Pave the way for cran Submission

adrientaudiere · Feb 6, 2024 · 7e1da5e · 7e1da5e
1 parent d81b9b5
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^paper$
 ^.vscode$
 ^citation.cff$
+^vignettes/articles$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -38,6 +38,16 @@ jobs:
          && make check \
          && sudo make install 
 
+      - name: Install swarm
+        run: |
+        git clone https://github.com/torognes/swarm.git \
+        && cd swarm/ \
+        && make
+
+      - name: Install cutadapt
+        run: |
+        sudo python3 -m pip install cutadapt
+
       - name: Test coverage
         run: |
           covr::codecov(

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.0
+Version: 0.7.1
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatic pipeline in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerfull by integrating a large number of analysis, some of them from other R packages.  
 License: AGPL-3
 Encoding: UTF-8
-LazyData: false
+LazyData: true
 Depends:
     R (>= 3.5.0),
     phyloseq,
@@ -21,17 +21,14 @@ Suggests:
     Biostrings,
     circlize,
     ComplexUpset,
-    data.table,
     DECIPHER,
     DESeq2,
     devtools,
     DT,
     edgeR,
-    formattable,
     gghalves,
     ggh4x,
     ggstatsplot,
-    ggtree,
     ggridges,
     ggVennDiagram,
     gtsummary,
@@ -48,7 +45,6 @@ Suggests:
     metacoder,
     methods,
     mia,
-    MicrobiotaProcess,
     mixtools,
     multcompView,
     networkD3,
@@ -73,14 +69,24 @@ Suggests:
     testthat (>= 3.0.0),
     tibble,
     tidyr,
-    tidytree,
-    treeio,
     treemapify,
     vegan,
     venneuler,
     vctrs,
     viridis,
-    withr
+    withr,
+    datawizard,
+    formattable,
+    ggforce,
+    ggtree,
+    gtExtras,
+    MicrobiotaProcess,
+    pillar,
+    pointblank,
+    summarytools,   
+    svglite,
+    tidytree,
+    treeio
 RoxygenNote: 7.3.1
 URL: https://github.com/adrientaudiere/MiscMetabar,
     https://adrientaudiere.github.io/MiscMetabar/
@@ -93,10 +99,6 @@ Imports:
     lifecycle,
     rlang,
     stats
-Remotes: 
-    bioc::phyloseq,
-    bioc::dada2,
-    bioc::ANCOMBC
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr

diff --git a/R/MiscMetabar-package.R b/R/MiscMetabar-package.R
@@ -22,7 +22,8 @@ if (getRversion() >= "2.15.1") {
     "tax", "tax_col", "teststat", "Time", "tnrs_match_names", "tol_induced_subtree",
     "update", "upr", "upViewport", "val", "value", "vegdist", "viewport",
     "write.table", "x", "x1", "X1", "x2", "y", "y1", "y2", "ymax",
-    "ymin", ".group", "archetype", "nOTUid", "taxon", "total"
+    "ymin", ".group", "archetype", "nOTUid", "taxon", "total",
+    "chim_rm", "condition", "physeq", "seq_tab_Pairs"
   ))
 }
 

diff --git a/R/blast.R b/R/blast.R
@@ -45,7 +45,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' data(data_fungi)
+#' # data(data_fungi)
 #' blastpath <- "...YOUR_PATH_TO_BLAST..."
 #' blast_to_phyloseq(data_fungi,
 #'   seq2search = system.file("extdata", "ex.fasta",

diff --git a/R/controls.R b/R/controls.R
@@ -145,7 +145,7 @@ dist_pos_control <- function(physeq, samples_names, method = "bray") {
 #' @export
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #'
 #' subset_taxa_tax_control(data_fungi,
 #'   as.numeric(data_fungi@otu_table[, 300]),

