
+ initialization to median (instead of mode).
66
+ * 1.4.2: Solved bug #36.
67
+ * 1.4.0: New option `pos.breaks.tsv` for `enve.recplot2`.
68
+ * 1.3.4: Gracefully handles and plots recruitment plots with insufficient data
69
+ to find peaks.
70
+ * 1.3.3: New function `enve.recplot2.windowDepthThreshold`.
71
+ * 1.3.2: New option `panel.fun` for `plot.enve.RecPlot2`.
72
+ * 1.3.1: New function enve.truncate.
73
+ * 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
74
+ * 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve
75
+ with S3 methods plot and summary.
76
+ * 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and
77
+ solved a minor bug in enve.recplot2 that caused failures in low-coverage
78
+ datasets when using too many threads.
79
+ * 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a
80
+ bin per subject sequence.
81
+
@@ -0,0 +1,16 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/growthcurve.R
3
+ \name{$,enve.GrowthCurve-method}
4
+ \alias{$,enve.GrowthCurve-method}
5
+ \title{Attribute accessor}
6
+ \usage{
7
+ \S4method{$}{enve.GrowthCurve}(x, name)
8
+ }
9
+ \arguments{
10
+ \item{x}{Object}
11
+
12
+ \item{name}{Attribute name}
13
+ }
14
+ \description{
15
+ Attribute accessor
16
+ }
@@ -0,0 +1,16 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/recplot2.R
3
+ \name{$,enve.RecPlot2-method}
4
+ \alias{$,enve.RecPlot2-method}
5
+ \title{Attribute accessor}
6
+ \usage{
7
+ \S4method{$}{enve.RecPlot2}(x, name)
8
+ }
9
+ \arguments{
10
+ \item{x}{Object}
11
+
12
+ \item{name}{Attribute name}
13
+ }
14
+ \description{
15
+ Attribute accessor
16
+ }
@@ -0,0 +1,16 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/recplot2.R
3
+ \name{$,enve.RecPlot2.Peak-method}
4
+ \alias{$,enve.RecPlot2.Peak-method}
5
+ \title{Attribute accessor}
6
+ \usage{
7
+ \S4method{$}{enve.RecPlot2.Peak}(x, name)
8
+ }
9
+ \arguments{
10
+ \item{x}{Object}
11
+
12
+ \item{name}{Attribute name}
13
+ }
14
+ \description{
15
+ Attribute accessor
16
+ }
@@ -0,0 +1,25 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/growthcurve.R
3
+ \docType{class}
4
+ \name{enve.GrowthCurve-class}
5
+ \alias{enve.GrowthCurve-class}
6
+ \alias{enve.GrowthCurve}
7
+ \title{Enveomics: Growth Curve S4 Class}
8
+ \description{
9
+ Enve-omics representation of fitted growth curves.
10
+ }
11
+ \section{Slots}{
12
+
13
+ \describe{
14
+ \item{\code{design}}{\code{(array)} Experimental design of the experiment.}
15
+
16
+ \item{\code{models}}{\code{(list)} Fitted growth curve models.}
17
+
18
+ \item{\code{predict}}{\code{(list)} Fitted growth curve values.}
19
+
20
+ \item{\code{call}}{\code{(call)} Call producing this object.}
21
+ }}
22
+
23
+ \author{
24
+ Luis M. Rodriguez-R [aut, cre]
25
+ }
@@ -0,0 +1,46 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/tribs.R
3
+ \docType{class}
4
+ \name{enve.TRIBS-class}
5
+ \alias{enve.TRIBS-class}
6
+ \alias{enve.TRIBS}
7
+ \title{Enveomics: TRIBS S4 Class}
8
+ \description{
9
+ Enve-omics representation of "Transformed-space Resampling In Biased Sets
10
+ (TRIBS)". This object represents sets of distances between objects,
11
+ sampled nearly-uniformly at random in "distance space". Subsampling
12
+ without selection is trivial, since both the distances space and the
13
+ selection occur in the same transformed space. However, it's useful to
14
+ compare randomly subsampled sets against a selected set of objects. This
15
+ is intended to identify overdispersion or overclustering (see
16
+ \code{\link{enve.TRIBStest}}) of a subset against the entire collection of objects
17
+ with minimum impact of sampling biases. This object can be produced by
18
+ \code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
