Merge pull request #98 from adrientaudiere/dev

 Minor fix for CRAN resubmission

.vscode/settings.json

@@ -1,7 +1,23 @@
 {
     "workbench.colorCustomizations": {
-        "activityBar.background": "#253202",
-        "titleBar.activeBackground": "#344602",
-        "titleBar.activeForeground": "#F4FEDC"
-    }
+        "activityBar.activeBackground": "#ab307e",
+        "activityBar.background": "#ab307e",
+        "activityBar.foreground": "#e7e7e7",
+        "activityBar.inactiveForeground": "#e7e7e799",
+        "activityBarBadge.background": "#25320e",
+        "activityBarBadge.foreground": "#e7e7e7",
+        "commandCenter.border": "#e7e7e799",
+        "sash.hoverBorder": "#ab307e",
+        "statusBar.background": "#832561",
+        "statusBar.foreground": "#e7e7e7",
+        "statusBarItem.hoverBackground": "#ab307e",
+        "statusBarItem.remoteBackground": "#832561",
+        "statusBarItem.remoteForeground": "#e7e7e7",
+        "titleBar.activeBackground": "#832561",
+        "titleBar.activeForeground": "#e7e7e7",
+        "titleBar.inactiveBackground": "#83256199",
+        "titleBar.inactiveForeground": "#e7e7e799",
+        "tab.activeBorder": "#ab307e"
+    },
+    "peacock.color": "#832561"
 }

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.9.2
+Version: 0.9.3
 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>.
@@ -79,7 +79,7 @@ Suggests:
     vctrs,
     viridis,
     withr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://github.com/adrientaudiere/MiscMetabar,
     https://adrientaudiere.github.io/MiscMetabar/
 biocViews: Sequencing, Microbiome, Metagenomics,

NAMESPACE

@@ -40,6 +40,7 @@ export(dist_pos_control)
 export(distri_1_taxa)
 export(fac2col)
 export(filter_asv_blast)
+export(filter_taxa_blast)
 export(filter_trim)
 export(formattable_pq)
 export(funguild_assign)
@@ -98,6 +99,7 @@ export(plot_mt)
 export(plot_tax_pq)
 export(plot_tsne_pq)
 export(plot_var_part_pq)
+export(postcluster_pq)
 export(psmelt_samples_pq)
 export(rarefy_sample_count_by_modality)
 export(read_phyloseq)

NEWS.md

@@ -1,4 +1,21 @@
-# MiscMetabar 0.9.2 (in development)
+
+# MiscMetabar 0.9.3 (in development)
+
+- Homogenize terminology replacing ASV by taxa/taxon in documentation and code
+- Build an alias function `filter_taxa_blast()` for 
+`filter_asv_blast()`
+- Build an alias function `postcluster_pq()` for 
+`asv2otu()`
+
+
+## BREAKING CHANGES
+
+- Replacing misnamed param `rename_asv` by `rename_taxons` in `clean_pq()`
+- Replacing misnamed param `reorder_asv` by `reorder_taxons` in `clean_pq()`
+
+
+
+# MiscMetabar 0.9.2
 
 - Add param `default_fun` in function `merge_samples2()` in order to replace the default function that change the sample data in case of merging. A useful parameter is `default_fun=diff_fct_diff_class`.
 - Add param `kruskal_test` to `hill_pq()` function to prevent user to mis-interpret Tuckey HSD result (and letters) if the global effect of the tested factor on Hill diversity is non significant.

R/Deseq2_edgeR.R

@@ -1,13 +1,13 @@
 ################################################################################
 #' Plot edgeR results for a phyloseq or a edgeR object.
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-maturing-blue" alt="lifecycle-maturing"></a>
 #'
 #' Graphical representation of edgeR result.
-#' 
+#'
 #' @inheritParams clean_pq
 #' @param contrast (required):This argument specifies what comparison
 #'   to extract from the object to build a results table.
@@ -125,12 +125,12 @@ plot_edgeR_pq <-
 # Plot the result of a DESeq2 test
 ################################################################################
 #' Plot DESeq2 results for a phyloseq or a DESeq2 object.
-#' 
+#'
 #' @description
 #'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
-#' 
+#'
 #' Graphical representation of DESeq2 analysis.
 #'
 #' @param data (required) a \code{\link{phyloseq-class}} or a

