Merge pull request #85 from adrientaudiere/dev

V0.7.7 getting closer to CRAN

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.5
+Version: 0.7.7
 Authors@R: person("Adrien", "Taudière", email = "adrien.taudiere@zaclys.net",
   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 powerful by integrating a large number of analysis, some of them from other R packages.  
+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.  
 License: AGPL-3
 Encoding: UTF-8
 LazyData: true

R/Deseq2_edgeR.R

@@ -22,10 +22,11 @@
 #' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' data("GlobalPatterns", package = "phyloseq")
 #' GP_archae <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
+#' \donttest{
 #' plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
 #'   color_tax = "Kingdom"
 #' )
-#' \dontrun{
+#'
 #' plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
 #'   taxolev = "Class", color_tax = "Kingdom"
 #' )
@@ -153,6 +154,7 @@ plot_edgeR_pq <-
 #' @details
 #'   Please cite `DESeq2` package if you use chis function.
 #' @examples
+#' \donttest{
 #' data("GlobalPatterns", package = "phyloseq")
 #' GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
 #' GP <- subset_samples(GP, SampleType %in% c("Soil", "Skin"))
@@ -170,6 +172,7 @@ plot_edgeR_pq <-
 #'   tax_table = GP@tax_table, color_tax = "Class",
 #'   select_taxa = c("522457", "271582")
 #' )
+#' }
 #' @author Adrien Taudière
 #'
 #' @return A \code{\link{ggplot}}2 plot representing DESeq2 results

R/beta_div_test.R

@@ -25,7 +25,9 @@
 #' @examples
 #' data(enterotype)
 #' graph_test_pq(enterotype, fact = "SeqTech")
+#' \donttest{
 #' graph_test_pq(enterotype, fact = "Enterotype", na_remove = TRUE)
+#' }
 #' @author Adrien Taudière
 #'
 #' @return A \code{\link{ggplot}}2 plot with a subtitle indicating the pvalue
@@ -123,10 +125,11 @@ graph_test_pq <- function(physeq,
 #'   more information.
 #' @examples
 #' data(enterotype)
+#' \donttest{
 #' adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE)
-#' adonis_pq(enterotype, "SeqTech")
 #' adonis_pq(enterotype, "SeqTech", dist_method = "jaccard")
 #' adonis_pq(enterotype, "SeqTech", dist_method = "robust.aitchison")
+#' }
 #' @export
 #' @author Adrien Taudière
 #' @details
@@ -234,7 +237,9 @@ adonis_pq <- function(physeq,
 #' str(res)
 #' length(res$LCBD)
 #' length(res$SCBD)
+#' \donttest{
 #' LCBD_pq(data_fungi_sp_known, nperm = 5, method = "jaccard")
+#' }
 #'
 #' @author Adrien Taudière
 #' This function is mainly a wrapper of the work of others.
@@ -291,6 +296,7 @@ LCBD_pq <- function(physeq,
 #'   nperm = 100, only_plot_significant = FALSE,
 #'   pval = 0.2
 #' )
+#' \donttest{
 #' plot_LCBD_pq(data_fungi_mini,
 #'   nperm = 100, only_plot_significant = TRUE,
 #'   pval = 0.2
@@ -309,6 +315,7 @@ LCBD_pq <- function(physeq,
 #'     legend.text = element_text(size = 10),
 #'     axis.title.x = element_text(size = 6)
 #'   )
+#' }
 #' @author Adrien Taudière
 #' @details
 #' This function is mainly a wrapper of the work of others.
@@ -430,9 +437,10 @@ plot_LCBD_pq <- function(physeq,
 #' plot_SCBD_pq(data_fungi) +
 #'   geom_text(aes(label = paste(Genus, Species)), hjust = 1, vjust = 2) +
 #'   xlim(c(0, NA))
-#'
+#' \donttest{
 #' plot_SCBD_pq(data_fungi, tax_level = "Class", tax_col = "Phylum", min_SCBD = 0) +
 #'   geom_jitter()
+#' }
 #' @author Adrien Taudière
 #' @details
 #' This function is mainly a wrapper of the work of others.
@@ -488,10 +496,12 @@ plot_SCBD_pq <- function(physeq,
 #' data(data_fungi)
 #' data_fungi_ab <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 10000)
 #' multipatt_pq(subset_samples(data_fungi_ab, !is.na(Time)), fact = "Time")
+#' \donttest{
 #' multipatt_pq(subset_samples(data_fungi_ab, !is.na(Time)),
 #'   fact = "Time",
 #'   max.order = 1, control = permute::how(nperm = 99)
 #' )
+#' }
 #' @author Adrien Taudière
 #' @details
 #' This function is mainly a wrapper of the work of others.
@@ -562,6 +572,7 @@ multipatt_pq <- function(physeq,
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' res_height <- ancombc_pq(
 #'   data_fungi_mini,
 #'   fact = "Height",
@@ -591,6 +602,7 @@ multipatt_pq <- function(physeq,
 #'   tax_level = "Family",
 #'   verbose = TRUE
 #' )
+#' }
 #' @author Adrien Taudière
 #' @details
 #' This function is mainly a wrapper of the work of others.

