miga-base 1.2.17.0 → 1.2.17.2

data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec

@@ -0,0 +1,233 @@
+8528	8627	97.03	169	2
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+554	653	96.00	161	6
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+8316	8415	95.00	156	436
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+7692	7791	96.04	163	470
+51	150	95.00	158	471
+1397	1496	98.00	172	472
+42	141	94.00	152	475
+2117	2216	96.00	161	476
+5481	5579	93.94	147	482
+7809	7908	95.00	158	485
+4991	5089	94.00	148	486
+9059	9158	97.00	167	487
+2	73	95.83	115	487
+133	232	95.10	158	488
+6966	7065	95.10	159	490
+6296	6390	96.84	158	492
+4728	4827	97.00	169	495
+4205	4304	96.08	165	498
+6833	6932	98.00	172	499

data/utils/enveomics/Tests/phyla_counts.tsv

@@ -0,0 +1,10 @@
+OTU	Site A	Site B	Site C	Site D
+Actinobacteria	22	1	2	22
+Dehalococcoidia	44	3	2	44
+Fusobacteria	1	4	2	32
+Nitrospirae	32	3	6	1
+Planctomycetes	11	2	1	11
+Proteobacteria	77	25	38	7
+Spirochaetes	4	11	7	3
+Thermotogae	2	11	1	2
+unclassified	1	1	1	1

data/utils/enveomics/Tests/primate_lentivirus.ogs

@@ -0,0 +1,11 @@
+hiv1	hiv2	siv
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	-
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	-
+lcl|AF033819.3_prot_AAD20388.1_7	-	-
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6
+-	lcl|NC_001722.1_prot_NP_056840.1_4	-

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm

@@ -0,0 +1,9 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|AF033819.3_prot_AAC82593.1_1	100.00	500	0	0	1	500	1	500	0.0	1044	500	500
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|AF033819.3_prot_AAC82598.2_2	100.00	1003	0	0	1	1003	1	1003	0.0	2062	1003	1003
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|AF033819.3_prot_AAC82594.1_3	100.00	192	0	0	1	192	1	192	6e-147	400	192	192
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|AF033819.3_prot_AAC82595.1_4	100.00	78	0	0	1	78	1	78	4e-56	161	78	78
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|AF033819.3_prot_AAC82591.1_5	100.00	86	0	0	1	86	1	86	6e-63	179	86	86
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|AF033819.3_prot_AAC82592.1_6	100.00	116	0	0	1	116	1	116	1e-82	231	116	116
+lcl|AF033819.3_prot_AAD20388.1_7	lcl|AF033819.3_prot_AAD20388.1_7	100.00	82	0	0	1	82	1	82	2e-54	157	82	82
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|AF033819.3_prot_AAC82596.1_8	100.00	856	0	0	1	856	1	856	0.0	1770	856	856
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|AF033819.3_prot_AAC82597.1_9	100.00	123	0	0	1	123	1	123	1e-92	257	123	123

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm

@@ -0,0 +1,8 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001722.1_prot_NP_056837.1_2	58.19	452	178	7	1	448	1	445	0.0	526	500	521
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001722.1_prot_NP_663784.1_1	58.24	953	397	1	42	994	498	1449	0.0	1169	1003	1550
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	33.75	160	91	6	2	153	4	156	2e-20	75.9	192	215
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001722.1_prot_NP_056841.1_5	40.79	76	45	0	2	77	7	82	1e-18	65.9	78	87
+lcl|AF033819.3_prot_AAC82591.1_5	lcl|NC_001722.1_prot_NP_056842.1_6	67.74	31	9	1	18	47	46	76	9e-12	47.8	86	130
+lcl|AF033819.3_prot_AAC82592.1_6	lcl|NC_001722.1_prot_NP_056843.1_7	46.43	28	14	1	8	34	5	32	0.004	25.0	116	103
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	34.47	879	492	22	25	856	19	860	3e-146	447	856	860
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	56.90	58	25	0	66	123	98	155	2e-22	80.1	123	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm

