Merge pull request #49 from adrientaudiere/dev

Merge pull request #36 from adrientaudiere/master

.Rbuildignore

@@ -8,3 +8,7 @@
 ^LICENSE\.md$
 ^doc$
 ^Meta$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^paper$
+^.vscode$

.github/ISSUE_TEMPLATE/bug_report.md

@@ -11,28 +11,17 @@ assignees: ''
 A clear and concise description of what the bug is.
 
 **To Reproduce**
-Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+Please provide a Minimal Reproducible Example (MRE). See
+[Wikipedia](https://en.wikipedia.org/wiki/Minimal_reproducible_example)
+ and [stackoverflow](https://stackoverflow.com/help/minimal-reproducible-example) for more information.
+
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
 
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
+**System information (please complete the following information):**
+Please copy the result of the commande `sessionInfo()`
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -16,5 +16,3 @@ A clear and concise description of what you want to happen.
 **Describe alternatives you've considered**
 A clear and concise description of any alternative solutions or features you've considered.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: MiscMetabar
 Type: Package
-Title: Miscellaneous functions for metabarcoding analysis
-Version: 0.5
+Title: Miscellaneous Functions for Metabarcoding Analysis
+Version: 0.51
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1088-1182"))
 Maintainer: Adrien Taudière <[email protected]>
 Description: Functions to help analyze and visualize metabarcoding data. Mainly build on the top of phyloseq, dada2 and targets R packages.
-License: AGPL-3 + file LICENSE
+License: AGPL-3
 Encoding: UTF-8
 LazyData: true
 Depends:
@@ -17,35 +17,46 @@ Depends:
     magrittr,
     phyloseq
 Suggests: 
+    adespatial,
+    BiocManager,
     Biostrings,
     circlize,
     ComplexUpset,
     data.table,
     DECIPHER,
     DESeq2,
+    devtools,
     DT,
     edgeR,
     formattable,
+    FUNGuildR,
     gghalves,
     ggh4x,
+    ggtree,
     ggridges,
     ggVennDiagram,
     gtsummary,
+    graphics, 
     grDevices,
     grid,
     gridExtra,
     here,
     iNEXT,
+    indicspecies,
     knitr,
     lulu,
     metacoder,
     methods,
+    mia,
     MicrobiotaProcess,
     microViz,
     mixtools,
     multcompView,
-    networkD3,
+    networkD3, 
+    pak,
     patchwork,
+    permute,
+    phangorn,
     pbapply,
     plotly,
     plyr,
@@ -60,7 +71,10 @@ Suggests:
     testthat (>= 3.0.0),
     tibble,
     tidyr,
+    tidytree,
+    treeio,
     treemapify,
+    utils, 
     vegan,
     venneuler,
     viridis
@@ -81,8 +95,9 @@ Remotes:
     github::adrientaudiere/lulu,
     github::david-barnett/microViz,
     github::erocoar/gghalves,
-    bioc::phyloseq,
-    bioc::dada2
+    bioc::release/phyloseq,
+    bioc::release/dada2,
+    github::brendanf/FUNGuildR
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr

LICENSE.md

@@ -1,6 +1,6 @@
-MiscMetabar is licensed under the GNU AGPLv3. MiscMetabar takes some code and
+MiscMetabar is licensed under the GNU AGPL-3.0. MiscMetabar takes some code and
 documentation from the Speedyseq R package. Speedyseq is also licensed under the
-GNU AGPLv3; its source code is available at https://github.com/mikemc/speedyseq/.
+GNU AGPL-3.0; its source code is available at https://github.com/mikemc/speedyseq/.
 
                     GNU AFFERO GENERAL PUBLIC LICENSE
                        Version 3, 19 November 2007

MiscMetabar.Rproj

@@ -1,8 +1,8 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes

NAMESPACE

@@ -6,6 +6,7 @@ export(accu_plot)
 export(accu_samp_threshold)
 export(add_blast_info)
 export(add_dna_to_phyloseq)
+export(add_funguild_info)
 export(add_new_taxonomy_pq)
 export(adonis_phyloseq)
 export(adonis_pq)
@@ -17,6 +18,7 @@ export(biplot_pq)
 export(blast_pq)
 export(blast_to_derep)
 export(blast_to_phyloseq)
+export(build_phytree_pq)
 export(circle_pq)
 export(clean_physeq)
 export(clean_pq)
@@ -37,6 +39,7 @@ export(hill_pq)
 export(hill_tuckey_phyloseq)
 export(hill_tuckey_pq)
 export(iNEXT_pq)
+export(install_pkg_needed)
 export(krona)
 export(list_fastq_files)
 export(lulu_phyloseq)
@@ -46,6 +49,7 @@ export(multi_biplot_pq)
 export(multipatt_pq)
 export(multiplot)
 export(multitax_bar_pq)
+export(mumu_pq)
 export(otu_circle)
 export(perc)
 export(phyloseq_to_edgeR)
@@ -56,6 +60,7 @@ export(plot_deseq2_phyloseq)
 export(plot_deseq2_pq)
 export(plot_edgeR_phyloseq)
 export(plot_edgeR_pq)
+export(plot_guild_pq)
 export(plot_mt)
 export(plot_tax_pq)
 export(plot_tsne_pq)