19
+ }
20
+ \section{Slots}{
21
+
22
+ \describe{
23
+ \item{\code{distance}}{\code{(numeric)} Centrality measurement of the distances
24
+ between the selected objects (without subsampling).}
25
+
26
+ \item{\code{points}}{\code{(matrix)} Position of the different objects in distance
27
+ space.}
28
+
29
+ \item{\code{distances}}{\code{(matrix)} Subsampled distances, where the rows are
30
+ replicates and the columns are subsampling levels.}
31
+
32
+ \item{\code{spaceSize}}{\code{(numeric)} Number of objects.}
33
+
34
+ \item{\code{selSize}}{\code{(numeric)} Number of selected objects.}
35
+
36
+ \item{\code{dimensions}}{\code{(numeric)} Number of dimensions in the distance space.}
37
+
38
+ \item{\code{subsamples}}{\code{(numeric)} Subsampling levels (as fractions, from
39
+ 0 to 1).}
40
+
41
+ \item{\code{call}}{\code{(call)} Call producing this object.}
42
+ }}
43
+
44
+ \author{
45
+ Luis M. Rodriguez-R [aut, cre]
46
+ }
@@ -0,0 +1,23 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/tribs.R
3
+ \name{enve.TRIBS.merge}
4
+ \alias{enve.TRIBS.merge}
5
+ \title{Enveomics: TRIBS Merge}
6
+ \usage{
7
+ enve.TRIBS.merge(x, y)
8
+ }
9
+ \arguments{
10
+ \item{x}{First \code{\link{enve.TRIBS}} object.}
11
+
12
+ \item{y}{Second \code{\link{enve.TRIBS}} object.}
13
+ }
14
+ \value{
15
+ Returns an \code{\link{enve.TRIBS}} object.
16
+ }
17
+ \description{
18
+ Merges two \code{\link{enve.TRIBS}} objects generated from the same objects at
19
+ different subsampling levels.
20
+ }
21
+ \author{
22
+ Luis M. Rodriguez-R [aut, cre]
23
+ }
@@ -0,0 +1,47 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/tribs.R
3
+ \docType{class}
4
+ \name{enve.TRIBStest-class}
5
+ \alias{enve.TRIBStest-class}
6
+ \alias{enve.TRIBStest}
7
+ \title{Enveomics: TRIBS Test S4 Class}
8
+ \description{
9
+ Test of significance of overclustering or overdispersion in a selected
10
+ set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}). This
11
+ object can be produced by \code{\link{enve.tribs.test}} and supports S4 methods
12
+ \code{plot} and \code{summary}.
13
+ }
14
+ \section{Slots}{
15
+
16
+ \describe{
17
+ \item{\code{pval.gt}}{\code{(numeric)}
18
+ P-value for the overdispersion test.}
19
+
20
+ \item{\code{pval.lt}}{\code{(numeric)}
21
+ P-value for the overclustering test.}
22
+
23
+ \item{\code{all.dist}}{\code{(numeric)}
24
+ Empiric PDF of distances for the entire dataset (subsampled at selection
25
+ size).}
26
+
27
+ \item{\code{sel.dist}}{\code{(numeric)}
28
+ Empiric PDF of distances for the selected objects (without subsampling).}
29
+
30
+ \item{\code{diff.dist}}{\code{(numeric)}
31
+ Empiric PDF of the difference between \code{all.dist} and \code{sel.dist}.
32
+ The p-values are estimating by comparing areas in this PDF greater than and
33
+ lesser than zero.}
34
+
35
+ \item{\code{dist.mids}}{\code{(numeric)}
36
+ Midpoints of the empiric PDFs of distances.}
37
+
38
+ \item{\code{diff.mids}}{\code{(numeric)}
39
+ Midpoints of the empiric PDF of difference of distances.}
40
+
41
+ \item{\code{call}}{\code{(call)}
42
+ Call producing this object.}
43
+ }}
44
+
45
+ \author{
46
+ Luis M. Rodriguez-R [aut, cre]
47
+ }
@@ -0,0 +1,23 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/autoprune.R
3
+ \name{enve.__prune.iter}
4
+ \alias{enve.__prune.iter}
5
+ \title{Enveomics: Prune Iter (Internal Function)}
6
+ \usage{
7
+ enve.__prune.iter(t, dist, min_dist, quiet)
8
+ }
9
+ \arguments{
10
+ \item{t}{A \strong{phylo} object}
11
+
12
+ \item{dist}{Cophenetic distance matrix}
13
+
14
+ \item{min_dist}{Minimum distance}
15
+
16
+ \item{quiet}{If running quietly}
17
+ }
18
+ \description{
19
+ Internal function for \code{\link{enve.prune.dist}}.