@@ -0,0 +1,6 @@
+lcl|AF033819.3_prot_AAC82593.1_1	lcl|NC_001549.1_prot_NP_054369.1_2	52.67	524	208	9	1	496	1	512	0.0	518	500	513
+lcl|AF033819.3_prot_AAC82598.2_2	lcl|NC_001549.1_prot_NP_687035.1_1	60.25	966	373	6	36	994	487	1448	0.0	1196	1003	1472
+lcl|AF033819.3_prot_AAC82594.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	38.71	155	87	7	2	152	4	154	1e-25	90.9	192	219
+lcl|AF033819.3_prot_AAC82595.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	30.43	69	40	3	11	73	21	87	4e-07	34.3	78	118
+lcl|AF033819.3_prot_AAC82596.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	36.16	874	464	26	34	855	22	853	5e-154	467	856	854
+lcl|AF033819.3_prot_AAC82597.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	60.34	58	23	0	66	123	82	139	5e-21	75.9	123	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm

@@ -0,0 +1,9 @@
+lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001722.1_prot_NP_663784.1_1	100.00	1550	0	0	1	1550	1	1550	0.0	3210	1550	1550
+lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001722.1_prot_NP_056837.1_2	100.00	521	0	0	1	521	1	521	0.0	1077	521	521
+lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001722.1_prot_NP_056839.1_3	100.00	215	0	0	1	215	1	215	5e-164	446	215	215
+lcl|NC_001722.1_prot_NP_056840.1_4	lcl|NC_001722.1_prot_NP_056840.1_4	100.00	113	0	0	1	113	1	113	6e-85	237	113	113
+lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001722.1_prot_NP_056841.1_5	100.00	87	0	0	1	87	1	87	5e-63	179	87	87
+lcl|NC_001722.1_prot_NP_056842.1_6	lcl|NC_001722.1_prot_NP_056842.1_6	100.00	130	0	0	1	130	1	130	4e-94	262	130	130
+lcl|NC_001722.1_prot_NP_056843.1_7	lcl|NC_001722.1_prot_NP_056843.1_7	100.00	103	0	0	1	103	1	103	2e-72	204	103	103
+lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001722.1_prot_NP_056844.1_8	100.00	860	0	0	1	860	1	860	0.0	1799	860	860
+lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001722.1_prot_NP_056845.1_9	100.00	257	0	0	1	257	1	257	0.0	536	257	257

data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm

@@ -0,0 +1,6 @@
+lcl|NC_001722.1_prot_NP_663784.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	56.99	1474	601	10	1	1458	1	1457	0.0	1697	1550	1472
+lcl|NC_001722.1_prot_NP_056837.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	57.39	528	203	7	1	521	1	513	0.0	593	521	513
+lcl|NC_001722.1_prot_NP_056839.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	44.97	169	88	5	1	167	1	166	6e-41	132	215	219
+lcl|NC_001722.1_prot_NP_056841.1_5	lcl|NC_001549.1_prot_NP_054371.1_4	35.21	71	42	2	17	83	22	92	3e-11	46.2	87	118
+lcl|NC_001722.1_prot_NP_056844.1_8	lcl|NC_001549.1_prot_NP_054372.1_5	44.90	873	401	14	25	859	23	853	0.0	714	860	854
+lcl|NC_001722.1_prot_NP_056845.1_9	lcl|NC_001549.1_prot_NP_054373.1_6	41.74	230	108	5	1	224	1	210	2e-50	158	257	223

data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm

@@ -0,0 +1,6 @@
+lcl|NC_001549.1_prot_NP_687035.1_1	lcl|NC_001549.1_prot_NP_687035.1_1	100.00	1472	0	0	1	1472	1	1472	0.0	3045	1472	1472
+lcl|NC_001549.1_prot_NP_054369.1_2	lcl|NC_001549.1_prot_NP_054369.1_2	100.00	513	0	0	1	513	1	513	0.0	1067	513	513
+lcl|NC_001549.1_prot_NP_054370.1_3	lcl|NC_001549.1_prot_NP_054370.1_3	100.00	219	0	0	1	219	1	219	7e-169	459	219	219
+lcl|NC_001549.1_prot_NP_054371.1_4	lcl|NC_001549.1_prot_NP_054371.1_4	100.00	118	0	0	1	118	1	118	3e-87	243	118	118
+lcl|NC_001549.1_prot_NP_054372.1_5	lcl|NC_001549.1_prot_NP_054372.1_5	100.00	854	0	0	1	854	1	854	0.0	1776	854	854
+lcl|NC_001549.1_prot_NP_054373.1_6	lcl|NC_001549.1_prot_NP_054373.1_6	100.00	223	0	0	1	223	1	223	5e-170	462	223	223

