miga-base 0.7.26.3 → 1.0.0.sr1

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Files changed (105) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/_data/aai-intax.blast.tsv.gz +0 -0
  3. data/lib/miga/_data/aai-intax.diamond.tsv.gz +0 -0
  4. data/lib/miga/_data/aai-novel.blast.tsv.gz +0 -0
  5. data/lib/miga/_data/aai-novel.diamond.tsv.gz +0 -0
  6. data/lib/miga/cli/action/doctor.rb +50 -19
  7. data/lib/miga/cli/action/doctor/base.rb +20 -18
  8. data/lib/miga/cli/action/init.rb +11 -7
  9. data/lib/miga/cli/action/init/files_helper.rb +1 -0
  10. data/lib/miga/cli/action/ncbi_get.rb +3 -3
  11. data/lib/miga/cli/action/tax_dist.rb +2 -2
  12. data/lib/miga/cli/action/wf.rb +5 -4
  13. data/lib/miga/daemon.rb +11 -4
  14. data/lib/miga/dataset/result.rb +10 -6
  15. data/lib/miga/json.rb +1 -2
  16. data/lib/miga/metadata.rb +5 -1
  17. data/lib/miga/parallel.rb +11 -6
  18. data/lib/miga/project.rb +8 -8
  19. data/lib/miga/project/base.rb +4 -4
  20. data/lib/miga/project/result.rb +2 -2
  21. data/lib/miga/sqlite.rb +7 -0
  22. data/lib/miga/version.rb +23 -9
  23. data/scripts/aai_distances.bash +16 -18
  24. data/scripts/ani_distances.bash +16 -17
  25. data/scripts/assembly.bash +31 -16
  26. data/scripts/haai_distances.bash +3 -27
  27. data/scripts/miga.bash +6 -4
  28. data/scripts/p.bash +1 -1
  29. data/scripts/read_quality.bash +9 -18
  30. data/scripts/trimmed_fasta.bash +14 -30
  31. data/scripts/trimmed_reads.bash +36 -36
  32. data/test/parallel_test.rb +31 -0
  33. data/test/project_test.rb +2 -1
  34. data/utils/distance/commands.rb +1 -0
  35. data/utils/distance/runner.rb +2 -4
  36. data/utils/enveomics/Manifest/Tasks/fasta.json +39 -3
  37. data/utils/enveomics/Manifest/Tasks/fastq.json +50 -2
  38. data/utils/enveomics/Manifest/Tasks/mapping.json +70 -0
  39. data/utils/enveomics/Manifest/Tasks/other.json +77 -0
  40. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +138 -1
  41. data/utils/enveomics/Manifest/categories.json +13 -4
  42. data/utils/enveomics/Scripts/Aln.cat.rb +206 -148
  43. data/utils/enveomics/Scripts/FastA.N50.pl +33 -29
  44. data/utils/enveomics/Scripts/FastA.fragment.rb +69 -61
  45. data/utils/enveomics/Scripts/FastA.sample.rb +61 -46
  46. data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
  47. data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
  48. data/utils/enveomics/Scripts/FastQ.tag.rb +59 -52
  49. data/utils/enveomics/Scripts/SRA.download.bash +6 -8
  50. data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
  51. data/utils/enveomics/Scripts/aai.rb +3 -2
  52. data/utils/enveomics/Scripts/anir.rb +137 -0
  53. data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
  54. data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
  55. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +17 -17
  56. data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
  57. data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
  58. data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +63 -0
  59. data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
  60. data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
  61. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
  62. data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
  63. data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +73 -0
  64. data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
  65. data/utils/enveomics/Scripts/rbm.rb +87 -133
  66. data/utils/enveomics/Scripts/sam.filter.rb +148 -0
  67. data/utils/enveomics/enveomics.R/DESCRIPTION +2 -2
  68. data/utils/enveomics/enveomics.R/NAMESPACE +1 -1
  69. data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
  70. data/utils/enveomics/enveomics.R/R/utils.R +30 -0
  71. data/utils/enveomics/enveomics.R/README.md +1 -0
  72. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -1
  73. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -1
  74. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -1
  75. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +10 -2
  76. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +16 -4
  77. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +13 -3
  78. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +8 -2
  79. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +8 -2
  80. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +9 -2
  81. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +13 -5
  82. data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
  83. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +9 -2
  84. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +23 -6
  85. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +13 -4
  86. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +8 -2
  87. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +7 -2
  88. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +14 -3
  89. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +10 -2
  90. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +8 -2
  91. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +17 -9
  92. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +6 -2
  93. data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
  94. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +14 -5
  95. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +19 -4
  96. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +11 -3
  97. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +11 -4
  98. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +26 -12
  99. data/utils/multitrim/Multitrim How-To.pdf +0 -0
  100. data/utils/multitrim/README.md +67 -0
  101. data/utils/multitrim/multitrim.py +1555 -0
  102. data/utils/multitrim/multitrim.yml +13 -0
  103. data/utils/requirements.txt +4 -3
  104. metadata +33 -6
  105. data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +0 -30
@@ -0,0 +1,50 @@
1
+ % Generated by roxygen2: do not edit by hand
2
+ % Please edit documentation in R/prefscore.R
3
+ \name{enve.prefscore}
4
+ \alias{enve.prefscore}
5
+ \title{Enveomics: Pref Score}
6
+ \usage{
7
+ enve.prefscore(
8
+ x,
9
+ set,
10
+ ignore = NULL,
11
+ signif.thr,
12
+ plot = TRUE,
13
+ col.above = rgb(148, 17, 0, maxColorValue = 255),
14
+ col.equal = rgb(189, 189, 189, maxColorValue = 255),
15
+ col.below = rgb(47, 84, 150, maxColorValue = 255),
16
+ ...