diff --git a/R/dada_phyloseq.R b/R/dada_phyloseq.R
@@ -437,7 +437,7 @@ track_wkflow <- function(list_of_objects,
 #' @author Adrien Taudière
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' tree_A10_005 <- subset_samples(data_fungi, Tree_name == "A10-005")
 #' track_wkflow_samples(tree_A10_005)
 track_wkflow_samples <- function(list_pq_obj, ...) {
@@ -619,7 +619,7 @@ asv2otu <- function(physeq = NULL,
 #'   ACCCTCAAGCCCCTTATTGCTTGGTGTTGGGAGTTTAGCTGGCTTTATAGCGGTTAACTCCCTAAATATACTGGCG",
 #'   file = file_dna, names = "seq1"
 #' )
-#' data(data_fungi)
+#' # data(data_fungi)
 #' res <- vs_search_global(data_fungi, file_dna)
 #' unlink(file_dna)
 #'
@@ -753,7 +753,7 @@ vs_search_global <- function(physeq,
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' # write_pq(data_fungi, path = "phyloseq")
 #' # write_pq(data_fungi, path = "phyloseq", one_file = TRUE)
 #' @seealso [MiscMetabar::save_pq()]
@@ -960,7 +960,7 @@ write_pq <- function(physeq,
 #' @author Adrien Taudière
 #' @examples
 #' \dontrun{
-#' data(data_fungi)
+#' # data(data_fungi)
 #' save_pq(data_fungi, path = "phyloseq")
 #' }
 #' @seealso [MiscMetabar::write_pq()]
@@ -1478,7 +1478,7 @@ verify_pq <- function(
 #'   the number of samples
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' cond_samp <- grepl("A1", data_fungi@sam_data[["Sample_names"]])
 #' subset_samples_pq(data_fungi, cond_samp)
 #'
@@ -1532,7 +1532,7 @@ subset_samples_pq <- function(physeq, condition) {
 #'   of this function if you use this parameter. No effect if the condition
 #'   is of class `tax_table`.
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' subset_taxa_pq(data_fungi, data_fungi@tax_table[, "Phylum"] == "Ascomycota")
 #'
 #' cond_taxa <- grepl("Endophyte", data_fungi@tax_table[, "Guild"])
@@ -1637,7 +1637,7 @@ subset_taxa_pq <- function(physeq,
 #' @author Adrien Taudière
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' A8_005 <- select_one_sample(data_fungi, "A8-005_S4_MERGED.fastq.gz")
 #' A8_005
 select_one_sample <- function(physeq, sam_name, silent = FALSE) {
@@ -1784,7 +1784,7 @@ tbl_sum_samdata <- function(physeq, remove_col_unique_value = TRUE, ...) {
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 5000)
 #' \dontrun{
 #' df <- add_funguild_info(df,
@@ -1853,7 +1853,7 @@ add_funguild_info <- function(physeq,
 #' @author Adrien Taudière
 #' @examples
 #' \dontrun{
-#' data(data_fungi)
+#' # data(data_fungi)
 #' df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 5000)
 #' df <- add_funguild_info(df,
 #'   taxLevels = c(
@@ -2016,7 +2016,7 @@ plot_guild_pq <-
 #'   use this function.
 #' @examples
 #' library("phangorn")
-#' data(data_fungi)
+#' # data(data_fungi)
 #' df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 9000)
 #' df_tree <- build_phytree_pq(df, nb_bootstrap = 5)
 #' plot(df_tree$UPGMA)
@@ -2153,7 +2153,7 @@ build_phytree_pq <- function(physeq,
 #' @author Adrien Taudière
 #' @importFrom stats kruskal.test
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' are_modality_even_depth(data_fungi, "Time")$p.value
 #' are_modality_even_depth(rarefy_even_depth(data_fungi), "Time")$p.value
 #' are_modality_even_depth(data_fungi, "Height", boxplot = TRUE)
@@ -2191,7 +2191,7 @@ are_modality_even_depth <- function(physeq, fact, boxplot = FALSE) {
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' data_fungi_ordered_by_genus <- reorder_taxa_pq(
 #'   data_fungi,
 #'   taxa_names(data_fungi)[order(as.vector(data_fungi@tax_table[, "Genus"]))]
@@ -2263,7 +2263,7 @@ reorder_taxa_pq <- function(physeq, names_ordered, remove_phy_tree = FALSE) {
 #' @export
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' data_fungi <- add_info_to_sam_data(data_fungi)
 #' boxplot(data_fungi@sam_data$nb_otu ~ data_fungi@sam_data$Time)
 #'
@@ -2293,7 +2293,7 @@ add_info_to_sam_data <- function(physeq,
     df_info <-
       df_info[match(sample_names(physeq), rownames(df_info)), ]
     physeq@sam_data <- sample_data(cbind(
-      as_tibble(physeq@sam_data),
+      as.data.frame(physeq@sam_data),
       df_info
     ))
   }
@@ -2347,15 +2347,25 @@ add_info_to_sam_data <- function(physeq,
 #' @export
 #' @examples
 #' \dontrun{
-#' data(data_fungi)
+#' # data(data_fungi)
 #' summary_plot_pq(data_fungi)
 #' # Change with your PATH
 #' path_to_swarm <- "/home/adrien/miniconda3/bin/swarm"
 #'
 #' data_fungi_swarm <- swarm_clustering(data_fungi, swarmpath = path_to_swarm)
 #' summary_plot_pq(data_fungi_swarm)
 #'
-#' sequences_ex <- c("TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG", "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG", "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG", "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG")
+#' sequences_ex <- c(
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACC",
+#'   "CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
+#' )
 #'
 #' sequences_ex_swarm <- swarm_clustering(
 #'   dna_seq = sequences_ex,
@@ -2520,11 +2530,21 @@ swarm_clustering <- function(physeq = NULL,
 #' @export
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' dna <- physeq_or_string_to_dna(data_fungi)
 #' dna
 #'
-#' sequences_ex <- c("TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG", "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCAACCTACCCTGTACACCGCGCCTGGGTCTACCCTCCGGATGACATTTTTAAGACTCTTGTTTTATAGTGAAATTCTGAGTTTTTATACTTAATAAGTTAAAACTTTCAATCTCGGATCTCTTGGCTCTGGCATCGATGAAGAACGCTACGAAATGCTGATAAATAATGTGAATTGCCGAATTCATTGAATCATCGAATCTTTGAACGCACATTGCACCCATTAGTATTCTAGAGTGCATGCCTGTTCCAGCGTCATTTTCAATCCTCAAGCCCCTTATTGCTTGGTGTTGGCAGTTTAGCTGGCTTTATAGTGCTTAACTCCCTAAATATACTGCCTGATTCGCGGTGACCCCAAGCGTAATAATTATTTTCTCGCTTGAGGTG")
+#' sequences_ex <- c(
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTAATAACGAATTCATTGAATCA",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAAGGCCCACTT",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACCCGGGATTTGATGGGGCGAATTACCTGGTAGAGGTG",
+#'   "TACCTATGTTGCCTTGGCGGCTAAACCTACC",
+#'   "CGGGATTTGATGGCGAATTACCTGGTATTTTAGCCCACTTACCCGGTACCATGAGGTG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACCTGG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG",
+#'   "GCGGCTAAACCTACCCGGGATTTGATGGCGAATTACAAAG"
+#' )
 #' dna2 <- physeq_or_string_to_dna(dna_seq = sequences_ex)
 #' dna2
 #'
@@ -2602,7 +2622,7 @@ physeq_or_string_to_dna <- function(physeq = NULL,
 #' @author Adrien Taudière
 #'
 #' @examples
-#' data(data_fungi)
+#' # data(data_fungi)
 #' summary_plot_pq(data_fungi)
 #' d_vs <- vsearch_clustering(data_fungi)
 #' summary_plot_pq(d_vs)
@@ -2776,7 +2796,7 @@ cutadapt_remove_primers <- function(path_to_fastq,
                                     args_before_cutadapt = "source ~/miniconda3/etc/profile.d/conda.sh && conda activate cutadaptenv && ") {
   cmd <- list()
   if (!dir.exists(folder_output)) {
-      dir.create(folder_output)
+    dir.create(folder_output)
   }
 