data/utils/enveomics/build_enveomics_r.bash

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+cd $(dirname -- $0)/enveomics.R
+rm man/*
+echo '
+\name{phyla.counts}
+\docType{data}
+\alias{phyla.counts}
+\title{Counts of microbial phyla in four sites}
+\description{
+  This data set gives the counts of phyla in three different
+  sites.
+}
+\usage{phyla.counts}
+\format{A data frame with 9 rows (phyla) and 4 rows (sites).}
+\keyword{datasets}
+' > man/phyla.counts.Rd
+echo '
+\name{growth.curves}
+\docType{data}
+\alias{growth.curves}
+\title{Bacterial growth curves for three Escherichia coli mutants}
+\description{
+  This data set provides time (first column) and three triplicated growth
+  curves as optical density at 600nm (OD_600nm) for different mutants of E.
+  coli.
+}
+\usage{growth.curves}
+\format{A data frame with 16 rows (times) and 10 rows (times and OD_600nm).}
+\keyword{datasets}
+' > man/growth.curves.Rd
+echo 'roxygen2::roxygenise();' | R --vanilla
+#echo "
+#library(inlinedocs)
+#package.skeleton.dx('./');
+#" | R --vanilla
+#cat man/enveomics.R-package.Rd | tr -d '\r' \
+#  | grep -v '^}$' | grep -v '^\\author{' \
+#  | grep -v '^Maintainer' \
+#  | perl -pe 's/^\\keyword/}\n\\author{Luis M. Rodriguez-R <lmrodriguezr\@gmail.com> [aut, cre]}\n\n\\keyword/' \
+#  | perl -lwe '$/=\0; $_=<>; s/^\\details{\n+([^}].*\n+)*}\n+//mg; print' \
+#  > o && mv o man/enveomics.R-package.Rd
+#[[ ! -d inst/doc ]] && mkdir -p inst/doc
+#pandoc -o inst/doc/enveomics.R.pdf -f markdown_github README.md
+

data/utils/enveomics/enveomics.R/DESCRIPTION

@@ -0,0 +1,31 @@
+Package: enveomics.R
+Version: 1.9.0
+Authors@R: c(person("Luis M.", "Rodriguez-R", role = c("aut", "cre"),
+	   email = "lmrodriguezr@gmail.com"))
+Title: Various Utilities for Microbial Genomics and Metagenomics
+Description: A collection of functions for microbial ecology and other
+   applications of genomics and metagenomics. Companion package for the
+   Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
+   <DOI:10.7287/peerj.preprints.1900v1>).
+Author: Luis M. Rodriguez-R [aut, cre]
+Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
+URL: http://enve-omics.ce.gatech.edu/enveomics/
+Depends:
+   R (>= 2.9),
+   stats,
+   methods,
+   parallel,
+   fitdistrplus,
+   sn,
+   investr
+Suggests:
+   tools,
+   vegan,
+   ape,
+   picante,
+   gplots,
+   optparse
+License: Artistic-2.0
+LazyData: yes
+Encoding: UTF-8
+RoxygenNote: 7.1.2