17
+ )
18
+ }
19
+ \arguments{
20
+ \item{x}{Occupancy matrix (logical or numeric binary) with species as rows and samples
21
+ as columns}
22
+
23
+ \item{set}{Vector indicating samples in the test set. It can be any selection vector:
24
+ boolean (same length as the number of columns in \code{x}), or numeric or
25
+ character vector with indexes of the \code{x} columns.}
26
+
27
+ \item{ignore}{Vector indicating species to ignore. It can be any selection vector with
28
+ respect to the rows in \code{x} (see \code{set}).}
29
+
30
+ \item{signif.thr}{Absolute value of the significance threshold}
31
+
32
+ \item{plot}{Indicates if a plot should be generated}
33
+
34
+ \item{col.above}{Color for points significantly above zero}
35
+
36
+ \item{col.equal}{Color for points not significantly different from zero}
37
+
38
+ \item{col.below}{Color for points significantly below zero}
39
+
40
+ \item{...}{Any additional parameters supported by \code{plot}}
41
+ }
42
+ \value{
43
+ Returns a named vector of preference scores.
44
+ }
45
+ \description{
46
+ Estimate preference score of species based on occupancy in biased sample sets
47
+ }
48
+ \author{
49
+ Luis M. Rodriguez-R [aut, cre]
50
+ }
@@ -4,8 +4,15 @@
4
4
  \alias{enve.prune.dist}
5
5
  \title{Enveomics: Prune Dist}
6
6
  \usage{
7
- enve.prune.dist(t, dist.quantile = 0.25, min_dist, quiet = FALSE,
8
- max_iters = 100, min_nodes_random = 40000, random_nodes_frx = 1)
7
+ enve.prune.dist(
8
+ t,
9
+ dist.quantile = 0.25,
10
+ min_dist,
11
+ quiet = FALSE,
12
+ max_iters = 100,
13
+ min_nodes_random = 40000,
14
+ random_nodes_frx = 1
15
+ )
9
16
  }
10
17
  \arguments{
11
18
  \item{t}{A \strong{phylo} object or a path to the Newick file.}
@@ -4,12 +4,29 @@
4
4
  \alias{enve.recplot}
5
5
  \title{Enveomics: Recruitment Plots}
6
6
  \usage{
7
- enve.recplot(prefix, id.min = NULL, id.max = NULL, id.binsize = NULL,
8
- id.splines = 0, id.metric = "id", id.summary = "sum",
9
- pos.min = 1, pos.max = NULL, pos.binsize = 1000, pos.splines = 0,
10
- rec.col1 = "white", rec.col2 = "black", main = NULL,
11
- contig.col = grey(0.85), ret.recplot = FALSE, ret.hist = FALSE,
12
- ret.mode = FALSE, id.cutoff = NULL, verbose = TRUE, ...)
7
+ enve.recplot(
8
+ prefix,
9
+ id.min = NULL,
10
+ id.max = NULL,
11
+ id.binsize = NULL,
12
+ id.splines = 0,
13
+ id.metric = "id",
14
+ id.summary = "sum",
15
+ pos.min = 1,
16
+ pos.max = NULL,
17
+ pos.binsize = 1000,
18
+ pos.splines = 0,
19
+ rec.col1 = "white",
20
+ rec.col2 = "black",
21
+ main = NULL,
22
+ contig.col = grey(0.85),
23
+ ret.recplot = FALSE,
24
+ ret.hist = FALSE,
25
+ ret.mode = FALSE,
26
+ id.cutoff = NULL,
27
+ verbose = TRUE,
28
+ ...
