v 0.12

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.11.1
+Version: 0.12.0
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 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>.

NAMESPACE

@@ -19,6 +19,7 @@ export(all_object_size)
 export(ancombc_pq)
 export(are_modality_even_depth)
 export(as_binary_otu_table)
+export(assign_idtaxa)
 export(assign_sintax)
 export(assign_vsearch_lca)
 export(asv2otu)
@@ -71,6 +72,7 @@ export(is_mumu_installed)
 export(is_swarm_installed)
 export(is_vsearch_installed)
 export(krona)
+export(learn_idtaxa)
 export(list_fastq_files)
 export(lulu)
 export(lulu_phyloseq)
@@ -137,6 +139,7 @@ export(taxa_as_columns)
 export(taxa_as_rows)
 export(taxa_only_in_one_level)
 export(tbl_sum_samdata)
+export(tbl_sum_taxtable)
 export(track_wkflow)
 export(track_wkflow_samples)
 export(transp)

NEWS.md

@@ -1,3 +1,11 @@
+# MiscMetabar 0.2.0 (in development) 
+
+- Add function [assign_idtaxa()] and [learn_idtaxa()] to facilitate the taxonomic assignation using the idtaxa algorithm from the  DECIPHER R package.
+- Add option `idtaxa` to method in [add_new_taxonomy_pq()]
+- Add function [tbl_sum_taxtable()] to summarize tax_table from a phyloseq object 
+- In function [assign_sintax()], add params `too_few` (default value "align_start") and `too_many` (default "merge") to authorize db with variable numbers of rank and parenthesis in taxonomic name, 
+
+
 # MiscMetabar 0.11.1 (in development) 
 
 - Add param `suffix` to `add_blast_info()` allowing multiple use of the function on the same phyloseq object (e.g. in order to used different database)

R/MiscMetabar-package.R

@@ -27,7 +27,8 @@ if (getRversion() >= "2.15.1") {
     "X1_lim1", "X1_lim2", "aicc", "variable", "pos_letters", "alluvium",
     "na_remove", "stratum", "to_lodes_form", "clean_fastq", "clean_sam",
     "samples_names_common", "seq_id", "alpha_hill", "Modality", "Type", "complexity",
-    "value_bootstrap"
+    "value_bootstrap", "LearnTaxa", "OrientNucleotides", "RemoveGaps",
+    "method", "readDNAStringSet"
   ))
 }
 

R/blast.R

@@ -631,9 +631,7 @@ blast_to_derep <- function(derep,
 #' @param fasta_for_db path to a fasta file to make the blast database
 #' @param silent (logical) If true, no message are printing.
 #' @param suffix (character) The suffix to name the new columns.
-#'   If set to NULL (the default), the basename of the file reFasta
-#'   is used with the name of the method. Set suffix to "" in order
-#'   to remove any suffix.
+#'   Set the suffix to "" in order to remove any suffix.
 #' @param ... Other arguments passed on to [blast_pq()] function.
 #' @return A new \code{\link[phyloseq]{phyloseq-class}} object with more information in tax_table based on a
 #'   blast on a given database
@@ -642,11 +640,8 @@ blast_to_derep <- function(derep,
 #'
 #' @author Adrien Taudière
 
-add_blast_info <- function(physeq, fasta_for_db, silent = FALSE, suffix=NULL, ...) {
+add_blast_info <- function(physeq, fasta_for_db, silent = FALSE, suffix = "blast_info", ...) {
   verify_pq(physeq)
-  if (is.null(suffix)) {
-    suffix <- paste0(basename(fasta_for_db), "_", method)
-  }
   res_blast <- blast_pq(physeq,
     fasta_for_db = fasta_for_db,
     unique_per_seq = TRUE,
@@ -655,15 +650,17 @@ add_blast_info <- function(physeq, fasta_for_db, silent = FALSE, suffix=NULL, ..
   )
   new_physeq <- physeq
 
-  new_physeq@tax_table <- tax_table(cbind(
+  new_taxtab <- cbind(
     new_physeq@tax_table,
     as.matrix(res_blast[match(
       taxa_names(new_physeq),
       res_blast$`Query name`
     ), ])
-  ))
+  )
+
+  # colnames(new_taxtab) <- c(colnames(new_physeq@tax_table), paste0(colnames(physeq), suffix))
 
-  colnames(new_physeq) <- c(colnames(physeq), paste0(colnames(), suffix))
+  new_physeq@tax_table <- tax_table(new_taxtab)
 
   verify_pq(new_physeq)
   if (!silent) {