20
+ }
21
+ \author{
22
+ Luis M. Rodriguez-R [aut, cre]
23
+ }
@@ -0,0 +1,23 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/autoprune.R
3
+ \name{enve.__prune.reduce}
4
+ \alias{enve.__prune.reduce}
5
+ \title{Enveomics: Prune Reduce (Internal Function)}
6
+ \usage{
7
+ enve.__prune.reduce(t, nodes, min_dist, quiet)
8
+ }
9
+ \arguments{
10
+ \item{t}{A \strong{phylo} object}
11
+
12
+ \item{nodes}{Vector of nodes}
13
+
14
+ \item{min_dist}{Minimum distance}
15
+
16
+ \item{quiet}{If running quietly}
17
+ }
18
+ \description{
19
+ Internal function for \code{\link{enve.prune.dist}}.
20
+ }
21
+ \author{
22
+ Luis M. Rodriguez-R [aut, cre]
23
+ }
@@ -0,0 +1,40 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/tribs.R
3
+ \name{enve.__tribs}
4
+ \alias{enve.__tribs}
5
+ \title{Enveomics: TRIBS - Internal Ancillary Function}
6
+ \usage{
7
+ enve.__tribs(
8
+ rep,
9
+ frx,
10
+ selection,
11
+ dimensions,
12
+ dots,
13
+ dist.method,
14
+ summary.fx,
15
+ dist
16
+ )
17
+ }
18
+ \arguments{
19
+ \item{rep}{Replicates}
20
+
21
+ \item{frx}{Fraction}
22
+
23
+ \item{selection}{Selection}
24
+
25
+ \item{dimensions}{Dimensions}
26
+
27
+ \item{dots}{Sampling points}
28
+
29
+ \item{dist.method}{Distance method}
30
+
31
+ \item{summary.fx}{Summary function}
32
+
33
+ \item{dist}{Distance}
34
+ }
35
+ \description{
36
+ Internal ancillary function (see \code{\link{enve.tribs}}).
37
+ }
38
+ \author{
39
+ Luis M. Rodriguez-R [aut, cre]
40
+ }
@@ -0,0 +1,103 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/barplot.R
3
+ \name{enve.barplot}
4
+ \alias{enve.barplot}
5
+ \title{Enveomics: Barplot}
6
+ \usage{
7
+ enve.barplot(
8
+ x,
9
+ sizes,
10
+ top = 25,
11
+ colors.per.group = 9,
12
+ bars.width = 4,
13
+ legend.ncol = 1,
14
+ other.col = "#000000",
15
+ add.trend = FALSE,
16
+ organic.trend = FALSE,
17
+ sort.by = median,
18
+ min.report = 101,
19
+ order = NULL,
20
+ col,
21
+ ...
22
+ )
23
+ }
24
+ \arguments{
25
+ \item{x}{Can be either the input data or the path to the file containing
26
+ the table.
27
+ \itemize{
28
+ \item{If it contains the data, it must be a data frame or an
29
+ object coercible to a data frame.}
30
+ \item{If it is a path, it must point to a
31
+ tab-delimited file containing a header (first row) and row names
32
+ (first column).}
33
+ }}
34
+
35
+ \item{sizes}{A numeric vector containing the real size of the samples
36
+ (columns) in the same order of the input table. If set, the values are
37
+ assumed to be 100\%. Otherwise, the sum of the columns is used.}
38
+
39
+ \item{top}{Maximum number of categories to display. Any additional
40
+ categories will be listed as "Others".}
41
+
42
+ \item{colors.per.group}{Number of categories in the first two saturation
43
+ groups of colors. The third group contains the remaining categories if
44
+ needed.}
45
+
46
+ \item{bars.width}{Width of the barplot with respect to the legend.}
47
+
48
+ \item{legend.ncol}{Number of columns in the legend.}
49
+
50
+ \item{other.col}{Color of the "Others" category.}
51
+
52
+ \item{add.trend}{Controls if semi-transparent areas are to be plotted
53
+ between the bars to connect the regions (trend regions).}
54
+
55
+ \item{organic.trend}{Controls if the trend regions are to be smoothed
56
+ (curves). By default, trend regions have straight edges. If \code{TRUE},
57
+ forces \code{add.trend=TRUE}.}
58
+
59
+ \item{sort.by}{Any function that takes a numeric vector and returns a
60
+ numeric scalar. This function is applied to each row, and the resulting
61
+ values are used to sort the rows (decreasingly). Good options include:
62
+ \code{sd, min, max, mean, median}.}
63
+
64
+ \item{min.report}{Minimum percentage to report the value in the plot.