R/MiscMetabar-package.R

@@ -8,13 +8,13 @@ NULL
 
 if (getRversion() >= "2.15.1") {
   utils::globalVariables(c(
-    ".id", "%>%", "Ab", "Abundance", "ASV_names", "beta.div", "calc_taxon_abund",
+    ".id", "%>%", "Ab", "Abundance", "taxon_names", "beta.div", "calc_taxon_abund",
     "character_method", "Class", "col_tax", "colors", "combn", "complement",
     "e-value", "Family", "Genus", "grid.draw", "grid.layout",
     "group_by", "Guild", "heat_tree", "hill_0", "Hill_0", "hill_1",
     "Hill_1", "hill_2", "Hill_2", "how name", "install_github", "install.packages",
     "LCBD", "log2FoldChange", "logFC", "LVL1", "LVL3", "lwr", "max_Hill",
-    "modality", "multcompLetters", "name", "nb_asv", "nb_seq", "nb_values",
+    "modality", "multcompLetters", "name", "nb_taxa", "nb_seq", "nb_values",
     "ott_id", "OTU", "p.adj", "p.adjust", "plot_layout",
     "plot_layout value", "Proportion", "pushViewport", "Query name",
     "rarefy", "read.delim", "reverse", "reverseComplement", "rgb",

R/alpha_div_test.R

@@ -105,11 +105,11 @@ hill_tuckey_pq <- function(
 #' Test multiple times effect of factor on Hill diversity
 #'   with different rarefaction even depth
 #'
-#' @description 
+#' @description
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
-#' 
-#' This reduce the risk of a random drawing of a exceptional situation of an unique rarefaction. 
+#'
+#' This reduce the risk of a random drawing of a exceptional situation of an unique rarefaction.
 #' @inheritParams clean_pq
 #' @param fact (required) Name of the factor in `physeq@sam_data` used to plot
 #'    different lines
@@ -272,12 +272,12 @@ hill_test_rarperm_pq <- function(physeq,
 ################################################################################
 #' Automated model selection and multimodel inference with (G)LMs for phyloseq
 #'
-#' @description 
+#' @description
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' See [glmulti::glmulti()] for more information.
-#' 
+#'
 #' @inheritParams clean_pq
 #' @param formula (required) a formula for [glmulti::glmulti()]
 #'   Variables must be present in the `physeq@sam_data` slot or be one

R/beta_div_test.R

@@ -220,15 +220,15 @@ adonis_pq <- function(physeq,
 ################################################################################
 #' Permanova (adonis) on permutations of rarefaction even depth
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
-#' Permanova are computed on a given number of rarefaction with different 
-#' seed.number. This reduce the risk of a random drawing of a exceptional 
-#' situation of an unique rarefaction. 
-#' 
+#' Permanova are computed on a given number of rarefaction with different
+#' seed.number. This reduce the risk of a random drawing of a exceptional
+#' situation of an unique rarefaction.
+#'
 #' @inheritParams adonis_pq
 #' @param nperm (int, default = 99) The number of permutations to perform.
 #' @param progress_bar (logical, default TRUE) Do we print progress during
@@ -578,7 +578,7 @@ plot_LCBD_pq <- function(physeq,
 #'   Please make a reference to `vegan::beta.div()` if you
 #'   use this function.
 plot_SCBD_pq <- function(physeq,
-                         tax_level = "ASV",
+                         tax_level = "Taxa",
                          tax_col = "Order",
                          min_SCBD = 0.01,
                          ...) {
@@ -587,7 +587,7 @@ plot_SCBD_pq <- function(physeq,
   tax_tab <- data.frame(physeq@tax_table)
 
   resSCBD <- tibble(
-    "ASV" = taxa_names(physeq),
+    "Taxa" = taxa_names(physeq),
     "SCBD" = resBeta$SCBD,
     tax_tab
   )
@@ -663,7 +663,7 @@ multipatt_pq <- function(physeq,
 
   res_df <- res$sign
   res_df$p.adj <- p.adjust(res_df$p.value, method = p_adjust_method)
-  res_df$ASV_names <- rownames(res_df)
+  res_df$taxon_names <- rownames(res_df)
   res_df_signif <-
     res_df %>%
     filter(p.adj < pval) %>%
@@ -672,7 +672,7 @@ multipatt_pq <- function(physeq,
   p <- ggplot(
     res_df_signif,
     aes(
-      x = ASV_names,
+      x = taxon_names,
       y = name,
       size = 2 * value,
       color = stat
@@ -775,12 +775,12 @@ ancombc_pq <- function(physeq, fact, levels_fact = NULL, tax_level = "Class", ..
 ################################################################################
 #' Filter ancombc_pq results
 #'
-#' @description 
+#' @description
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' Internally used in [plot_ancombc_pq()].
-#' 
+#'
 #' @param ancombc_res (required) the result of the ancombc_pq function
 #'   For the moment only bimodal factors are possible.
 #' @param filter_passed (logical, default TRUE) Do we filter using the column
@@ -857,12 +857,12 @@ signif_ancombc <- function(ancombc_res,
 ################################################################################
 #' Plot ANCOMBC2 result for phyloseq object
 #'
-#' @description 
+#' @description
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' Graphical representation of ANCOMBC2 result.
-#' 
+#'
 #' @inheritParams clean_pq
 #' @param ancombc_res (required) the result of the ancombc_pq function
 #'   For the moment only bimodal factors are possible.
@@ -961,7 +961,7 @@ plot_ancombc_pq <-
       )
 