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

@@ -524,13 +524,16 @@ track_wkflow_samples <- function(list_pq_obj, ...) {
 #'
 #' @examples
 #' asv2otu(data_fungi_mini)
+#' \donttest{
 #' asv2otu(data_fungi_mini, method_clusterize = "longest")
+#'
 #' if (MiscMetabar:::is_swarm_installed()) {
 #'   d_swarm <- asv2otu(data_fungi_mini, method = "swarm")
 #' }
 #' if (MiscMetabar:::is_vsearch_installed()) {
 #'   d_vs <- asv2otu(data_fungi_mini, method = "vsearch")
 #' }
+#' }
 #' @references
 #'   VSEARCH can be downloaded from
 #'   \url{https://github.com/torognes/vsearch}.
@@ -910,10 +913,8 @@ save_pq <- function(physeq, path = NULL, ...) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' read_pq(path = "phyloseq_data")
-#' read_pq(path = "phyloseq_data", taxa_are_rows = TRUE)
-#' }
+#' # read_pq(path = "phyloseq_folder")
+#' # read_pq(path = "phyloseq_folder", taxa_are_rows = TRUE)
 #'
 read_pq <- function(path = NULL,
                     taxa_are_rows = FALSE,
@@ -1162,7 +1163,6 @@ lulu_pq <- function(physeq,
 #' @export
 #' @examples
 #' \dontrun{
-#' data(data_fungi_sp_known)
 #' mumu_pq(data_fungi_sp_known)
 #' }
 #' @author Frédéric Mahé
@@ -1403,7 +1403,7 @@ subset_samples_pq <- function(physeq, condition) {
   if (length(condition) != nsamples(physeq)) {
     stop("Length of condition is different from the number of samples.")
   }
-  if (is.null(sample_data(physeq))) {
+  if (is.null(physeq@sam_data)) {
     message("Nothing subset. No sample_data in physeq.\n")
     return(physeq)
   } else {
@@ -1927,6 +1927,7 @@ plot_guild_pq <-
 #'   Please make a reference to `phangorn` package if you
 #'   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)
@@ -1946,6 +1947,7 @@ plot_guild_pq <-
 #' plot(consensusNet(df_tree$ML_bs))
 #' plot(consensusNet(df_tree$NJ_bs))
 #' ps_tree <- merge_phyloseq(df, df_tree$ML$tree)
+#' }
 build_phytree_pq <- function(physeq,
                              nb_bootstrap = 0,
                              model = "GTR",
@@ -2065,9 +2067,9 @@ build_phytree_pq <- function(physeq,
 #' @importFrom stats kruskal.test
 #' @examples
 #'
-#' 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)
+#' are_modality_even_depth(data_fungi_mini, "Time")$p.value
+#' are_modality_even_depth(rarefy_even_depth(data_fungi_mini), "Time")$p.value
+#' are_modality_even_depth(data_fungi_mini, "Height", boxplot = TRUE)
 are_modality_even_depth <- function(physeq, fact, boxplot = FALSE) {
   nb_seq <- sample_sums(physeq)
   fact <- factor(unclass(physeq@sam_data[, fact])[[1]])
@@ -2108,9 +2110,9 @@ are_modality_even_depth <- function(physeq, fact, boxplot = FALSE) {
 #'   taxa_names(data_fungi)[order(as.vector(data_fungi@tax_table[, "Genus"]))]
 #' )
 #'
-#' data_fungi_asc_ordered_by_abundance <- reorder_taxa_pq(
-#'   data_fungi,
-#'   taxa_names(data_fungi)[order(taxa_sums(data_fungi))]
+#' data_fungi_mini_asc_ordered_by_abundance <- reorder_taxa_pq(
+#'   data_fungi_mini,
+#'   taxa_names(data_fungi_mini)[order(taxa_sums(data_fungi_mini))]
 #' )
 reorder_taxa_pq <- function(physeq, names_ordered, remove_phy_tree = FALSE) {
   new_physeq <- physeq
@@ -2337,7 +2339,7 @@ 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.

R/miscellanous.R

@@ -202,7 +202,10 @@ perc <- function(x, y = NULL, accuracy = 0, add_symbol = FALSE) {
 #'   package = "MiscMetabar",
 #'   mustWork = TRUE
 #' ))
-#' count_seq(folder_path = "extdata/", pattern = "*.fasta")
+#' count_seq(
+#'   folder_path = system.file("extdata", package = "MiscMetabar"),
+#'   pattern = "*.fasta"
+#' )
 count_seq <- function(file_path = NULL, folder_path = NULL, pattern = NULL) {
   if (is.null(file_path) && is.null(folder_path)) {
     stop("You need to specify one of file_path or folder_path param!")