Merge pull request #87 from adrientaudiere/dev

Second release on CRAN

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.8
+Version: 0.7.10
 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 bioinformatics pipelines in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerful by integrating a large number of analysis, some of them from other R packages.  
+Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
 License: AGPL-3
 Encoding: UTF-8
 LazyData: true
 Depends:
     R (>= 3.5.0),
     phyloseq,
-    ggplot2,
+    ggplot2 (>= 3.5.0),
     dada2,
     dplyr
 Suggests: 

NAMESPACE

@@ -51,7 +51,12 @@ export(hill_pq)
 export(hill_tuckey_phyloseq)
 export(hill_tuckey_pq)
 export(iNEXT_pq)
-export(install_pkg_needed)
+export(is_cutadapt_installed)
+export(is_falco_installed)
+export(is_krona_installed)
+export(is_mumu_installed)
+export(is_swarm_installed)
+export(is_vsearch_installed)
 export(krona)
 export(list_fastq_files)
 export(lulu)

NEWS.md

@@ -1,3 +1,9 @@
+# MiscMetabar 0.8 (in development)
+
+- Add param `plot_with_tuckey` to `hill_pq()`.
+
+
+
 # MiscMetabar 0.7 (in development)
 
 - Add functions `chimera_detection_vs()` and `chimera_removal_vs()` to process chimera detection and removal using [vsearch](https://github.com/torognes/vsearch) software 
@@ -8,7 +14,7 @@
 - Add function `cutadapt_remove_primers()` to remove primers using [cutadapt](https://github.com/marcelm/cutadapt/)
 - Add internal functions `is_swarm_installed()`, `is_cutadapt_installed()`, `is_vsearch_installed()` and `is_falco_installed()` to test for the availability of external software in order to run examples and test from testthat.
 
-- Submit to CRAN and change code to comply with their rules (patch 0.7.1 to 0.7.8)
+- Submit to CRAN and change code to comply with their rules (patch 0.7.1 to 0.7.9)
 - Numerous examples and tests are skipped on CRAN because it spends to much time to run. Rules vignettes is updated to details the strategy for this.
 
 
@@ -25,6 +31,7 @@
   - `sequences` -> `seq2search` in function `search_exact_seq_pq()`
   - `seq_names` -> `dna_seq` in function `asv2otu`
 
+- Removing the function `install_pkg_needed()` which do not comply with CRAN policies
 
 # MiscMetabar 0.6.0 
 

R/beta_div_test.R

@@ -23,9 +23,9 @@
 #'   [phyloseqGraphTest::graph_perm_test()] function
 #'
 #' @examples
+#' \donttest{
 #' data(enterotype)
 #' graph_test_pq(enterotype, fact = "SeqTech")
-#' \donttest{
 #' graph_test_pq(enterotype, fact = "Enterotype", na_remove = TRUE)
 #' }
 #' @author Adrien Taudière
@@ -119,6 +119,7 @@ graph_test_pq <- function(physeq,
 #'    `phyloseq::rarefy_even_depth()`.
 #'   if `correction_for_sample_size` is TRUE, rarefy_nb_seqs will have no
 #'   effect.
+#' @param verbose (logical, default TRUE) If TRUE, prompt some messages.
 #' @param ... Other arguments passed on to [vegan::adonis2()] function.
 #' @return The function returns an anova.cca result object with a
 #'   new column for partial R^2. See help of [vegan::adonis2()] for
@@ -144,6 +145,7 @@ adonis_pq <- function(physeq,
                       na_remove = FALSE,
                       correction_for_sample_size = FALSE,
                       rarefy_nb_seqs = FALSE,
+                      verbose = TRUE,
                       ...) {
   physeq <- clean_pq(
     physeq,
@@ -175,7 +177,9 @@ adonis_pq <- function(physeq,
   if (na_remove) {
     new_physeq <- physeq
     for (tl in term_lab) {
-      print(tl)
+      if (verbose) {
+        message(tl)
+      }
       new_physeq <-
         subset_samples_pq(new_physeq, !is.na(physeq@sam_data[[tl]]))
     }
@@ -257,8 +261,6 @@ LCBD_pq <- function(physeq,
     silent = TRUE
   )
 
-  install_pkg_needed("adespatial")
-
   mat <- as.matrix(unclass(physeq@otu_table))
   resBeta <- adespatial::beta.div(mat, adj = FALSE, ...)
 
