Merge pull request #100 from adrientaudiere/dev

docs: Fix bugs for devel cran test
adrientaudiere · Sep 27, 2024 · c9d0a46 · c9d0a46
2 parents 76a25f8 + 3f565a2
commit c9d0a46
Show file tree

Hide file tree

Showing 188 changed files with 393 additions and 257 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.9.3
+Version: 0.9.4
 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>.

diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,16 @@
 
-# MiscMetabar 0.9.3 (in development)
+# MiscMetabar 0.9.5 (in development)
+
+# MiscMetabar 0.9.4 
+
+- Set a seed in the example of `build_tree_pq` to resubmit to CRAN
+
+# MiscMetabar 0.9.3
 
 - 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()`
+- Build an alias function `filter_taxa_blast()` for `filter_asv_blast()`
+- Build an alias function `postcluster_pq()` for `asv2otu()`
+- Add param `return_data_for_venn` in function `ggvenn_pq` in order to make more customizable plot following [ggVennDiagram tutorial](https://gaospecial.github.io/ggVennDiagram/articles/fully-customed.html)
 
 
 ## BREAKING CHANGES

diff --git a/R/blast.R b/R/blast.R
@@ -437,7 +437,7 @@ filter_taxa_blast <- filter_asv_blast
 ################################################################################
 
 
-#' Blast some sequence against sequences from of a \code{\link{derep-class}}
+#' Blast some sequence against sequences from of a \code{\link[dada2]{derep-class}}
 #'   object.
 #'
 #' @description

diff --git a/R/dada_phyloseq.R b/R/dada_phyloseq.R
@@ -1786,7 +1786,7 @@ tbl_sum_samdata <- function(physeq, remove_col_unique_value = TRUE, ...) {
 #' @details
 #' This function is mainly a wrapper of the work of others.
 #'   Please make a reference to `FUNGuildR` package and the associate
-#'   [publication](https://www.sciencedirect.com/science/article/abs/pii/S1754504815000847) if you
+#'   publication (\doi{10.1016/j.funeco.2015.06.006}) if you
 #'   use this function.
 #' @seealso [plot_guild_pq()]
 
@@ -2019,6 +2019,7 @@ plot_guild_pq <-
 #' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' \donttest{
 #' if (requireNamespace("phangorn")) {
+#'   set.seed(22)
 #'   df <- subset_taxa_pq(data_fungi_mini, taxa_sums(data_fungi_mini) > 9000)
 #'   df_tree <- build_phytree_pq(df, nb_bootstrap = 2)
 #'   plot(df_tree$UPGMA)

diff --git a/R/funguild.R b/R/funguild.R
@@ -7,7 +7,7 @@
 #' The original function and documentation was written by Brendan Furneaux
 #' in the [FUNGuildR](https://github.com/brendanf/FUNGuildR/) package.
 #'
-#' Please cite this [publication](https://www.sciencedirect.com/science/article/abs/pii/S1754504815000847).
+#' Please cite this publication (\doi{10.1016/j.funeco.2015.06.006}).
 #'
 #' @param db_url a length 1 character string giving the URL to retrieve the database
 #'     from

diff --git a/R/plot_functions.R b/R/plot_functions.R
@@ -1195,6 +1195,9 @@ venn_pq <-
 #'   modalities of args `fact`. Use `phyloseq::rarefy_even_depth()` function
 #' @param rarefy_after_merging Rarefy each sample after merging by the
 #'   modalities of args `fact`.
+#' @param return_data_for_venn (logical, default FALSE) If TRUE, the plot is
+#'   not returned, but the resulting dataframe to plot with ggVennDiagram package
+#'   is returned.
 #' @param ... Other arguments for the `ggVennDiagram::ggVennDiagram` function
 #'   for ex. `category.names`.
 #' @return A \code{\link[ggplot2]{ggplot}}2 plot representing Venn diagram of
@@ -1225,6 +1228,35 @@ venn_pq <-
 #'   ggvenn_pq(data_fungi, fact = "Height", rarefy_before_merging = TRUE)
 #'   ggvenn_pq(data_fungi, fact = "Height", rarefy_after_merging = TRUE) +
 #'     scale_x_continuous(expand = expansion(mult = 0.5))
+#'
+#'   # For more flexibility, you can save the dataset for more precise construction
+#'   # with ggplot2 and ggVennDiagramm
+#'   # (https://gaospecial.github.io/ggVennDiagram/articles/fully-customed.html)
+#'   res_venn <- ggvenn_pq(data_fungi, fact = "Height", return_data_for_venn = TRUE)
+#'
+#'   ggplot() +
+#'     # 1. region count layer
+#'     geom_polygon(aes(X, Y, group = id, fill = name),
+#'       data = ggVennDiagram::venn_regionedge(res_venn)
+#'     ) +
+#'     # 2. set edge layer
+#'     geom_path(aes(X, Y, color = id, group = id),
+#'       data = ggVennDiagram::venn_setedge(res_venn),
+#'       show.legend = FALSE, linewidth = 3
+#'     ) +
+#'     # 3. set label layer
+#'     geom_text(aes(X, Y, label = name),
+#'       data = ggVennDiagram::venn_setlabel(res_venn)
+#'     ) +
+#'     # 4. region label layer
+#'     geom_label(
+#'       aes(X, Y, label = paste0(
+#'         count, " (",
+#'         scales::percent(count / sum(count), accuracy = 2), ")"
+#'       )),
+#'       data = ggVennDiagram::venn_regionlabel(res_venn)
+#'     ) +
+#'     theme_void()
 #' }
 #' }
 #' @export
@@ -1240,6 +1272,7 @@ ggvenn_pq <- function(physeq = NULL,
                       add_nb_seq = FALSE,
                       rarefy_before_merging = FALSE,
                       rarefy_after_merging = FALSE,
+                      return_data_for_venn = FALSE,
                       ...) {
   if (!is.factor(physeq@sam_data[[fact]])) {
     physeq@sam_data[[fact]] <- as.factor(physeq@sam_data[[fact]])
@@ -1323,7 +1356,11 @@ ggvenn_pq <- function(physeq = NULL,
         ggtitle(moda)
     }
   }
-  return(p)
+  if (return_data_for_venn) {
+    return(ggVennDiagram::process_data(ggVennDiagram::Venn(res)))
+  } else {
+    return(p)
+  }
 }
 ################################################################################
 