NEWS.md

@@ -2,6 +2,10 @@
 
 - Add function `LCBD_pq()` and `plot_LCBD_pq()` to compute, test and plot local contributions to beta diversity (LCBD) of samples
 - Add function `tbl_sum_samdata()` to summarize information from sample data in a table
+- Add function `mumu_pq()` to use [mumu](https://github.com/frederic-mahe/mumu), a fast and robust C++ implementation of lulu.
+- Add (a mostly internal) function `install_pkg_needed()` to install pkg (mostly for package list in *Suggest* in DESCRIPTION) if needed by a function.
+- Add function `add_funguild_info()` and `plot_guild_pq()` to add and plot fungal guild information from taxonomy using `FUNGuild` package
+- Add function `build_phytree_pq()` to build 3 phylogenetic trees (NJ, UPGMA and ML using `phangorn` R package) from the `refseq` slot of a `phyloseq` object, possibly with bootstrap values. See the vignettes [Tree visualization](https://adrientaudiere.github.io/MiscMetabar/articles/tree_visualization.html) for an introduction to tree visualization using `ggtree` R package.
 
 # MiscMetabar 0.5
 
@@ -10,7 +14,7 @@
 ## BREAKING CHANGES
 
 - Rename param `log_10` in function `biplot_pq()` into `log10trans`
-- Rename param `log10trans` in function `circle_pq()` into `log10trans`
+- Rename param `log10transform` in function `circle_pq()` into `log10trans`
 
 # MiscMetabar 0.42 
 
@@ -23,8 +27,8 @@
 # MiscMetabar 0.41
 
 - Add function `iNEXT_pq()` to calculate hill diversity using the [iNEXT](https://github.com/AnneChao/iNEXT) package.
-- Add argument `paires` to `multi_biplot_pq()` in order to indicate all paires of samples we want to print.
-- Improve `compare_pairs_pq()` with information about the number of shared sequences among paires.
+- Add argument `pairs` to `multi_biplot_pq()` in order to indicate all pairs of samples we want to print.
+- Improve `compare_pairs_pq()` with information about the number of shared sequences among pairs.
 - Add function `upset_pq()` to plot upset of phyloseq object using the [ComplexUpset](https://krassowski.github.io/complex-upset/) package.
 - Add function `upset_test_pq` to test for differences between intersections (wrapper of `ComplexUpset::upset_test()` for `phyloseq-object`).
 - Add info (param `add_info`) in subtitle of the `hill_pq()` function.
@@ -52,7 +56,7 @@
 * Improve the documentation of `asv2otu()` and fix a little bug in the name of the conserved ASV after `asv2otu()`.
 * Test coverage largely improved leading to numerous minor bug fixes.
 * Add function `search_exact_seq_pq()` to search for exact matching of sequences using complement, reverse and reverse-complement against a phyloseq object.
-* Add function `add_new_taxonomy_pq()` to add new taxonomic rank to a phyloseq object. For exemple to add taxonomic assignment from a new database.
+* Add function `add_new_taxonomy_pq()` to add new taxonomic rank to a phyloseq object. For example to add taxonomic assignment from a new database.
 * Add a battery of test using `test_that` package and improve code compatibility with cran recommendations.
 