@@ -301,20 +303,21 @@ LCBD_pq <- function(physeq,
 #'   nperm = 100, only_plot_significant = TRUE,
 #'   pval = 0.2
 #' )
-#' library("patchwork")
-#' plot_LCBD_pq(data_fungi_mini,
-#'   nperm = 100, only_plot_significant = FALSE,
-#'   sam_variables = c("Time", "Height")
-#' )
-#' plot_LCBD_pq(data_fungi_mini,
-#'   nperm = 100, only_plot_significant = TRUE, pval = 0.2,
-#'   sam_variables = c("Time", "Height", "Tree_name")
-#' ) &
-#'   theme(
-#'     legend.key.size = unit(0.4, "cm"),
-#'     legend.text = element_text(size = 10),
-#'     axis.title.x = element_text(size = 6)
+#' if (!requireNamespace("patchwork")) {
+#'   plot_LCBD_pq(data_fungi_mini,
+#'     nperm = 100, only_plot_significant = FALSE,
+#'     sam_variables = c("Time", "Height")
 #'   )
+#'   plot_LCBD_pq(data_fungi_mini,
+#'     nperm = 100, only_plot_significant = TRUE, pval = 0.2,
+#'     sam_variables = c("Time", "Height", "Tree_name")
+#'   ) &
+#'     theme(
+#'       legend.key.size = unit(0.4, "cm"),
+#'       legend.text = element_text(size = 10),
+#'       axis.title.x = element_text(size = 6)
+#'     )
+#' }
 #' }
 #' @author Adrien Taudière
 #' @details

R/blast.R

@@ -46,13 +46,13 @@
 #' @examples
 #' \dontrun{
 #'
-#' # blastpath <- "...YOUR_PATH_TO_BLAST..."
-#' # blast_to_phyloseq(data_fungi,
-#' #   seq2search = system.file("extdata", "ex.fasta",
-#' #     package = "MiscMetabar", mustWork = TRUE
-#' #   ),
-#' #   blastpath = blastpath
-#' # )
+#' blastpath <- "...YOUR_PATH_TO_BLAST..."
+#' blast_to_phyloseq(data_fungi,
+#'   seq2search = system.file("extdata", "ex.fasta",
+#'     package = "MiscMetabar", mustWork = TRUE
+#'   ),
+#'   blastpath = blastpath
+#' )
 #' }
 blast_to_phyloseq <- function(physeq,
                               seq2search,

R/dada_phyloseq.R

@@ -527,10 +527,10 @@ track_wkflow_samples <- function(list_pq_obj, ...) {
 #' \donttest{
 #' asv2otu(data_fungi_mini, method_clusterize = "longest")
 #'
-#' if (MiscMetabar:::is_swarm_installed()) {
+#' if (MiscMetabar::is_swarm_installed()) {
 #'   d_swarm <- asv2otu(data_fungi_mini, method = "swarm")
 #' }
-#' if (MiscMetabar:::is_vsearch_installed()) {
+#' if (MiscMetabar::is_vsearch_installed()) {
 #'   d_vs <- asv2otu(data_fungi_mini, method = "vsearch")
 #' }
 #' }
@@ -667,11 +667,9 @@ asv2otu <- function(physeq = NULL,
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' \dontrun{
-#' write_pq(data_fungi, path = "phyloseq")
-#' write_pq(data_fungi, path = "phyloseq", one_file = TRUE)
-#' }
-
+#' write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
+#' write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"), one_file = TRUE)
+#' unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)
 #' @seealso [MiscMetabar::save_pq()]
 