     taxtable <- data.frame(physeq@tax_table)
-    taxtable$taxon <- taxa_names(physeq)
+    taxtable$taxa <- taxa_names(physeq)
 
     df <-
       left_join(signif_ancombc_res, taxtable, by = join_by("taxon" == "taxon"))
@@ -1080,13 +1080,13 @@ taxa_only_in_one_level <- function(physeq,
 ################################################################################
 #' Distribution of sequences across a factor for one taxon
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
-#' Focus on one taxon and one factor. 
-#' 
+#' Focus on one taxon and one factor.
+#'
 #' @inheritParams clean_pq
 #' @param fact (required) Name of the factor in `physeq@sam_data` used to plot
 #'    different lines

R/blast.R

@@ -2,17 +2,17 @@
 #' Blast some sequence against `refseq` slot of a \code{\link{phyloseq-class}}
 #'   object.
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-maturing-blue" alt="lifecycle-maturing"></a>
-#' 
+#'
 #' Use the blast software.
-#' 
+#'
 #' @param physeq (required): a \code{\link{phyloseq-class}} object obtained
 #'   using the `phyloseq` package.
 #' @param seq2search (required) path to a fasta file defining the sequences
-#'   you want to blast against the ASV sequences from the physeq object.
+#'   you want to blast against the taxa (ASV, OTU) sequences from the physeq object.
 #' @param blastpath path to blast program
 #' @param id_cut (default: 90) cut of in identity percent to keep result
 #' @param bit_score_cut (default: 50) cut of in bit score to keep result
@@ -184,13 +184,13 @@ blast_to_phyloseq <- function(physeq,
 #' Blast all sequence of `refseq` slot of a \code{\link{phyloseq-class}}
 #'   object against a custom database.
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' Use the blast software.
-#' 
+#'
 #' @inheritParams blast_to_phyloseq
 #' @param fasta_for_db path to a fasta file to make the blast database
 #' @param database path to a blast database
@@ -338,23 +338,21 @@ blast_pq <- function(physeq,
   return(blast_tab)
 }
 
-
-
 ################################################################################
 #' Filter undesirable taxa using blast against a custom database.
 #'
-#' @description 
-#' 
+#' @description
+#'
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' Use the blast software.
-#' 
+#'
 #' @inheritParams blast_to_phyloseq
 #' @param fasta_for_db path to a fasta file to make the blast database
 #' @param database path to a blast database
 #' @param clean_pq (logical)
-#'   If set to TRUE, empty samples and empty ASV are discarded
+#'   If set to TRUE, empty samples and empty taxa (ASV, OTU) are discarded
 #'   after filtering.
 #' @param id_filter (default: 90) cut of in identity percent to keep result
 #' @param bit_score_filter (default: 50) cut of in bit score to keep result
@@ -432,20 +430,27 @@ filter_asv_blast <- function(physeq,
 }
 
 
+################################################################################
+#' @rdname filter_asv_blast
+#' @export
+filter_taxa_blast <- filter_asv_blast
+################################################################################
+
+
 #' Blast some sequence against sequences from of a \code{\link{derep-class}}
 #'   object.
 #'
-#' @description 
+#' @description
 #' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
 #' <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
 #'
 #' Use the blast software.
-#' 
+#'
 #' @inheritParams blast_to_phyloseq
 #' @param derep The result of `dada2::derepFastq()`. A list of `derep-class`
 #'   object.
 #' @param seq2search (required) path to a fasta file defining the sequences
-#'   you want to blast against the ASV sequences from the physeq object.
+#'   you want to blast against the taxa (ASV, OTU) sequences from the physeq object.
 #' @param min_length_seq (default: 200) Removed sequences with less than
 #'   `min_length_seq` from derep before blast. Set to 0 to discard filtering
 #'    sequences by length.