Merge pull request #92 from adrientaudiere/dev

Change v0.9.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.8.00
+Version: 0.9.1
 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>.
@@ -28,11 +28,14 @@ Suggests:
     DT,
     edgeR,
     formattable,
+    ggalluvial,
+    ggfittext,
     gghalves,
     ggh4x,
     ggstatsplot,
     ggridges,
     ggVennDiagram,
+    glmulti,
     gtsummary,
     grDevices,
     grid,

NAMESPACE

@@ -5,6 +5,7 @@ S3method(unique_or_na,factor)
 export(LCBD_pq)
 export(SRS_curve_pq)
 export(accu_plot)
+export(accu_plot_balanced_modality)
 export(accu_samp_threshold)
 export(add_blast_info)
 export(add_dna_to_phyloseq)
@@ -13,6 +14,7 @@ export(add_info_to_sam_data)
 export(add_new_taxonomy_pq)
 export(adonis_phyloseq)
 export(adonis_pq)
+export(adonis_rarperm_pq)
 export(all_object_size)
 export(ancombc_pq)
 export(are_modality_even_depth)
@@ -45,12 +47,16 @@ export(funky_color)
 export(get_file_extension)
 export(get_funguild_db)
 export(ggVenn_phyloseq)
+export(ggaluv_pq)
 export(ggbetween_pq)
+export(ggscatt_pq)
 export(ggvenn_pq)
+export(glmutli_pq)
 export(graph_test_pq)
 export(heat_tree_pq)
 export(hill_phyloseq)
 export(hill_pq)
+export(hill_test_rarperm_pq)
 export(hill_tuckey_phyloseq)
 export(hill_tuckey_pq)
 export(iNEXT_pq)
@@ -91,7 +97,9 @@ export(plot_guild_pq)
 export(plot_mt)
 export(plot_tax_pq)
 export(plot_tsne_pq)
+export(plot_var_part_pq)
 export(psmelt_samples_pq)
+export(rarefy_sample_count_by_modality)
 export(read_phyloseq)
 export(read_pq)
 export(rename_samples)
@@ -116,6 +124,8 @@ export(summary_plot_pq)
 export(swarm_clustering)
 export(tax_bar_pq)
 export(tax_datatable)
+export(taxa_as_columns)
+export(taxa_as_rows)
 export(taxa_only_in_one_level)
 export(tbl_sum_samdata)
 export(track_wkflow)
@@ -126,6 +136,8 @@ export(tsne_pq)
 export(unique_or_na)
 export(upset_pq)
 export(upset_test_pq)
+export(var_par_pq)
+export(var_par_rarperm_pq)
 export(venn_phyloseq)
 export(venn_pq)
 export(verify_pq)
@@ -141,10 +153,13 @@ import(purrr)
 importFrom(grDevices,col2rgb)
 importFrom(lifecycle,deprecated)
 importFrom(rlang,.data)
+importFrom(stats,anova)
+importFrom(stats,as.formula)
 importFrom(stats,ave)
 importFrom(stats,kruskal.test)
 importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
+importFrom(stats,quantile)
 importFrom(stats,reformulate)
 importFrom(stats,reorder)
 importFrom(stats,runif)

NEWS.md

@@ -1,4 +1,25 @@
-# MiscMetabar 0.8 (in development)
+# MiscMetabar 0.9.1 (in development)
+
+## New functions 
+- Add functions [taxa_as_rows()] and [taxa_as_columns()] to replace verbose called to [clean_pq()]
+- Add function [ggscatt_pq()] to plot and test for effect of a numerical columns in sam_data on Hill number. Its the equivalent for numerical variables of [ggbetween_pq()] which focus on the effect of a factor. 
+- Add functions [var_par_pq()] , [var_par_rarperm_pq()] and [plot_var_part_pq()] to compute the partition of the variation of community and plot it. It introduce the notion of `rarperm` part in the function name. It refers to the fact that this function compute permutation of samples depth rarefaction to measure the variation due to the random process in rarefaction. 
+- Add function [hill_test_rarperm_pq()] to test the effect of a factor on hill diversity accounting for the variation due to random nature of the rarefaction by sample depth. 
+- Add function [rarefy_sample_count_by_modality()] to equalize the number of samples for each levels of a modality (factor)
+- Add function [accu_plot_balanced_modality()] to plot accumulation curves with balanced modality (same number of samples per level) and depth rarefaction (same number of sequences per sample) 
+- Add function [adonis_rarperm_pq()] to compute multiple Permanova analyses on different sample depth rarefaction.
+- Add function [ggaluv_pq()] to plot taxonomic distribution in alluvial fashion with ggplot2 (using the [ggalluvial] package)
+- Add function [glmutli_pq()] to use automated model selection and multimodel inference with (G)LMs for phyloseq object
+
+
+## New parameters
+
+- Add param `taxa_ranks` in function [psmelt_samples_pq()] to group results by samples AND taxonomic ranks. 
+- Add param `hill_scales` in functions [hill_tuckey_pq()] and [hill_pq()] to choose the level of the hill number. 
+- Add param `na_remove` in function `hill_pq()` to remove samples with NA in the factor fact.
+
+
+# MiscMetabar 0.8.1 
 
 - Add param `plot_with_tuckey` to `hill_pq()`.,
 - Add function `formattable_pq()` to make beautiful table of the distribution of taxa across a modality using visualization inside in the table.

R/MiscMetabar-package.R

@@ -23,7 +23,9 @@ if (getRversion() >= "2.15.1") {
     "update", "upr", "upViewport", "val", "value", "vegdist", "viewport",
     "write.table", "x", "x1", "X1", "x2", "y", "y1", "y2", "ymax",
     "ymin", ".group", "archetype", "nOTUid", "taxon", "total",
-    "chim_rm", "condition", "physeq", "seq_tab_Pairs", "nb_samp", "silent"
+    "chim_rm", "condition", "physeq", "seq_tab_Pairs", "nb_samp", "silent",
+    "X1_lim1", "X1_lim2", "aicc", "variable", "pos_letters", "alluvium",
+    "na_remove", "stratum", "to_lodes_form"
   ))
 }