re-styled code & roxygen2 docs, replaced jsonlite by yyjsonr, fixed removeNAs

Author: agusinac

.github/workflows/R-CMD-check.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main]
+    branches: [dev]
 
 name: R-CMD-check.yaml
 

.github/workflows/pkgdown.yaml

@@ -1,6 +1,6 @@
 Package: OmicFlow
 Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
-Version: 1.6.0
+Version: 1.6.0.9001
 Date: 2026-05-19
 Authors@R: c(
     person(
@@ -28,28 +28,23 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Depends: 
-    R (>= 4.3.0),
+    R (>= 4.3.0)
+Imports:
     R6,
     data.table,
-    Matrix
-Imports: 
+    Matrix,
     ape,
     ggpubr,
     ggrepel,
     ggplot2,
-    jsonlite,
     jsonvalidate,
-    magrittr,
     methods,
     patchwork,
     RColorBrewer,
     rhdf5,
     rstatix,
     Rcpp (>= 0.12.6),
     RcppParallel (>= 4.3.20),
-    stats,
-    tools,
-    utils,
     vegan,
     yyjsonr,
     cli

DESCRIPTION

@@ -23,58 +23,20 @@ export(plot_pairwise_stats)
 export(proteomics)
 export(unifrac)
 export(volcano_plot)
-import(Matrix)
 import(R6)
+import(data.table)
+import(ggplot2)
 import(rhdf5)
 importFrom(Matrix,sparseMatrix)
-importFrom(RColorBrewer,brewer.pal)
-importFrom(RColorBrewer,brewer.pal.info)
 importFrom(Rcpp,sourceCpp)
-importFrom(RcppParallel,setThreadOptions)
-importFrom(ape,keep.tip)
 importFrom(ape,read.tree)
 importFrom(data.table,":=")
 importFrom(data.table,.SD)
-importFrom(ggplot2,.data)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,coord_flip)
-importFrom(ggplot2,element_rect)
-importFrom(ggplot2,element_text)
-importFrom(ggplot2,facet_wrap)
-importFrom(ggplot2,geom_bar)
-importFrom(ggplot2,geom_boxplot)
-importFrom(ggplot2,geom_hline)
-importFrom(ggplot2,geom_label)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_segment)
-importFrom(ggplot2,geom_vline)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,position_jitter)
-importFrom(ggplot2,scale_color_gradient2)
-importFrom(ggplot2,scale_colour_manual)
-importFrom(ggplot2,scale_fill_manual)
-importFrom(ggplot2,scale_size_continuous)
-importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_x_discrete)
-importFrom(ggplot2,stat_ellipse)
-importFrom(ggplot2,theme)
-importFrom(ggplot2,theme_bw)
-importFrom(jsonlite,read_json)
-importFrom(jsonlite,toJSON)
 importFrom(jsonvalidate,json_validate)
-importFrom(magrittr,"%>%")
-importFrom(methods,as)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
-importFrom(stats,as.dist)
-importFrom(stats,median)
-importFrom(stats,na.omit)
-importFrom(stats,p.adjust)
-importFrom(stats,p.adjust.methods)
-importFrom(stats,quantile)
-importFrom(tools,file_ext)
 importFrom(utils,globalVariables)
+importFrom(yyjsonr,read_json_file)
 importFrom(yyjsonr,validate_json_file)
+importFrom(yyjsonr,write_json_file)
 useDynLib(OmicFlow, .registration = TRUE)

NAMESPACE

@@ -1,3 +1,15 @@
+# OmicFlow 1.6.0.9001
+
+## Changed
+- Re-factoring `roxygen2` code & documentation style [IN PROGRESS].
+- TODO: Add `tryCatch` where neccessary
+- Replaced `jsonlite` by `yyjsonr` functionality, much faster and cleaner code.
+- Replaced `tests/testthat/input/metagenomics/biom_with_taxonomy_json.biom` with one from BIOM v2 example.
+
+## Fixed
+- `omics$feature_merge` is optional in `omics$foldchange`
+- `omics$removeNAs` uses `stats::complete.cases` instead of `na.omit`
+
 # OmicFlow 1.6.0 (2026-05-19)
 
 ## Added

NEWS.md

@@ -2,11 +2,9 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom magrittr %>%
 #' @importFrom data.table := .SD
-#' @importFrom stats na.omit p.adjust
-#' @useDynLib OmicFlow, .registration = TRUE
 #' @importFrom Rcpp sourceCpp
+#' @useDynLib OmicFlow, .registration = TRUE
 #' @importFrom utils globalVariables
 ## usethis namespace: end
 