 write_pq <- function(physeq,
@@ -875,9 +873,8 @@ write_pq <- function(physeq,
 #' @export
 #' @author Adrien Taudière
 #' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
-#' \dontrun{
-#' save_pq(data_fungi, path = "phyloseq")
-#' }
+#' save_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
+#' unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)
 #' @seealso [MiscMetabar::write_pq()]
 save_pq <- function(physeq, path = NULL, ...) {
   write_pq(physeq,
@@ -913,9 +910,9 @@ save_pq <- function(physeq, path = NULL, ...) {
 #' @export
 #'
 #' @examples
-#' # read_pq(path = "phyloseq_folder")
-#' # read_pq(path = "phyloseq_folder", taxa_are_rows = TRUE)
-#'
+#' write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
+#' read_pq(path = paste0(tempdir(), "/phyloseq"))
+#' unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)
 read_pq <- function(path = NULL,
                     taxa_are_rows = FALSE,
                     sam_names = NULL,
@@ -1016,9 +1013,8 @@ read_pq <- function(path = NULL,
 #' - "merged_ASV": the data.frame used to merged ASV
 #'
 #' @export
-#' @examples
-#' \dontrun{
-#' data(data_fungi_sp_known)
+#' @examplesIf MiscMetabar::is_vsearch_installed()
+#' \donttest{
 #' lulu_pq(data_fungi_sp_known)
 #' }
 #' @author Tobias Guldberg Frøslev \email{[email protected]}
@@ -1163,7 +1159,7 @@ lulu_pq <- function(physeq,
 #'   bash to obtain details about columns' signification.
 #'
 #' @export
-#' @examples
+#' @examplesIf MiscMetabar::is_mumu_installed()
 #' \dontrun{
 #' mumu_pq(data_fungi_sp_known)
 #' }
@@ -1327,7 +1323,7 @@ mumu_pq <- function(physeq,
 #' Mostly for internal use in MiscMetabar functions.
 #'
 #' @inheritParams clean_pq
-#' @param verbose (logical, default FALSE) If true, prompt some warnings.
+#' @param verbose (logical, default FALSE) If TRUE, prompt some warnings.
 #' @param min_nb_seq_sample (numeric) Only used if verbose = TRUE.
 #'   Minimum number of sequences per samples to not show warning.
 #' @param min_nb_seq_taxa (numeric) Only used if verbose = TRUE.
@@ -1652,7 +1648,6 @@ add_new_taxonomy_pq <- function(physeq, ref_fasta, suffix = NULL, ...) {
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' data(data_fungi)
 #' tbl_sum_samdata(data_fungi) %>%
 #'   gtsummary::as_kable()
 #'
@@ -1661,11 +1656,12 @@ add_new_taxonomy_pq <- function(physeq, ref_fasta, suffix = NULL, ...) {
 #'   type = list(Time ~ "continuous2", Height ~ "categorical"),
 #'   statistic = list(Time ~ c("{median} ({p25}, {p75})", "{min}, {max}"))
 #' )
-#'
+#' \donttest{
 #' data(enterotype)
 #'
 #' summary_samdata <- tbl_sum_samdata(enterotype)
 #' summary_samdata <- tbl_sum_samdata(enterotype, include = !contains("SampleId"))
+#' }
 #' @details
 #' This function is mainly a wrapper of the work of others.
 #'   Please make a reference to `gtsummary::tbl_summary()` if you
@@ -1698,16 +1694,19 @@ tbl_sum_samdata <- function(physeq, remove_col_unique_value = TRUE, ...) {
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#'
-#' df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 5000)
-#' \dontrun{
-#' df <- add_funguild_info(df,
+#' \donttest{
+#' d_fung_mini <- add_funguild_info(data_fungi_mini,
 #'   taxLevels = c(
-#'     "Domain", "Phylum", "Class", "Order",
-#'     "Family", "Genus", "Species"
+#'     "Domain",
+#'     "Phylum",
+#'     "Class",
+#'     "Order",
+#'     "Family",
+#'     "Genus",
+#'     "Species"
 #'   )
 #' )
-#' sort(table(df@tax_table[, "guild"]), decreasing = TRUE)
+#' sort(table(d_fung_mini@tax_table[, "guild"]), decreasing = TRUE)
 #' }
 #' @details
 #' This function is mainly a wrapper of the work of others.
@@ -1766,23 +1765,29 @@ add_funguild_info <- function(physeq,
 #' @export
 #' @author Adrien Taudière
 #' @examples
-#' \dontrun{
-#'
-#' df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 5000)
-#' df <- add_funguild_info(df,
+#' \donttest{
+#' d_fung_mini <- add_funguild_info(data_fungi_mini,
 #'   taxLevels = c(
-#'     "Domain", "Phylum", "Class", "Order",
-#'     "Family", "Genus", "Species"
+#'     "Domain",
+#'     "Phylum",
+#'     "Class",
+#'     "Order",
+#'     "Family",
+#'     "Genus",
+#'     "Species"
 #'   )
 #' )
-#' p <- plot_guild_pq(df)
-#' library("patchwork")
-#' (plot_guild_pq(subset_samples(df, Height == "Low"),
-#'   levels_order = p$data$Guild[order(p$data$nb_seq)]
-#' ) + theme(legend.position = "none")) +
-#'   (plot_guild_pq(subset_samples(df, Height == "High"),
+#' sort(table(d_fung_mini@tax_table[, "guild"]), decreasing = TRUE)
+#'
+#' p <- plot_guild_pq(d_fung_mini)
+#' if (!requireNamespace("patchwork")) {
+#'   (plot_guild_pq(subset_samples(d_fung_mini, Height == "Low"),
 #'     levels_order = p$data$Guild[order(p$data$nb_seq)]
-#'   ) + ylab("") + theme(axis.text.y = element_blank()))
+#'   ) + theme(legend.position = "none")) +
+#'     (plot_guild_pq(subset_samples(d_fung_mini, Height == "High"),
+#'       levels_order = p$data$Guild[order(p$data$nb_seq)]
+#'     ) + ylab("") + theme(axis.text.y = element_blank()))
+#' }
 #' }
 #' @seealso [add_funguild_info()]
 