65
+ Any value above 100 indicates that no values are to be reported.}
66
+
67
+ \item{order}{Controls how the rows should be ordered.
68
+ \itemize{
69
+ \item{If \code{NULL}
70
+ (default), \code{sort.by} is applied per row and the results are
71
+ sorted decreasingly.}
72
+ \item{If \code{NA}, no sorting is performed, i.e., the original
73
+ order is respected.}
74
+ \item{If a vector is provided, it is assumed to be the
75
+ custom order to be used (either by numeric index or by row names).}
76
+ }}
77
+
78
+ \item{col}{Colors to use. If provided, overrides the variables \code{top}
79
+ and \code{colors.per.group}, but \code{other.col} is still used if the
80
+ vector is insufficient for all the rows. An additional palette is available with
81
+ \code{col='coto'} (contributed by Luis (Coto) Orellana).}
82
+
83
+ \item{...}{Any additional parameters to be passed to barplot.}
84
+ }
85
+ \description{
86
+ Creates nice barplots from tab-delimited tables.
87
+ }
88
+ \examples{
89
+ # Load data
90
+ data("phyla.counts", package="enveomics.R", envir=environment())
91
+ # Create a barplot sorted by variance with organic trends
92
+ enve.barplot(
93
+ phyla.counts, # Counts of phyla in four sites
94
+ sizes=c(250,100,75,200), # Total sizes of the datasets of each site
95
+ bars.width=2, # Decrease from default, so the names are fully displayed
96
+ organic.trend=TRUE, # Nice curvy background
97
+ sort.by=var # Sort by variance across sites
98
+ )
99
+
100
+ }
101
+ \author{
102
+ Luis M. Rodriguez-R [aut, cre]
103
+ }
@@ -0,0 +1,67 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/cliopts.R
3
+ \name{enve.cliopts}
4
+ \alias{enve.cliopts}
5
+ \title{Enveomics: Cliopts}
6
+ \usage{
7
+ enve.cliopts(
8
+ fx,
9
+ rd_file,
10
+ positional_arguments,
11
+ usage,
12
+ mandatory = c(),
13
+ vectorize = c(),
14
+ ignore = c(),
15
+ number = c(),
16
+ defaults = list(),
17
+ o_desc = list(),
18
+ p_desc = ""
19
+ )
20
+ }
21
+ \arguments{
22
+ \item{fx}{Function for which the interface should be generated.}
23
+
24
+ \item{rd_file}{(Optional) .Rd file with the standard documentation of
25
+ the function.}
26
+
27
+ \item{positional_arguments}{(Optional) Number of \strong{positional}
28
+ arguments passed to \code{\link[optparse]{parse_args}}
29
+ (package: \pkg{optparse}).}
30
+
31
+ \item{usage}{(Optional) Usage passed to \code{\link[optparse]{OptionParser}}
32
+ (package: \pkg{optparse}).}
33
+
34
+ \item{mandatory}{Mandatory arguments.}
35
+
36
+ \item{vectorize}{Arguments of the function to vectorize (comma-delimited).
37
+ If numeric, use also \code{number}.}
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+
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+ \item{ignore}{Arguments of the function to ignore.}
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+
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+ \item{number}{Force these arguments as numerics. Useful for numeric
42
+ vectors (see \code{vectorize}) or arguments with no defaults.}
43
+
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+ \item{defaults}{Defaults to use instead of the ones provided by the
45
+ formals.}
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+
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+ \item{o_desc}{Descriptions of the options. Help from \code{rd} is ignored
48
+ for arguments present in this list.}
49
+
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+ \item{p_desc}{Description Description of the function. Help from \code{rd}
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+ is ignored for the function description unless this value is an empty string.}
52
+ }
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+ \value{
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+ Returns a list with keys:
55
+ \itemize{
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+ \item{\code{options}, a named list with the values for the function's
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+ arguments}
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+ \item{\code{args}, a vector with zero or more strings containing the
59
+ positional arguments}}
60
+ }
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+ \description{
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+ Generates nicely formatted command-line interfaces for functions
63
+ (\strong{closures} only).
