Merge dev

.github/workflows/R-CMD-check.yaml

@@ -20,7 +20,6 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -1,6 +1,8 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
+  push:
+    branches: [main, master]
   pull_request:
     branches: [main, master]
   workflow_dispatch:
@@ -40,9 +42,9 @@ jobs:
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
+        # if: github.event_name != 'pull_request'
         uses: JamesIves/[email protected]
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.6.0
+Version: 0.6.1
 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.  

NEWS.md

@@ -1,4 +1,6 @@
-# MiscMetabar 0.6.1  (in development)
+# MiscMetabar 0.6.1 (in development) 
+
+- Minor bugs fix to pass R CMD CHECK
 
 # MiscMetabar 0.6.0 
 

R/beta_div_test.R

@@ -35,15 +35,14 @@
 #'   Please cite `phyloseqGraphTest` package.
 #' @export
 
-graph_test_pq <- function(
-        physeq,
-        fact,
-        merge_sample_by = NULL,
-        nperm = 999,
-        return_plot = TRUE,
-        title = "Graph Test",
-        na_remove = FALSE,
-        ...) {
+graph_test_pq <- function(physeq,
+                          fact,
+                          merge_sample_by = NULL,
+                          nperm = 999,
+                          return_plot = TRUE,
+                          title = "Graph Test",
+                          na_remove = FALSE,
+                          ...) {
   verify_pq(physeq)
 
   if (!is.null(merge_sample_by)) {
@@ -135,15 +134,14 @@ graph_test_pq <- function(
 #'   Please make a reference to `vegan::adonis2()` if you
 #'   use this function.
 
-adonis_pq <- function(
-        physeq,
-        formula,
-        dist_method = "bray",
-        merge_sample_by = NULL,
-        na_remove = FALSE,
-        correction_for_sample_size = FALSE,
-        rarefy_nb_seqs = FALSE,
-        ...) {
+adonis_pq <- function(physeq,
+                      formula,
+                      dist_method = "bray",
+                      merge_sample_by = NULL,
+                      na_remove = FALSE,
+                      correction_for_sample_size = FALSE,
+                      rarefy_nb_seqs = FALSE,
+                      ...) {
   physeq <- clean_pq(
     physeq,
     force_taxa_as_columns = TRUE,
@@ -243,10 +241,9 @@ adonis_pq <- function(
 #' This function is mainly a wrapper of the work of others.
 #'   Please make a reference to `adespatial::beta.div()` if you
 #'   use this function.
-LCBD_pq <- function(
-        physeq,
-        p_adjust_method = "BH",
-        ...) {
+LCBD_pq <- function(physeq,
+                    p_adjust_method = "BH",
+                    ...) {
   physeq <- clean_pq(
     physeq,
     force_taxa_as_columns = TRUE,
@@ -290,6 +287,7 @@ LCBD_pq <- function(
 #' @seealso [LCBD_pq], [adespatial::beta.div()]
 #'
 #' @examples
+#' data(data_fungi)
 #' plot_LCBD_pq(data_fungi,
 #'   nperm = 100, only_plot_significant = FALSE,
 #'   pval = 0.2
@@ -317,13 +315,12 @@ LCBD_pq <- function(
 #' This function is mainly a wrapper of the work of others.
 #'   Please make a reference to `vegan::beta.div()` if you
 #'   use this function.
-plot_LCBD_pq <- function(
-        physeq,
-        p_adjust_method = "BH",
-        pval = 0.05,
-        sam_variables = NULL,
-        only_plot_significant = TRUE,
-        ...) {
+plot_LCBD_pq <- function(physeq,
+                         p_adjust_method = "BH",
+                         pval = 0.05,
+                         sam_variables = NULL,
+                         only_plot_significant = TRUE,
+                         ...) {
   resBeta <- LCBD_pq(physeq,
     p_adjust_method = p_adjust_method,
     ...
@@ -430,6 +427,7 @@ plot_LCBD_pq <- function(
 #' @seealso [LCBD_pq], [adespatial::beta.div()]
 #'
 #' @examples
+#' data(data_fungi)
 #' plot_SCBD_pq(data_fungi) +
 #'   geom_text(aes(label = paste(Genus, Species)), hjust = 1, vjust = 2) +
 #'   xlim(c(0, NA))
@@ -441,12 +439,11 @@ plot_LCBD_pq <- function(
 #' This function is mainly a wrapper of the work of others.
 #'   Please make a reference to `vegan::beta.div()` if you
 #'   use this function.
-plot_SCBD_pq <- function(
-        physeq,
-        tax_level = "ASV",
-        tax_col = "Order",
-        min_SCBD = 0.01,
-        ...) {
+plot_SCBD_pq <- function(physeq,
+                         tax_level = "ASV",
+                         tax_col = "Order",
+                         min_SCBD = 0.01,
+                         ...) {
   resBeta <- LCBD_pq(physeq, nperm = 0, ...)
 
   tax_tab <- data.frame(physeq@tax_table)
@@ -489,6 +486,7 @@ plot_SCBD_pq <- function(
 #' @return A ggplot object
 #' @export
 #' @examples
+#' 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")
 #' multipatt_pq(subset_samples(data_fungi_ab, !is.na(Time)),
@@ -501,13 +499,12 @@ plot_SCBD_pq <- function(
 #'   Please make a reference to `indicspecies::multipatt()` if you
 #'   use this function.
 
