Merge pull request #91 from adrientaudiere/dev

Submission 0.8.00 to CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.12
+Version: 0.8.00
 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>.
@@ -13,7 +13,8 @@ Depends:
     phyloseq,
     ggplot2 (>= 3.5.0),
     dada2,
-    dplyr
+    dplyr,
+    purrr
 Suggests: 
     adespatial,
     ANCOMBC,
@@ -57,7 +58,6 @@ Suggests:
     pbapply,
     plotly,
     plyr,
-    purrr,
     reshape2,
     rmarkdown,
     rotl,

NAMESPACE

@@ -91,6 +91,7 @@ export(plot_guild_pq)
 export(plot_mt)
 export(plot_tax_pq)
 export(plot_tsne_pq)
+export(psmelt_samples_pq)
 export(read_phyloseq)
 export(read_pq)
 export(rename_samples)
@@ -136,6 +137,7 @@ import(dada2)
 import(dplyr)
 import(ggplot2)
 import(phyloseq)
+import(purrr)
 importFrom(grDevices,col2rgb)
 importFrom(lifecycle,deprecated)
 importFrom(rlang,.data)

NEWS.md

@@ -6,9 +6,12 @@
 - Add functions `signif_ancombc()` and `plot_ancombc_pq()` to plot significant results from `ancombc_pq()` function
 - Add function `distri_1_taxa()` to summarize the distribution of one given taxa across level of a modality
 - Add function `normalize_prop_pq()` to implement the method proposed by [McKnight et al. 2018](https://doi.org/10.5061/dryad.tn8qs35)
+- Add function `psmelt_samples_pq()` to build data frame of samples information including the number of sequences (Abundance) and Hill diversity metrics. Useful to use with the [ggstatsplot](https://indrajeetpatil.github.io/ggstatsplot/) packages (see examples).
+- Replace param `variable` by `fact` in function `ggbetween_pq()` and `hill_pq()` (keeping the variable option in `hill_pq()` for backward compatibility)
+- Fix a bug in the class of the return object of function `chimera_removal_vs()`. Now it return a matrix to be able to be parsed on to [dada2::getUniques()] 
 
 # 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 
 - Add functions `filter_trim()`, `sample_data_with_new_names()` and `rename_samples()` to facilitate the use of [targets](https://books.ropensci.org/targets/) for bioinformatic pipeline.
 - Add function `add_info_to_sam_data()` to expand sam_data slot using a data.frame and using nb_asv and nb_seq 

R/Deseq2_edgeR.R

@@ -23,13 +23,15 @@
 #' 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"
-#' )
+#' if (requireNamespace("edgeR")) {
+#'   plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
+#'     color_tax = "Kingdom"
+#'   )
 #'
-#' plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
-#'   taxolev = "Class", color_tax = "Kingdom"
-#' )
+#'   plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),
+#'     taxolev = "Class", color_tax = "Kingdom"
+#'   )
+#' }
 #' }
 #' @author Adrien Taudière
 #'
@@ -155,23 +157,26 @@ plot_edgeR_pq <-
 #'   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"))
-#' res <- DESeq2::DESeq(phyloseq_to_deseq2(GP, ~SampleType),
-#'   test = "Wald", fitType = "local"
-#' )
-#' plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
-#'   tax_table = GP@tax_table, color_tax = "Kingdom"
-#' )
-#' plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
-#'   tax_table = GP@tax_table, color_tax = "Kingdom",
-#'   pval = 0.7
-#' )
-#' plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
-#'   tax_table = GP@tax_table, color_tax = "Class",
-#'   select_taxa = c("522457", "271582")
-#' )
+#' if (requireNamespace("DESeq2")) {
+#'   res <- DESeq2::DESeq(phyloseq_to_deseq2(GP, ~SampleType),
+#'     test = "Wald", fitType = "local"
+#'   )
+#'   plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
+#'     tax_table = GP@tax_table, color_tax = "Kingdom"
+#'   )
+#'   plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
+#'     tax_table = GP@tax_table, color_tax = "Kingdom",
+#'     pval = 0.7
+#'   )
+#'   plot_deseq2_pq(res, c("SampleType", "Soil", "Skin"),
+#'     tax_table = GP@tax_table, color_tax = "Class",
+#'     select_taxa = c("522457", "271582")
+#'   )
+#' }
 #' }
 #' @author Adrien Taudière
 #'

R/MiscMetabar-package.R

@@ -3,7 +3,7 @@
 #' Functions to help analyze and visualize metabarcoding data. Mainly based on
 #' the phyloseq and dada2 packages.
 #' @name MiscMetabar-package
-#' @import ggplot2 phyloseq dada2 dplyr
+#' @import ggplot2 phyloseq dada2 dplyr purrr
 NULL
 
 if (getRversion() >= "2.15.1") {