64
+ }
65
+ \author{
66
+ Luis M. Rodriguez-R [aut, cre]
67
+ }
@@ -0,0 +1,24 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/utils.R
3
+ \name{enve.col.alpha}
4
+ \alias{enve.col.alpha}
5
+ \title{Enveomics: Color Alpha}
6
+ \usage{
7
+ enve.col.alpha(col, alpha = 1/2)
8
+ }
9
+ \arguments{
10
+ \item{col}{Color or vector of colors. It can be any value supported by
11
+ \code{\link[grDevices]{col2rgb}}, such as \code{darkred} or \code{#009988}.}
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+
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+ \item{alpha}{Alpha value to add to the color, from 0 to 1.}
14
+ }
15
+ \value{
16
+ Returns a color or a vector of colors in \emph{hex} notation,
17
+ including \code{alpha}.
18
+ }
19
+ \description{
20
+ Modify alpha in a color (or vector of colors).
21
+ }
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+ \author{
23
+ Luis M. Rodriguez-R [aut, cre]
24
+ }
@@ -0,0 +1,19 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/growthcurve.R
3
+ \name{enve.col2alpha}
4
+ \alias{enve.col2alpha}
5
+ \title{Enveomics: Color to Alpha}
6
+ \usage{
7
+ enve.col2alpha(x, alpha)
8
+ }
9
+ \arguments{
10
+ \item{x}{A vector of any value base colors.}
11
+
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+ \item{alpha}{Alpha level to set (in the 0-1 range).}
13
+ }
14
+ \description{
15
+ Takes a vector of colors and sets the alpha.
16
+ }
17
+ \author{
18
+ Luis M. Rodriguez-R [aut, cre]
19
+ }
@@ -0,0 +1,45 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/df2dist.R
3
+ \name{enve.df2dist}
4
+ \alias{enve.df2dist}
5
+ \title{Enveomics: Data Frame to Dist}
6
+ \usage{
7
+ enve.df2dist(
8
+ x,
9
+ obj1.index = 1,
10
+ obj2.index = 2,
11
+ dist.index = 3,
12
+ default.d = NA,
13
+ max.sim = 0
14
+ )
15
+ }
16
+ \arguments{
17
+ \item{x}{A dataframe (or coercible object) with at least three columns:
18
+ \enumerate{
19
+ \item ID of the object 1,
20
+ \item ID of the object 2, and
21
+ \item distance between the two objects.}}
22
+
23
+ \item{obj1.index}{Index of the column containing the ID of the object 1.}
24
+
25
+ \item{obj2.index}{Index of the column containing the ID of the object 2.}
26
+
27
+ \item{dist.index}{Index of the column containing the distance.}
28
+
29
+ \item{default.d}{Default value (for missing values).}
30
+
31
+ \item{max.sim}{If not zero, assumes that the values are similarity
32
+ (not distance) and this is the maximum similarity (corresponding to
33
+ distance 0). Applies transformation:
34
+ \eqn{distance = (max.sim - values)/max.sim.}}
35
+ }
36
+ \value{
37
+ Returns a \strong{dist} object.
38
+ }
39
+ \description{
40
+ Transform a dataframe (or coercible object, like a table) into a
41
+ \strong{dist} object.
42
+ }
43
+ \author{
44
+ Luis M. Rodriguez-R [aut, cre]
45
+ }
@@ -0,0 +1,44 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/df2dist.R
3
+ \name{enve.df2dist.group}
4
+ \alias{enve.df2dist.group}
5
+ \title{Enveomics: Data Frame to Dist (Group)}
6
+ \usage{
7
+ enve.df2dist.group(
8
+ x,
9
+ obj1.index = 1,
10
+ obj2.index = 2,
11
+ dist.index = 3,
12
+ summary = median,
13
+ empty.rm = TRUE
14
+ )
15
+ }
16
+ \arguments{
17
+ \item{x}{A dataframe (or coercible object) with at least three columns:
18
+ \enumerate{
19
+ \item ID of the object 1,
20
+ \item ID of the object 2, and
21
+ \item distance between the two objects.}}
22
+
23
+ \item{obj1.index}{Index of the column containing the ID of the object 1.}
24
+
25
+ \item{obj2.index}{Index of the column containing the ID of the object 2.}
26
+
27
+ \item{dist.index}{Index of the column containing the distance.}
28
+
29
+ \item{summary}{Function summarizing the different distances between the
30
+ two objects.}
31
+
32
+ \item{empty.rm}{Remove rows with empty or \code{NA} groups.}
33
+ }
34
+ \value{
35
+ Returns a \strong{dist} object.
36
+ }
37
+ \description{
38
+ Transform a dataframe (or coercible object, like a table) into a
39
+ \strong{dist} object, where there are 1 or more distances between each pair
40
+ of objects.
41
+ }
42
+ \author{
43
+ Luis M. Rodriguez-R [aut, cre]
44
+ }