@@ -1930,25 +1935,26 @@ plot_guild_pq <-
 #'   use this function.
 #' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' \donttest{
-#' library("phangorn")
-#' df <- subset_taxa_pq(data_fungi_mini, taxa_sums(data_fungi_mini) > 9000)
-#' df_tree <- build_phytree_pq(df, nb_bootstrap = 2)
-#' plot(df_tree$UPGMA)
-#' plotBS(df_tree$UPGMA, df_tree$UPGMA_bs, main = "UPGMA")
-#' plot(df_tree$NJ, "unrooted")
-#' plot(df_tree$ML)
-#' # plotBS(df_tree$ML_bs)
-#' plotBS(df_tree$ML$tree, df_tree$ML_bs, p = 20, frame = "circle")
-#' plotBS(
-#'   df_tree$ML$tree,
-#'   df_tree$ML_bs,
-#'   p = 20,
-#'   frame = "circle",
-#'   method = "TBE"
-#' )
-#' plot(consensusNet(df_tree$ML_bs))
-#' plot(consensusNet(df_tree$NJ_bs))
-#' ps_tree <- merge_phyloseq(df, df_tree$ML$tree)
+#' if (!requireNamespace("phangorn")) {
+#'   df <- subset_taxa_pq(data_fungi_mini, taxa_sums(data_fungi_mini) > 9000)
+#'   df_tree <- build_phytree_pq(df, nb_bootstrap = 2)
+#'   plot(df_tree$UPGMA)
+#'   phangorn::plotBS(df_tree$UPGMA, df_tree$UPGMA_bs, main = "UPGMA")
+#'   plot(df_tree$NJ, "unrooted")
+#'   plot(df_tree$ML)
+#'
+#'   phangorn::plotBS(df_tree$ML$tree, df_tree$ML_bs, p = 20, frame = "circle")
+#'   phangorn::plotBS(
+#'     df_tree$ML$tree,
+#'     df_tree$ML_bs,
+#'     p = 20,
+#'     frame = "circle",
+#'     method = "TBE"
+#'   )
+#'   plot(phangorn::consensusNet(df_tree$ML_bs))
+#'   plot(phangorn::consensusNet(df_tree$NJ_bs))
+#'   ps_tree <- merge_phyloseq(df, df_tree$ML$tree)
+#' }
 #' }
 build_phytree_pq <- function(physeq,
                              nb_bootstrap = 0,
@@ -2341,7 +2347,7 @@ physeq_or_string_to_dna <- function(physeq = NULL,
 #' )
 #'
 #'
-#' # unlink(tempdir(), recursive = TRUE)
+#' unlink(tempdir(), recursive = TRUE)
 #' }
 #' @details
 #' This function is mainly a wrapper of the work of others.