   if (is.null(primer_rev)) {
@@ -2813,8 +2833,8 @@ cutadapt_remove_primers <- function(path_to_fastq,
       nb_files = nb_files
     )
 
-    primer_fw_RC <- dada2:::rc(primer_fw)
-    primer_rev_RC <- dada2:::rc(primer_rev)
+    primer_fw_RC <- dada2::rc(primer_fw)
+    primer_rev_RC <- dada2::rc(primer_rev)
     for (f in lff$fnfs) {
       cmd[[f]] <-
         paste0(

diff --git a/R/funguild.R b/R/funguild.R
@@ -13,8 +13,6 @@
 #'     to the `db` argument of [funguild_assign()]
 #' @export
 #'
-#' @examples
-#' get_funguild_db()
 #' @references Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J,
 #' Schilling JS, Kennedy PG. 2016. *FUNGuild: An open annotation tool for
 #' parsing fungal community datasets by ecological guild*. Fungal Ecology
@@ -135,6 +133,9 @@ funguild_assign <- function(otu_table, db_funguild = get_funguild_db(),
     dplyr::ungroup() %>%
     dplyr::mutate_all(as.character) %>%
     dplyr::left_join(otu_table, ., by = "taxkey") %>%
-    dplyr::left_join(db_funguild, by = "searchkey", suffix = c("", ".funguild")) %>%
+    dplyr::left_join(db_funguild,
+      by = "searchkey",
+      suffix = c("", ".funguild")
+    ) %>%
     dplyr::select(-taxkey, -searchkey)
 }