-multipatt_pq <- function(
-        physeq,
-        fact,
-        p_adjust_method = "BH",
-        pval = 0.05,
-        control = permute::how(nperm = 999),
-        ...) {
+multipatt_pq <- function(physeq,
+                         fact,
+                         p_adjust_method = "BH",
+                         pval = 0.05,
+                         control = permute::how(nperm = 999),
+                         ...) {
   physeq <- clean_pq(physeq,
     clean_samples_names = FALSE,
     force_taxa_as_columns = TRUE

R/blast.R

@@ -54,21 +54,20 @@
 #'   blastpath = blastpath
 #' )
 #' }
-blast_to_phyloseq <- function(
-        physeq,
-        seq2search,
-        blastpath = NULL,
-        id_cut = 90,
-        bit_score_cut = 50,
-        min_cover_cut = 50,
-        e_value_cut = 1e-30,
-        unique_per_seq = FALSE,
-        score_filter = TRUE,
-        list_no_output_query = FALSE,
-        args_makedb = NULL,
-        args_blastn = NULL,
-        nproc = 1,
-        keep_temporary_files = FALSE) {
+blast_to_phyloseq <- function(physeq,
+                              seq2search,
+                              blastpath = NULL,
+                              id_cut = 90,
+                              bit_score_cut = 50,
+                              min_cover_cut = 50,
+                              e_value_cut = 1e-30,
+                              unique_per_seq = FALSE,
+                              score_filter = TRUE,
+                              list_no_output_query = FALSE,
+                              args_makedb = NULL,
+                              args_blastn = NULL,
+                              nproc = 1,
+                              keep_temporary_files = FALSE) {
   verify_pq(physeq)
   dna <- Biostrings::DNAStringSet(physeq@refseq)
   Biostrings::writeXStringSet(dna, paste0(tempdir(), "/", "db.fasta"))
@@ -196,21 +195,20 @@ blast_to_phyloseq <- function(
 #' @return  a blast table
 #' @export
 #'
-blast_pq <- function(
-        physeq,
-        fasta_for_db = NULL,
-        database = NULL,
-        blastpath = NULL,
-        id_cut = 90,
-        bit_score_cut = 50,
-        min_cover_cut = 50,
-        e_value_cut = 1e-30,
-        unique_per_seq = FALSE,
-        score_filter = TRUE,
-        nproc = 1,
-        args_makedb = NULL,
-        args_blastn = NULL,
-        keep_temporary_files = FALSE) {
+blast_pq <- function(physeq,
+                     fasta_for_db = NULL,
+                     database = NULL,
+                     blastpath = NULL,
+                     id_cut = 90,
+                     bit_score_cut = 50,
+                     min_cover_cut = 50,
+                     e_value_cut = 1e-30,
+                     unique_per_seq = FALSE,
+                     score_filter = TRUE,
+                     nproc = 1,
+                     args_makedb = NULL,
+                     args_blastn = NULL,
+                     keep_temporary_files = FALSE) {
   verify_pq(physeq)
   dna <- Biostrings::DNAStringSet(physeq@refseq)
   Biostrings::writeXStringSet(
@@ -363,17 +361,16 @@ blast_pq <- function(
 #' @return A new \code{\link{phyloseq-class}} object.
 
 
-filter_asv_blast <- function(
-        physeq,
-        fasta_for_db = NULL,
-        database = NULL,
-        clean_pq = TRUE,
-        add_info_to_taxtable = TRUE,
-        id_filter = 90,
-        bit_score_filter = 50,
-        min_cover_filter = 50,
-        e_value_filter = 1e-30,
-        ...) {
+filter_asv_blast <- function(physeq,
+                             fasta_for_db = NULL,
+                             database = NULL,
+                             clean_pq = TRUE,
+                             add_info_to_taxtable = TRUE,
+                             id_filter = 90,
+                             bit_score_filter = 50,
+                             min_cover_filter = 50,
+                             e_value_filter = 1e-30,
+                             ...) {
   blast_tab <- blast_pq(
     physeq = physeq,
     fasta_for_db = fasta_for_db,
@@ -446,22 +443,21 @@ filter_asv_blast <- function(
 #'   against un custom database and [MiscMetabar::blast_to_phyloseq()]  to use
 #'    `refseq` slot as a database
 #' @author Adrien Taudière
-blast_to_derep <- function(
-        derep,
-        seq2search,
-        blastpath = NULL,
-        id_cut = 90,
-        bit_score_cut = 50,
-        min_cover_cut = 50,
-        e_value_cut = 1e-30,
-        unique_per_seq = FALSE,
-        score_filter = FALSE,
-        list_no_output_query = FALSE,
-        min_length_seq = 200,
-        args_makedb = NULL,
-        args_blastn = NULL,
-        nproc = 1,
-        keep_temporary_files = FALSE) {
+blast_to_derep <- function(derep,
+                           seq2search,
+                           blastpath = NULL,
+                           id_cut = 90,
+                           bit_score_cut = 50,
+                           min_cover_cut = 50,
+                           e_value_cut = 1e-30,
+                           unique_per_seq = FALSE,
+                           score_filter = FALSE,
+                           list_no_output_query = FALSE,
+                           min_length_seq = 200,
+                           args_makedb = NULL,
+                           args_blastn = NULL,
+                           nproc = 1,
+                           keep_temporary_files = FALSE) {
   if (!inherits(derep[[1]], "derep")) {
     stop("derep must be an object of class derep-class")
   }

R/controls.R

@@ -153,11 +153,10 @@ dist_pos_control <- function(physeq, samples_names, method = "bray") {
 #'
 #' @author Adrien Taudière
 subset_taxa_tax_control <-
-  function(
-        physeq,
-        taxa_distri,
-        method = "mean",
-        min_diff_for_cutoff = NULL) {
+  function(physeq,
+           taxa_distri,
+           method = "mean",
+           min_diff_for_cutoff = NULL) {
     verify_pq(physeq)
 
     cutoff_seq <- vector(mode = "numeric", length = nsamples(physeq))