feat: add function tbl_sum_samdata

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(LCBD_pq)
 export(SRS_curve_pq)
 export(accu_plot)
 export(accu_samp_threshold)
@@ -42,13 +43,15 @@ export(lulu_phyloseq)
 export(lulu_pq)
 export(merge_krona)
 export(multi_biplot_pq)
+export(multipatt_pq)
 export(multiplot)
 export(multitax_bar_pq)
 export(otu_circle)
 export(perc)
 export(phyloseq_to_edgeR)
 export(physeq_graph_test)
 export(physeq_heat_tree)
+export(plot_LCBD_pq)
 export(plot_deseq2_phyloseq)
 export(plot_deseq2_pq)
 export(plot_edgeR_phyloseq)
@@ -75,6 +78,7 @@ export(summary_plot_phyloseq)
 export(summary_plot_pq)
 export(tax_bar_pq)
 export(tax_datatable)
+export(tbl_sum_samdata)
 export(track_wkflow)
 export(track_wkflow_samples)
 export(treemap_pq)

NEWS.md

@@ -1,6 +1,7 @@
 # MiscMetabar 0.51 (in development) 
 
-- Add function `LCBD_pq()`  and `plot_LCBD_pq()` to compute, test and plot local contributions to beta diversity (LCBD) of samples
+- Add function `LCBD_pq()` and `plot_LCBD_pq()` to compute, test and plot local contributions to beta diversity (LCBD) of samples
+- Add function `tbl_sum_samdata()` to summarize information from sample data in a table
 
 # MiscMetabar 0.5
 

R/beta_div_test.R

@@ -355,24 +355,40 @@ plot_LCBD_pq <- function(physeq,
 }
 
 
+#' @title Test and plot multipatt result
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' A wrapper for the [indicspecies::multipatt()] function in the case of `physeq`
+#'   object.
+#' @inheritParams clean_pq
+#' @param fact (required) Name of the factor in `physeq@sam_data` used to plot
+#'    different lines
+#' @param p_adjust_method (chr, default "BH"): the method used to adjust p-value
+#' @param pval (int, default 0.05): the value to determine the significance of
+#'   LCBD
+#' @param control see `?indicspecies::multipatt()`
+#' @param ... Others arguments passed on to [indicspecies::multipatt()] function
+#'
+#' @return A ggplot object
+#' @export
 #' @examples 
 #' multipatt_pq(subset_samples(data_fungi, !is.na(Time)), fact="Time")
 #' multipatt_pq(subset_samples(data_fungi, !is.na(Time)), fact="Time",
 #'    max.order = 1, control = how(nperm=9999))
+#' @author Adrien Taudière
 
 multipatt_pq <- function(physeq,
 fact,
 p_adjust_method =  "BH",
 pval = 0.05,
 control = how(nperm = 999),
-max.order = 3, 
 ...){
 
 res <-
-  multipatt(as.matrix(physeq@otu_table),
+  indicspecies::multipatt(as.matrix(physeq@otu_table),
             physeq@sam_data[[fact]],
             control = control,
-            max.order = max.order,
             ...)
 
 res_df <- res$sign

R/plot_functions.R

@@ -1251,7 +1251,7 @@ hill_pq <-
     colnames(otu_hill) <- c("Hill_0", "Hill_1", "Hill_2")
 
     df_hill <- data.frame(otu_hill, physeq@sam_data)
-    df_hill[, c(1:3)] <- apply(df_hill[, c(1:3)], 2, as.numeric)
+    df_hill[, 1:3] <- apply(df_hill[, 1:3], 2, as.numeric)
 
     p_var <- hill_tuckey_pq(physeq, variable, correction_for_sample_size = correction_for_sample_size)
 
@@ -1654,7 +1654,7 @@ rotl_pq <- function(physeq,
 #' @inheritParams clean_pq
 #' @param taxonomic_level (default: NULL): a vector of selected
 #' taxonomic level using
-#'   their column numbers (e.g. taxonomic_level = c(1:7))
+#'   their column numbers (e.g. taxonomic_level = 1:7)
 #' @param ... Arguments passed on to \code{\link[metacoder]{heat_tree}}
 #'
 #' @return A plot