29
+ )
13
30
  }
14
31
  \arguments{
15
32
  \item{prefix}{Path to the prefix of the BlastTab.catsbj.pl output files. At
@@ -4,11 +4,20 @@
4
4
  \alias{enve.recplot2}
5
5
  \title{Enveomics: Recruitment Plot (2)}
6
6
  \usage{
7
- enve.recplot2(prefix, plot = TRUE, pos.breaks = 1000,
8
- pos.breaks.tsv = NA, id.breaks = 60, id.free.range = FALSE,
7
+ enve.recplot2(
8
+ prefix,
9
+ plot = TRUE,
10
+ pos.breaks = 1000,
11
+ pos.breaks.tsv = NA,
12
+ id.breaks = 60,
13
+ id.free.range = FALSE,
9
14
  id.metric = c("identity", "corrected identity", "bit score"),
10
- id.summary = sum, id.cutoff = 95, threads = 2, verbose = TRUE,
11
- ...)
15
+ id.summary = sum,
16
+ id.cutoff = 95,
17
+ threads = 2,
18
+ verbose = TRUE,
19
+ ...
20
+ )
12
21
  }
13
22
  \arguments{
14
23
  \item{prefix}{Path to the prefix of the \code{BlastTab.catsbj.pl} output files. At
@@ -4,8 +4,14 @@
4
4
  \alias{enve.recplot2.compareIdentities}
5
5
  \title{Enveomics: Recruitment Plot (2) Compare Identities}
6
6
  \usage{
7
- enve.recplot2.compareIdentities(x, y, method = "hellinger",
8
- smooth.par = NULL, pseudocounts = 0, max.deviation = 0.75)
7
+ enve.recplot2.compareIdentities(
8
+ x,
9
+ y,
10
+ method = "hellinger",
11
+ smooth.par = NULL,
12
+ pseudocounts = 0,
13
+ max.deviation = 0.75
14
+ )
9
15
  }
10
16
  \arguments{
11
17
  \item{x}{First \code{\link{enve.RecPlot2}} object.}
@@ -4,8 +4,13 @@
4
4
  \alias{enve.recplot2.extractWindows}
5
5
  \title{Enveomics: Recruitment Plot (2) Extract Windows}
6
6
  \usage{
7
- enve.recplot2.extractWindows(rp, peak, lower.tail = TRUE,
8
- significance = 0.05, seq.names = FALSE)
7
+ enve.recplot2.extractWindows(
8
+ rp,
9
+ peak,
10
+ lower.tail = TRUE,
11
+ significance = 0.05,
12
+ seq.names = FALSE
13
+ )
9
14
  }
10
15
  \arguments{
11
16
  \item{rp}{Recruitment plot, a \code{\link{enve.RecPlot2}} object.}
@@ -4,9 +4,20 @@
4
4
  \alias{enve.recplot2.findPeaks.__mow_one}
5
5
  \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1}
6
6
  \usage{
7
- enve.recplot2.findPeaks.__mow_one(lsd1, min.points, quant.est, mlv.opts,
8
- fitdist.opts, with.skewness, optim.rounds, optim.epsilon, n.total,
9
- merge.logdist, verbose, log)
7
+ enve.recplot2.findPeaks.__mow_one(
8
+ lsd1,
9
+ min.points,
10
+ quant.est,
11
+ mlv.opts,
12
+ fitdist.opts,
13
+ with.skewness,
14
+ optim.rounds,
15
+ optim.epsilon,
16
+ n.total,
17
+ merge.logdist,
18
+ verbose,
19
+ log
20
+ )
10
21
  }
11
22
  \arguments{
12
23
  \item{lsd1}{Vector of log-transformed sequencing depths}
@@ -4,8 +4,16 @@
4
4
  \alias{enve.recplot2.findPeaks.em}
5
5
  \title{Enveomics: Recruitment Plot (2) Em Peak Finder}
6
6
  \usage{
7
- enve.recplot2.findPeaks.em(x, max.iter = 1000, ll.diff.res = 1e-08,
8
- components = 2, rm.top = 0.05, verbose = FALSE, init, log = TRUE)
7
+ enve.recplot2.findPeaks.em(
8
+ x,
9
+ max.iter = 1000,
10
+ ll.diff.res = 1e-08,
11
+ components = 2,
12
+ rm.top = 0.05,
13
+ verbose = FALSE,
14
+ init,
15
+ log = TRUE
16
+ )
9
17
  }
10
18
  \arguments{
11
19
  \item{x}{An \code{\link{enve.RecPlot2}} object.}
@@ -4,8 +4,14 @@
4
4
  \alias{enve.recplot2.findPeaks.emauto}
5
5
  \title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
6
6
  \usage{
7
- enve.recplot2.findPeaks.emauto(x, components = seq(1, 5),
8
- criterion = "aic", merge.tol = 2L, verbose = FALSE, ...)
7
+ enve.recplot2.findPeaks.emauto(
8
+ x,
9
+ components = seq(1, 5),
10
+ criterion = "aic",
11
+ merge.tol = 2L,
12
+ verbose = FALSE,
13
+ ...