R/OmicFlow-package.R

@@ -12,8 +12,8 @@
 #' When weighted is set to FALSE, counts are replaced by presence/absence data.
 #'
 #' @param x A \link[base]{matrix}, \link[Matrix]{sparseMatrix} or \link[Matrix]{Matrix}.
-#' @param weighted A boolean value, to use abundances (\code{weighted = TRUE}) or absence/presence (\code{weighted=FALSE}) (default: TRUE).
-#' @param threads A wholenumber, the number of threads to use in \link[RcppParallel]{setThreadOptions} (default: 1).
+#' @param weighted A boolean value, to use abundances (\code{weighted = TRUE}) or absence/presence (\code{weighted=FALSE}) (default: \code{TRUE}).
+#' @param threads A wholenumber, the number of threads to use in \link[RcppParallel]{setThreadOptions} (default: \code{1}).
 #' @return A column x column \link[stats]{dist} object.
 #' @references
 #' Bray, J.R. & Curtis, J.T. (1957) An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecological Monographs, 27(4), 325–349.
@@ -36,17 +36,15 @@
 #' taxa$scale(method = "tss")
 #'
 #' bray(taxa$countData)
-#' @importFrom RcppParallel setThreadOptions
 #' @importFrom Matrix sparseMatrix
-#' @importFrom stats as.dist
 #' @export
 
 bray <- function(x, weighted = TRUE, threads = 1) {
 
     ## Error handling
     #--------------------------------------------------------------------#
     if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
-        x <- as(x, "CsparseMatrix")
+        x <- methods::as(x, "CsparseMatrix")
     } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
 
     if (!is.numeric(x@x))
@@ -67,5 +65,5 @@ bray <- function(x, weighted = TRUE, threads = 1) {
     if (!is.null(col_names))
         dimnames(out) <- list(col_names, col_names)
 
-    return(as.dist(out))
+    return(stats::as.dist(out))
 }

R/bray.R

@@ -11,9 +11,7 @@
 #' where \eqn{A_i} and \eqn{B_i} are the abundances of the \eqn{i}-th feature in sample \eqn{A} and \eqn{B}, respectively. NZ are the number of non-zero entries.
 #' When weighted is set to FALSE, counts are replaced by presence/absence data.
 #'
-#' @param x A \link[base]{matrix}, \link[Matrix]{sparseMatrix} or \link[Matrix]{Matrix}.
-#' @param weighted A boolean value, to use abundances (\code{weighted = TRUE}) or absence/presence (\code{weighted=FALSE}) (default: TRUE).
-#' @param threads A wholenumber, the number of threads to use in \link[RcppParallel]{setThreadOptions} (default: 1).
+#' @inheritParams bray
 #' @return A column x column \link[stats]{dist} object.
 #' @references
 #' Lance, G.N. & Williams, W.T. (1967) Mixed-data classificatory programs. I. Agglomerative systems. Australian Computer Journal, 1(1), 15-20.
@@ -36,9 +34,7 @@
 #' taxa$scale(method = "tss")
 #'
 #' canberra(taxa$countData)
-#' @importFrom RcppParallel setThreadOptions
 #' @importFrom Matrix sparseMatrix
-#' @importFrom stats as.dist
 #' @export
 
 canberra <- function(x, weighted = TRUE, threads = 1) {
@@ -49,7 +45,7 @@ canberra <- function(x, weighted = TRUE, threads = 1) {
         cli::cli_abort("Input must a matrix of class matrix or Matrix, not a vector.")
 
     if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
-        x <- as(x, "CsparseMatrix")
+        x <- methods::as(x, "CsparseMatrix")
     } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
 
     if (!is.numeric(x@x))
@@ -70,5 +66,5 @@ canberra <- function(x, weighted = TRUE, threads = 1) {
     if (!is.null(col_names))
         dimnames(out) <- list(col_names, col_names)
 