data/utils/enveomics/enveomics.R/NAMESPACE

@@ -0,0 +1,39 @@
+import(methods)
+import(parallel)
+import(fitdistrplus)
+import(sn)
+importFrom("investr", "predFit")
+importFrom("grDevices", "boxplot.stats", "col2rgb", "grey", "rainbow",
+  "rgb")
+importFrom("graphics", "abline", "axis", "barplot", "hist", "image",
+  "layout", "legend", "lines", "par", "points", "polygon",
+  "rect", "text")
+importFrom("stats", "as.dist", "cophenetic", "cor", "median",
+  "quantile", "runif", "smooth.spline", "nls", "nls.control", "qnorm",
+  "dnorm", "kmeans")
+importFrom("utils", "head", "read.table", "setTxtProgressBar", "tail",
+  "txtProgressBar")
+exportClasses(enve.RecPlot2, enve.RecPlot2.Peak, enve.TRIBS, enve.TRIBStest,
+  enve.GrowthCurve)
+S3method(plot, enve.RecPlot2)
+S3method(plot, enve.TRIBS)
+S3method(plot, enve.TRIBStest)
+S3method(plot, enve.GrowthCurve)
+S3method(summary, enve.TRIBS)
+S3method(summary, enve.TRIBStest)
+S3method(summary, enve.GrowthCurve)
+export(
+  enve.cliopts, enve.col.alpha,
+  enve.barplot, enve.recplot, enve.prune.dist,
+  enve.tribs, plot.enve.TRIBS, summary.enve.TRIBS, enve.tribs.test,
+  plot.enve.TRIBStest, summary.enve.TRIBStest,
+  enve.df2dist, enve.df2dist.group, enve.df2dist.list,
+  enve.recplot2, plot.enve.RecPlot2, enve.recplot2.findPeaks,
+  enve.recplot2.findPeaks.emauto, enve.recplot2.findPeaks.em,
+  enve.recplot2.findPeaks.mower,
+  enve.recplot2.corePeak, enve.recplot2.changeCutoff,
+  enve.recplot2.windowDepthThreshold, enve.recplot2.extractWindows,
+  enve.recplot2.compareIdentities,
+  enve.recplot2.coordinates, enve.recplot2.seqdepth, enve.recplot2.ANIr,
+  enve.growthcurve, plot.enve.GrowthCurve, summary.enve.GrowthCurve,
+  enve.col2alpha, enve.truncate, enve.selvector, enve.prefscore)