14
+ )
9
15
  }
10
16
  \arguments{
11
17
  \item{x}{An \code{\link{enve.RecPlot2}} object.}
@@ -4,15 +4,23 @@
4
4
  \alias{enve.recplot2.findPeaks.mower}
5
5
  \title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
6
6
  \usage{
7
- enve.recplot2.findPeaks.mower(x, min.points = 10, quant.est = c(0.002,
8
- 0.998), mlv.opts = list(method = "parzen"),
9
- fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1,
10
- 0.5, 0.8), start = list(omega = 1, alpha = -1), lower = c(0, -Inf,
11
- -Inf)), fitdist.opts.norm = list(distr = "norm", method = "qme", probs
12
- = c(0.4, 0.6), start = list(sd = 1), lower = c(0, -Inf)),
13
- rm.top = 0.05, with.skewness = TRUE, optim.rounds = 200,
14
- optim.epsilon = 1e-04, merge.logdist = log(1.75), verbose = FALSE,
15
- log = TRUE)
7
+ enve.recplot2.findPeaks.mower(
8
+ x,
9
+ min.points = 10,
10
+ quant.est = c(0.002, 0.998),
11
+ mlv.opts = list(method = "parzen"),
12
+ fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1, 0.5, 0.8), start =
13
+ list(omega = 1, alpha = -1), lower = c(0, -Inf, -Inf)),
14
+ fitdist.opts.norm = list(distr = "norm", method = "qme", probs = c(0.4, 0.6), start =
15
+ list(sd = 1), lower = c(0, -Inf)),
16
+ rm.top = 0.05,
17
+ with.skewness = TRUE,
18
+ optim.rounds = 200,
19
+ optim.epsilon = 1e-04,
20
+ merge.logdist = log(1.75),
21
+ verbose = FALSE,
22
+ log = TRUE
23
+ )
16
24
  }
17
25
  \arguments{
18
26
  \item{x}{An \code{\link{enve.RecPlot2}} object.}
@@ -4,8 +4,12 @@
4
4
  \alias{enve.recplot2.windowDepthThreshold}
5
5
  \title{Enveomics: Recruitment Plot (2) Window Depth Threshold}
6
6
  \usage{
7
- enve.recplot2.windowDepthThreshold(rp, peak, lower.tail = TRUE,
8
- significance = 0.05)
7
+ enve.recplot2.windowDepthThreshold(
8
+ rp,
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(dist, selection = labels(dist), replicates = 1000,
8
- summary.fx = median, dist.method = "euclidean", subsamples = seq(0,
9
- 1, by = 0.01), dimensions = ceiling(length(selection) * 0.05),
10
- metaMDS.opts = list(), threads = 2, verbosity = 1, points,
11
- pre.tribs)
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}(x, col, pt.alpha = 0.9, ln.alpha = 1,
8
- ln.lwd = 1, ln.lty = 1, band.alpha = 0.4, band.density = NULL,
9
- band.angle = 45, xp.alpha = 0.5, xp.lwd = 1, xp.lty = 1,
10
- pch = 19, new = TRUE, legend = new, add.params = FALSE, ...)
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}(x, new = TRUE, type = c("boxplot", "points"),
8
- col = "#00000044", pt.cex = 1/2, pt.pch = 19, pt.col = col,
9
- ln.col = col, ...)
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}(x, type = c("overlap", "difference"),
8
- col = "#00000044", col1 = col, col2 = "#44001144",
9
- ylab = "Probability", xlim = range(attr(x, "dist.mids")),
10
- ylim = c(0, max(c(attr(x, "all.dist"), attr(x, "sel.dist")))), ...)
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}(x, layout = matrix(c(5, 5, 2, 1, 4, 3), nrow
8
- = 2), panel.fun = list(), widths = c(1, 7, 2), heights = c(1, 2),
9
- palette = grey((100:0)/100), underlay.group = TRUE,
10
- peaks.col = "darkred", use.peaks, id.lim = range(x$id.breaks),
11
- pos.lim = range(x$pos.breaks), pos.units = c("Mbp", "Kbp", "bp"),
12
- mar = list(`1` = c(5, 4, 1, 1) + 0.1, `2` = c(ifelse(any(layout == 1),
13
- 1, 5), 4, 4, 1) + 0.1, `3` = c(5, ifelse(any(layout == 1), 1, 4), 1, 2) +
14
- 0.1, `4` = c(ifelse(any(layout == 1), 1, 5), ifelse(any(layout == 2), 1,
15
- 4), 4, 2) + 0.1, `5` = c(5, 3, 4, 1) + 0.1, `6` = c(5, 4, 4, 2) + 0.1),
16
- pos.splines = 0, id.splines = 1/2,
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", out.col = "lightblue", id.col = "black",
21
- breaks.col = "#AAAAAA40", peaks.opts = list(), ...)
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.}