diff --git a/README.Rmd b/README.Rmd
@@ -42,6 +42,15 @@ A CRAN version of MiscMetabar is available.
 install.packages("MiscMetabar")
 ```
 
+You may need to install required bioconductor packages (dada2 and phyloseq) first. See their installation pages. 
+One other solution is to use the package [pak](https://pak.r-lib.org/) to install MiscMetabar. It comes with the benefit to check for 
+uninstalled dependencies on your computer (system requirements), thank you [pak](https://pak.r-lib.org/)! 
+
+```{r, results = 'hide', eval=FALSE}
+pak::pkg_install("MiscMetabar")
+```
+
+
 
 You can also install the stable development version from [GitHub](https://github.com/) with:
 

diff --git a/README.md b/README.md
@@ -11,6 +11,7 @@ v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.06038/status.svg)](https://doi.org/10.21105/joss.06038)
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
+
 <!-- devtools::build_readme() -->
 
 # MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="https://adrientaudiere.github.io/MiscMetabar/reference/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
@@ -48,6 +49,16 @@ A CRAN version of MiscMetabar is available.
 install.packages("MiscMetabar")
 ```
 
+You may need to install required bioconductor packages (dada2 and
+phyloseq) first. See their installation pages. One other solution is to
+use the package [pak](https://pak.r-lib.org/) to install MiscMetabar. It
+comes with the benefit to check for uninstalled dependencies on your
+computer (system requirements), thank you [pak](https://pak.r-lib.org/)!
+
+``` r
+pak::pkg_install("MiscMetabar")
+```
+
 You can also install the stable development version from
 [GitHub](https://github.com/) with:
 
@@ -138,7 +149,7 @@ ggvenn_pq(data_fungi, fact = "Height") +
   labs(title = "Share number of ASV among Height in tree")
 ```
 
-<img src="man/figures/README-unnamed-chunk-7-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-8-1.png" width="100%" />
 
 ### Note for non-Linux users
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,20 +1,3 @@
-Resolved 2 Notes from CRAN submission
+Resolved 1 Error from CRAN "Additional issue"
 
-
-# Invalid URLs
-
-Found the following (possibly) invalid URLs:
-  URL: https://www.sciencedirect.com/science/article/abs/pii/S1754504815000847
-    From: man/add_funguild_info.Rd
-          man/get_funguild_db.Rd
-    Status: 403
-    Message: Forbidden
-
-> I don't understand why the URL is invalid. It works for me.
-
-
-# Bad \link{} for external packages
-
-Found the following Rd file(s) with Rd \link{} targets missing package
-
-> Solved in v. 0.9.3
+I add a seed (`set.seed(22)`) in the offending example of `build_phytree_pq`. I tried to find the error using a loop, but after 50 different seed numbers, the examples still work on my side.
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/MiscMetabar.html b/docs/articles/MiscMetabar.html
diff --git a/docs/articles/Reclustering.html b/docs/articles/Reclustering.html
diff --git a/docs/articles/Rules.html b/docs/articles/Rules.html
diff --git a/docs/articles/alpha-div.html b/docs/articles/alpha-div.html
diff --git a/docs/articles/beta-div.html b/docs/articles/beta-div.html
diff --git a/docs/articles/explore_data.html b/docs/articles/explore_data.html
diff --git a/docs/articles/fastq_quality_check.html b/docs/articles/fastq_quality_check.html
diff --git a/docs/articles/filter.html b/docs/articles/filter.html