Merge pull request #60 from adrientaudiere/dev

v 0.52
adrientaudiere · Dec 13, 2023 · a09750e · a09750e
2 parents 80e2122 + 3f9d492
commit a09750e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.51
+Version: 0.52
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1088-1182"))
 Maintainer: Adrien Taudière <[email protected]>

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
-# MiscMetabar 0.52 (in development) 
+# MiscMetabar 0.53 (in development) 
+
+# MiscMetabar 0.52 
 
 - Add function `ggbetween_pq()` to facilitate comparison of hill number using the power of `ggstatsplot::ggbetweenstats()`
 - Add function `plot_SCBD_pq()` to plot species contributions to beta diversity (SCBD) of samples

diff --git a/R/plot_functions.R b/R/plot_functions.R
@@ -82,7 +82,9 @@ plot_mt <-
 #' @examples
 #' data("GlobalPatterns", package = "phyloseq")
 #' GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
+#' GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
 #' p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, by.fact = TRUE, step = 10)
+#' p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, step = 10)
 #'
 #' p + theme(legend.position = "none")
 #'
@@ -288,6 +290,7 @@ accu_plot <-
 #' @examples
 #' data("GlobalPatterns", package = "phyloseq")
 #' GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
+#' GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
 #' p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, by.fact = TRUE, step = 10)
 #'
 #' val_threshold <- accu_samp_threshold(p)
@@ -1439,9 +1442,9 @@ ggbetween_pq <- function(physeq, variable, one_plot = FALSE, ...) {
   physeq <- clean_pq(physeq, force_taxa_as_columns = TRUE)
   df <- cbind(
     "nb_asv" = sample_sums(physeq@otu_table), physeq@sam_data,
-    "hill_0" = vegan::renyi(physeq@otu_table, scale = c(0), hill = TRUE),
-    "hill_1" = vegan::renyi(physeq@otu_table, scale = c(1), hill = TRUE),
-    "hill_2" = vegan::renyi(physeq@otu_table, scale = c(2), hill = TRUE)
+    "hill_0" = vegan::renyi(physeq@otu_table, scale = 0, hill = TRUE),
+    "hill_1" = vegan::renyi(physeq@otu_table, scale = 1, hill = TRUE),
+    "hill_2" = vegan::renyi(physeq@otu_table, scale = 2, hill = TRUE)
   )
   variable <- sym(variable)
   p0 <- ggstatsplot::ggbetweenstats(df, !!variable, hill_0, ...)

diff --git a/man/accu_plot.Rd b/man/accu_plot.Rd
diff --git a/man/accu_samp_threshold.Rd b/man/accu_samp_threshold.Rd
diff --git a/man/blast_to_phyloseq.Rd b/man/blast_to_phyloseq.Rd
diff --git a/man/count_seq.Rd b/man/count_seq.Rd
diff --git a/man/plot_SCBD_pq.Rd b/man/plot_SCBD_pq.Rd
diff --git a/man/subsample_fastq.Rd b/man/subsample_fastq.Rd
diff --git a/tests/testthat/test_figures_alpha_div.R b/tests/testthat/test_figures_alpha_div.R
@@ -11,6 +11,7 @@ data_fungi_2trees <-
   )
 GP_archae <-
   subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
+GP_archae <- rarefy_even_depth(subset_samples_pq(GP_archae, sample_sums(GP_archae) > 3000))
 data_basidio <- subset_taxa(data_fungi, Phylum == "Basidiomycota")
 
 test_that("hill_pq works with data_fungi dataset", {