-    return(as.dist(out))
+    return(stats::as.dist(out))
 }

R/canberra.R

@@ -18,7 +18,6 @@
 #'
 #' colors <- colormap(data = dt,
 #'                    col_name = "treatment")
-#' @importFrom RColorBrewer brewer.pal.info brewer.pal
 #' @export
 
 colormap <- function(data,

R/colormap.R

@@ -9,12 +9,8 @@
 #' @param title_name A character to set the \code{ggtitle} of the \link[ggplot2]{ggplot}, (Default: NULL).
 #' @param group_by A character variable to aggregate the stacked bars by group (Default: NULL).
 #' @return A \link[ggplot2]{ggplot2} object to be further modified
-#'
-#' @importFrom ggplot2 ggplot aes .data geom_bar coord_flip theme_bw theme element_text scale_x_discrete scale_fill_manual labs ggtitle
 #' 
 #' @examples
-#' library("ggplot2")
-#' 
 #' # Create mock_data as data.frame (data.table is also supported)
 #' mock_data <- data.frame(
 #'   SAMPLE_ID = rep(paste0("Sample", 1:10), each = 5),
@@ -67,6 +63,7 @@
 #'   title_name = "Mock Genus Composition by Group",
 #'   group_by = "Group"
 #' )
+#' @import ggplot2
 #' @export
 
 composition_plot <- function(data,
@@ -108,51 +105,60 @@ composition_plot <- function(data,
 
   # Generates a stacked barplot as base with custome palette
   if (!is.null(group_by)) {
-    plt <- data %>%
-      ggplot(mapping = aes(y = .data[["value"]],
-                           x = as.factor(.data[[ group_by ]]),
-                           fill = .data[[ feature_rank ]]))
+    plt <- ggplot2::ggplot(
+      data = data,
+      mapping = ggplot2::aes(
+        y = .data[["value"]],
+        x = as.factor(.data[[ group_by ]]),
+        fill = .data[[ feature_rank ]]
+      )
+    )
   } else {
-    plt <- data %>%
-      ggplot(mapping = aes(y = .data[["value"]],
-                           x = .data[["SAMPLE_ID"]],
-                           fill = base::get(feature_rank, data)))
+    plt <- ggplot2::ggplot(
+      data = data, 
+      mapping = ggplot2::aes(
+        y = .data[["value"]],
+        x = .data[["SAMPLE_ID"]],
+        fill = base::get(feature_rank, data)
+      )
+    )
   }
   # Required for stacked barplot
   plt <- plt +
-    geom_bar(
+    ggplot2::geom_bar(
       position = "fill",
       stat = "identity"
     )
 
   if (is.null(group_by)) {
     plt <- plt +
-      coord_flip()
+      ggplot2::coord_flip()
   }
   plt <- plt +
-    theme_bw() +
-    theme(
-      plot.title = element_text(size = 14, face = "bold"),
-      plot.subtitle = element_text(size = 13),
-      axis.text.x = element_text(angle = 90, size = 12,
-                                 vjust = 0.5, hjust=1,
-                                 colour = "black"),
-      axis.title.y = element_text(size = 12),
-      axis.title.x = element_text(size = 12, vjust=0.5),
-      legend.title = element_text(size = 14, face = "bold"),
-      legend.text = element_text(size = 12, colour = "black"),
-      axis.text.y = element_text(colour = "black", size = 12)
+    ggplot2::theme_bw() +
+    ggplot2::theme(
+      plot.title = ggplot2::element_text(size = 14, face = "bold"),
+      plot.subtitle = ggplot2::element_text(size = 13),
+      axis.text.x = ggplot2::element_text(
+        angle = 90, size = 12,
+        vjust = 0.5, hjust=1,
+        colour = "black"
+      ),
+      axis.title.y = ggplot2::element_text(size = 12),
+      axis.title.x = ggplot2::element_text(size = 12, vjust=0.5),
+      legend.title = ggplot2::element_text(size = 14, face = "bold"),
+      legend.text = ggplot2::element_text(size = 12, colour = "black"),
+      axis.text.y = ggplot2::element_text(colour = "black", size = 12)
     )
 
   if (is.null(group_by)) {
     plt <- plt +
-      scale_x_discrete(limits = rev(levels(as.factor(data[["SAMPLE_ID"]]))))
+      ggplot2::scale_x_discrete(limits = rev(levels(as.factor(data[["SAMPLE_ID"]]))))
   }
   plt <- plt +
-    scale_fill_manual(values = palette, name = feature_rank) +
-    labs(y = "Rel. Abun.",
-         x = NULL) +
-    ggtitle(title_name)
+    ggplot2::scale_fill_manual(values = palette, name = feature_rank) +
+    ggplot2::labs(y = "Rel. Abun.", x = NULL) +
+    ggplot2::ggtitle(title_name)
 
   return(plt)
 }