Merge pull request #89 from adrientaudiere/dev

Add functions (v 0.7.12)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.10
+Version: 0.7.12
 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>.
@@ -26,6 +26,7 @@ Suggests:
     devtools,
     DT,
     edgeR,
+    formattable,
     gghalves,
     ggh4x,
     ggstatsplot,

NAMESPACE

@@ -35,8 +35,11 @@ export(cutadapt_remove_primers)
 export(diff_fct_diff_class)
 export(dist_bycol)
 export(dist_pos_control)
+export(distri_1_taxa)
+export(fac2col)
 export(filter_asv_blast)
 export(filter_trim)
+export(formattable_pq)
 export(funguild_assign)
 export(funky_color)
 export(get_file_extension)
@@ -70,6 +73,7 @@ export(multipatt_pq)
 export(multiplot)
 export(multitax_bar_pq)
 export(mumu_pq)
+export(normalize_prop_pq)
 export(otu_circle)
 export(perc)
 export(phyloseq_to_edgeR)
@@ -78,6 +82,7 @@ export(physeq_heat_tree)
 export(physeq_or_string_to_dna)
 export(plot_LCBD_pq)
 export(plot_SCBD_pq)
+export(plot_ancombc_pq)
 export(plot_deseq2_phyloseq)
 export(plot_deseq2_pq)
 export(plot_edgeR_phyloseq)
@@ -99,6 +104,7 @@ export(sankey_pq)
 export(save_pq)
 export(search_exact_seq_pq)
 export(select_one_sample)
+export(signif_ancombc)
 export(simplify_taxo)
 export(subsample_fastq)
 export(subset_samples_pq)
@@ -109,9 +115,11 @@ export(summary_plot_pq)
 export(swarm_clustering)
 export(tax_bar_pq)
 export(tax_datatable)
+export(taxa_only_in_one_level)
 export(tbl_sum_samdata)
 export(track_wkflow)
 export(track_wkflow_samples)
+export(transp)
 export(treemap_pq)
 export(tsne_pq)
 export(unique_or_na)
@@ -128,6 +136,7 @@ import(dada2)
 import(dplyr)
 import(ggplot2)
 import(phyloseq)
+importFrom(grDevices,col2rgb)
 importFrom(lifecycle,deprecated)
 importFrom(rlang,.data)
 importFrom(stats,ave)
@@ -136,6 +145,8 @@ importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
 importFrom(stats,reformulate)
 importFrom(stats,reorder)
+importFrom(stats,runif)
+importFrom(stats,sd)
 importFrom(stats,terms)
 importFrom(utils,object.size)
 importFrom(utils,setTxtProgressBar)

NEWS.md

@@ -1,8 +1,11 @@
 # MiscMetabar 0.8 (in development)
 
-- Add param `plot_with_tuckey` to `hill_pq()`.
-
-
+- 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.
+- Add functions `fac2col()` and `transp()` to facilitate manipulation of colors, especially in function `formattable_pq()`
+- 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)
 
 # MiscMetabar 0.7 (in development)
 

R/MiscMetabar-package.R

@@ -23,7 +23,7 @@ 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"
+    "chim_rm", "condition", "physeq", "seq_tab_Pairs", "nb_samp", "silent"
   ))
 }