 ## BREAKING CHANGES
@@ -64,7 +68,7 @@
 # MiscMetabar 0.34
 
 * Add option `add_nb_samples` to `ggvenn_pq()` which add the number of samples to level name in the plot. Useful to see disequilibrium in the number of samples among the factor's levels.
-* Add option `args_makedb` and `args_blastn` to funtions `blast_pq()`, `blast_to_phyloseq()`, `blast_to_derep()` and `filter_asv_blast()`.
+* Add option `args_makedb` and `args_blastn` to functions `blast_pq()`, `blast_to_phyloseq()`, `blast_to_derep()` and `filter_asv_blast()`.
 * Add option `rarefy_nb_seqs` to `ggven_pq()` in order to rarefy samples before plotting. 
 * Add function `SRS_curve_pq()` to plot scaling with ranked subsampling (SRS) curves using the `SRS::SRS_curve()` function (see citation("SRS") for reference).
 * Add option `nb_samples_info` to `biplot_pq()` in order to add the number of samples merged by level of factors.
@@ -158,7 +162,7 @@
 
 * Add a function `multiple_share_bisamples()` to help compare samples by pairs
 
-* Add a new function (`ggVenn_phyloseq()`) for better venn diagramm but without area calculation (use `venn_phyloseq()` in this case).
+* Add a new function (`ggVenn_phyloseq()`) for better venn diagram but without area calculation (use `venn_phyloseq()` in this case).
 
 * Add two functions helpful for beta-diversity analysis (`adonis_phyloseq()` and `physeq_graph_test()`)
 

R/Deseq2_edgeR.R

@@ -19,7 +19,6 @@
 #'   or \code{\link[ggplot2]{ggplot}}
 #'
 #' @export
-#'
 #' @examples
 #' \dontrun{
 #' data(GlobalPatterns)
@@ -150,11 +149,12 @@ plot_edgeR_pq <-
 #'   or \code{\link[ggplot2]{ggplot}}
 #'
 #' @export
-#'
+#' @details
+#'   Please cite `DESeq2` package if you use chis function.
 #' @examples
-#' data("GlobalPatterns")
+#' data("GlobalPatterns", package = "phyloseq")
 #' GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
-#' GP <- subset_samples(GP, GP@sam_data$SampleType %in% c("Soil", "Skin"))
+#' GP <- subset_samples(GP, SampleType %in% c("Soil", "Skin"))
 #' res <- DESeq2::DESeq(phyloseq_to_deseq2(GP, ~SampleType),
 #'   test = "Wald", fitType = "local"
 #' )
@@ -380,6 +380,8 @@ plot_deseq2_pq <-
 #'
 #'  \code{c("TMM", "RLE", "upperquartile", "none")}.
 #'
+#' @return A DGEList object. See [edgeR::estimateTagwiseDisp()] for more details.
+#'
 #' @param ... Additional arguments passed on to \code{\link[edgeR]{DGEList}}
 #' @export
 #'

R/MiscMetabar-package.R

@@ -9,7 +9,7 @@ NULL
 
 if (getRversion() >= "2.15.1") {
   utils::globalVariables(c(
-    ".id", "%>%", "Ab", "Abundance", "character_method", "col_tax", "combn", "complement", "devtools", "e-value", "Family", "Genus", "grid.draw", "grid.layout", "group_by", "Hill_0", "Hill_1", "Hill_2", "install_github", "log2FoldChange", "logFC", "lwr", "max_Hill", "modality", "multcompLetters", "nb_values", "ott_id", "OTU", "Proportion", "pushViewport", "Query name", "rarefy", "reverse", "rgb", "reverseComplement", "rrarefy", "Sample", "Species", "summarise", "tax", "tax_col", "teststat", "tnrs_match_names", "tol_induced_subtree", "upr", "upViewport", "val", "vegdist", "viewport", "x", "x1", "X1", "x2", "y", "y1", "y2", "ymax", "ymin", "Class", "LVL1", "LVL3", "Time",  "calc_taxon_abund", "heat_tree", "parse_phyloseq"
+    ".id", "%>%", "Ab", "Abundance", "character_method", "col_tax", "combn", "complement", "devtools", "e-value", "Family", "Genus", "grid.draw", "grid.layout", "group_by", "Hill_0", "Hill_1", "Hill_2", "install_github", "log2FoldChange", "logFC", "lwr", "max_Hill", "modality", "multcompLetters", "nb_values", "ott_id", "OTU", "Proportion", "pushViewport", "Query name", "rarefy", "reverse", "rgb", "reverseComplement", "rrarefy", "Sample", "Species", "summarise", "tax", "tax_col", "teststat", "tnrs_match_names", "tol_induced_subtree", "upr", "upViewport", "val", "vegdist", "viewport", "x", "x1", "X1", "x2", "y", "y1", "y2", "ymax", "ymin", "Class", "LVL1", "LVL3", "Time", "calc_taxon_abund", "heat_tree", "parse_phyloseq", "ASV_names", "LCBD", "Sample_names", "beta.div", "how name", "p.adj", "p.adjust", "plot_layout value", "Guild", "colors", "install.packages", "name", "nb_asv", "nb_seq", "plot_layout", "read.delim", "update", "value", "write.table"
   ))
 }