R/table_functions.R

@@ -5,7 +5,7 @@
 #' @inheritParams clean_pq
 #' @param abundance (default: TRUE) Does the number of sequences is print
 #' @param taxonomic_level (default: NULL) a vector of selected taxonomic
-#' level using their column numbers (e.g. taxonomic_level = c(1:7))
+#' level using their column numbers (e.g. taxonomic_level = 1:7)
 #' @param modality (default: NULL) A sample modality to split
 #' OTU abundancy by level of the modality
 #' @param ... Other argument for the datatable function
@@ -229,7 +229,7 @@ compare_pairs_pq <- function(physeq = NULL,
   }
 
   res_df_t <- t(as_tibble(res, .name_repair = "minimal"))
-  colnames(res_df_t) <- paste0("V", seq_along(ncol(res_df_t))
+  colnames(res_df_t) <- paste0("V", seq_along(ncol(res_df_t)))
   res_df <- as_tibble(res_df_t)
   # res_df <- as_tibble(t(as_tibble(res, .name_repair = "universal")), .name_repair = "universal")
 

README.Rmd

@@ -24,7 +24,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# MiscMetabar
+# MiscMetabar <a href="https://adrientaudiere.github.io/MiscMetabar/"><img src="man/figures/logo.png" align="right" height="138" alt="MiscMetabar website" /></a>
 
 See the pkdown site [here](https://adrientaudiere.github.io/MiscMetabar/).
 

default.nix

@@ -0,0 +1,73 @@
+# This file was generated by the {rix} R package v0.4.1 on 2023-11-21
+# with following call:
+# >rix(r_ver = "976fa3369d722e76f37c77493d99829540d43845",
+#  > r_pkgs = c("quarto",
+#  > "dplyr",
+#  > "DT",
+#  > "flexdashboard",
+#  > "forcats",
+#  > "formattable",
+#  > "ggplot2",
+#  > "ggVennDiagram",
+#  > "grid",
+#  > "gridExtra",
+#  > "here",
+#  > "knitr",
+#  > "networkD3",
+#  > "optparse",
+#  > "plotly",
+#  > "qs",
+#  > "quarto",
+#  > "rmarkdown",
+#  > "stringr",
+#  > "targets",
+#  > "this.path",
+#  > "treemap",
+#  > "vegan",
+#  > "viridis",
+#  > "visNetwork"),
+#  > system_pkgs = "quarto",
+#  > tex_pkgs = c("amsmath",
+#  > "framed",
+#  > "fvextra",
+#  > "environ",
+#  > "fontawesome5",
+#  > "orcidlink",
+#  > "pdfcol",
+#  > "tcolorbox",
+#  > "tikzfill"),
+#  > ide = "rstudio",
+#  >      project_path = ".",
+#  > overwrite = TRUE,
+#  > print = TRUE,
+#  > shell_hook = "")
+# It uses nixpkgs' revision 976fa3369d722e76f37c77493d99829540d43845 for reproducibility purposes
+# which will install R version 4.3.1
+# Report any issues to https://github.com/b-rodrigues/rix
+let
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/976fa3369d722e76f37c77493d99829540d43845.tar.gz") {};
+ rpkgs = builtins.attrValues {
+  inherit (pkgs.rPackages) quarto dplyr DT flexdashboard forcats formattable ggplot2 ggVennDiagram grid gridExtra here knitr networkD3 optparse plotly qs quarto rmarkdown stringr targets this_path treemap vegan viridis visNetwork;
+};
+  tex = (pkgs.texlive.combine {
+  inherit (pkgs.texlive) scheme-small amsmath framed fvextra environ fontawesome5 orcidlink pdfcol tcolorbox tikzfill;
+});
+ system_packages = builtins.attrValues {
+  inherit (pkgs) R glibcLocalesUtf8 quarto;
+};
+ rstudio_pkgs = pkgs.rstudioWrapper.override {
+  packages = [  rpkgs ];
+};
+ in
+  pkgs.mkShell {
+    LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then  "${pkgs.glibcLocalesUtf8}/lib/locale/locale-archive" else "";
+    LANG = "en_US.UTF-8";
+    LC_ALL = "en_US.UTF-8";
+    LC_TIME = "en_US.UTF-8";
+    LC_MONETARY = "en_US.UTF-8";
+    LC_PAPER = "en_US.UTF-8";
+    LC_MEASUREMENT = "en_US.UTF-8";
+
+    buildInputs = [  rpkgs tex system_packages rstudio_pkgs ];
+
+  }