data/utils/enveomics/enveomics.R/R/autoprune.R

@@ -0,0 +1,167 @@
+#' Enveomics: Prune Dist
+#' 
+#' Automatically prunes a tree, to keep representatives of each clade.
+#'
+#' @param t A \strong{phylo} object or a path to the Newick file.
+#' @param dist.quantile The quantile of edge lengths.
+#' @param min_dist The minimum distance to allow between two tips.
+#' If not set, \code{dist.quantile} is used instead to calculate it.
+#' @param quiet Boolean indicating if the function must run without output.
+#' @param max_iters Maximum number of iterations.
+#' @param min_nodes_random 
+#' Minimum number of nodes to trigger \emph{tip-pairs} nodes sampling. 
+#' This sampling is less reproducible and more computationally expensive,
+#' but it's the only solution if the cophenetic matrix exceeds \code{2^31-1} 
+#' entries; above that, it cannot be represented in R.
+#' @param random_nodes_frx 
+#' Fraction of the nodes to be sampled if more than \code{min_nodes_random}.
+#'
+#' @return Returns a pruned \strong{phylo} object.
+#'
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.prune.dist <- function(
+  t,
+  dist.quantile = 0.25,
+  min_dist,
+  quiet = FALSE,
+  max_iters = 100,
+  min_nodes_random = 4e4,
+  random_nodes_frx = 1
+) {
+  if (!requireNamespace("ape", quietly = TRUE))
+    stop('Unavailable ape library.');
+  if (is.character(t)) t <- ape::read.tree(t)
+  if (missing(min_dist)) {
+    if (dist.quantile > 0) {
+      min_dist <- as.numeric(quantile(t$edge.length, dist.quantile))
+    } else {
+      min_dist <- as.numeric(min(t$edge.length[t$edge.length>0]))
+    }
+  }
+  if (!quiet)
+    cat("\nObjective minimum distance: ", min_dist, ", initial tips: ",
+        length(t$tip.label), "\n", sep = "")
+
+  round <- 1
+  while (round <= max_iters) {
+    if (length(t$tip.label) > min_nodes_random) {
+      if (!quiet)
+        cat("  | Iter: ", round - 1, ", Tips: ", length(t$tip.label),
+            ", reducing tip-pairs.\n", sep = "")
+      rnd.nodes <- sample(t$tip.label, length(t$tip.label) * random_nodes_frx)
+      t <- enve.__prune.reduce(t, rnd.nodes, min_dist, quiet)
+    } else {
+      if (!quiet) cat(" Gathering distances...\r")
+      d <- cophenetic(t)
+      diag(d) <- NA
+      if(!quiet)
+        cat("  | Iter: ", round - 1, ", Tips: ", length(t$tip.label),
+            ", Median distance: ", median(d, na.rm = TRUE),
+            ", Minimum distance: ", min(d, na.rm = TRUE), "\n", sep = "")
+      # Run iteration
+      if (min(d, na.rm = TRUE) < min_dist) {
+        t <- enve.__prune.iter(t, d, min_dist, quiet)
+      } else {
+        break
+      }
+    }
+    round <- round + 1
+  }
+  return(t)
+}
+
+#' Enveomics: Prune Reduce (Internal Function)
+#' 
+#' Internal function for \code{\link{enve.prune.dist}}.
+#'
+#' @param t A \strong{phylo} object.
+#' @param nodes Vector of nodes.
+#' @param min_dist Minimum distance.
+#' @param quiet If running quietly.
+#' 
+#' @return A \strong{phylo} object.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.__prune.reduce <- function(t, nodes, min_dist, quiet) {
+  if (!quiet) pb <- txtProgressBar(1, length(nodes), style = 3)
+  for (i in 1:length(nodes)) {
+    node.name <- nodes[i]
+    if (!quiet) setTxtProgressBar(pb, i)
+
+    # Get node ID
+    node <- which(t$tip.label == node.name)
+    if (length(node) == 0) next
+
+    # Get parent and distance to parent
+    parent.node <- t$edge[t$edge[, 2] == node, 1]
+
+    # Get edges to parent
+    parent.edges <- which(t$edge[, 1] == parent.node)
+    stopit <- FALSE
+    for (j in parent.edges) {
+      for (k in parent.edges) {
+        if (j != k & t$edge[j,2]<length(t$tip.label) &
+            t$edge[k,2]<length(t$tip.label) &
+            sum(t$edge.length[c(j,k)]) < min_dist) {
+          t <- ape::drop.tip(t, t$edge[k,2])
+          stopit <- TRUE
+          break
+        }
+      }
+      if (stopit) break
+    }
+  }
+  if (!quiet) cat("\n")
+  return(t)
+}
+
+#' Enveomics: Prune Iter (Internal Function)
+#' 
+#' Internal function for \code{\link{enve.prune.dist}}.
+#'
+#' @param t A \strong{phylo} object.
+#' @param dist Cophenetic distance matrix.
+#' @param min_dist Minimum distance.
+#' @param quiet If running quietly.
+#' 
+#' @return Returns a \strong{phylo} object.
+#' 
+#' @author Luis M. Rodriguez-R [aut, cre]
+#'
+#' @export
+
+enve.__prune.iter <- function(t, dist, min_dist, quiet) {
+  ori_len <- length(t$tip.label)
+
+  # Prune
+  if (!quiet) pb <- txtProgressBar(1, ncol(dist) - 1, style = 3)
+  ignore <- c()
+  for (i in 1:(ncol(dist) - 1)) {
+    if (i %in% ignore) next
+    for (j in (i + 1):nrow(dist)) {
+      if (dist[j, i] < min_dist) {
+        t <- ape::drop.tip(t, rownames(dist)[j])
+        ignore <- c(ignore, j)
+        break
+      }
+    }
+    if (!quiet) setTxtProgressBar(pb, i)
+  }
+  if(!quiet) cat("\n")
+
+  # Check if it droped tips
+  cur_len <- length(t$tip.label)
+  if (cur_len == ori_len){
+    stop(
+      "Internal error: small edge found in tree, with no equivalent in distance matrix.\n"
+    )
+  }
+  return(t)
+}
+