Merge branch 'dev' into add-parallelism

Author: agusinac

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OmicFlow
 Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
-Version: 1.6.0.9002
-Date: 2026-05-19
+Version: 1.6.0.9004
+Date: 2026-08-03
 Authors@R: c(
     person(
         "Alem", "Gusinac",
@@ -22,32 +22,34 @@ Description:
     which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class. 
     Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.
 License: MIT + file LICENSE
-URL: https://github.com/agusinac/OmicFlow, https://agusinac.github.io/OmicFlow/
+URL: https://agusinac.github.io/OmicFlow/
 BugReports: https://github.com/agusinac/OmicFlow/issues
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Depends: 
     R (>= 4.3.0)
 Imports:
-    R6,
-    data.table,
-    Matrix,
     ape,
+    cli,
+    data.table,
     ggpubr,
     ggrepel,
     ggplot2,
     jsonvalidate,
     methods,
+    Matrix,
     patchwork,
+    R6,
     RColorBrewer,
     rhdf5,
     rstatix,
     Rcpp (>= 0.12.6),
     RcppParallel (>= 4.3.20),
+    stats,
+    utils,
     vegan,
-    yyjsonr,
-    cli
+    yyjsonr
 Suggests: 
     DT,
     downloadthis,

NAMESPACE

@@ -3,7 +3,6 @@
 export(bray)
 export(canberra)
 export(colormap)
-export(column_exists)
 export(composition_plot)
 export(cosine)
 export(diversity)
@@ -13,7 +12,6 @@ export(hill_taxa)
 export(jaccard)
 export(jsd)
 export(manhattan)
-export(matrix_to_dtable)
 export(metagenomics)
 export(omics)
 export(ordination_plot)
@@ -29,6 +27,8 @@ import(ggplot2)
 import(rhdf5)
 importFrom(Matrix,sparseMatrix)
 importFrom(Rcpp,sourceCpp)
+importFrom(RcppParallel,RcppParallelLibs)
+importFrom(RcppParallel,setThreadOptions)
 importFrom(ape,read.tree)
 importFrom(data.table,":=")
 importFrom(data.table,.SD)

NEWS.md

@@ -1,12 +1,9 @@
-# OmicFlow 1.6.0.9003
+# OmicFlow 1.6.0.9005
 
 ## Changed
-- Re-factoring `roxygen2` code & documentation style & error handling.
-    - Follow order of `tests/testthat.R` file
-    - Finished:
-        - test-omics.R
-        - test-metagenomics.R
+- Re-factoring and improving `roxygen2` code, documentation style and error handling.
 - TODO: Add `tryCatch` where neccessary
+- Added `tryCatch` and better error handling in `omics$sample_subset`, `omics$feature_subset` and `omics$samplepair_subset`.
 - 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.
 - Re-combined `foldchange` into `omics` and option to use different fold-change computations via argument `method`.

R/OmicFlow-package.R

@@ -3,8 +3,10 @@
 
 ## usethis namespace: start
 #' @importFrom data.table := .SD
-#' @importFrom Rcpp sourceCpp
 #' @useDynLib OmicFlow, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
+#' @importFrom RcppParallel RcppParallelLibs
+#' @importFrom RcppParallel setThreadOptions
 #' @importFrom utils globalVariables
 ## usethis namespace: end
 

R/bray.R

@@ -43,15 +43,24 @@ bray <- function(x, weighted = TRUE, threads = 1) {
 
     ## Error handling
     #--------------------------------------------------------------------#
+    if (is.vector(x))
+        cli::cli_abort("{.val x} must be a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}, not a {.cls vector}.")
+    
     if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
         x <- methods::as(x, "CsparseMatrix")
-    } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
-
+    } else cli::cli_abort("{.val x} isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
+    
     if (!is.numeric(x@x))
-        cli::cli_abort("Input data must be numeric.")
+        cli::cli_abort("{.val x} must be numeric.")
+
+    if (!is.logical(weighted))
+        cli::cli_abort("{.val weighted} needs to be either `TRUE` or `FALSE`.")
 
-    if (!is.wholenumber(threads))
-        cli::cli_abort("{.val {threads}} must be a whole number.")
+    if (length(threads) != 1) {
+        cli::cli_abort("{.val threads} must be a single whole number.")
+    } else if (!is.wholenumber(threads)) {
+        cli::cli_abort("{.val threads} must be a whole number.")
+    }
 
     ## MAIN
     #--------------------------------------------------------------------#

R/canberra.R

@@ -42,17 +42,23 @@ canberra <- function(x, weighted = TRUE, threads = 1) {
     ## Error handling
     #--------------------------------------------------------------------#
     if (is.vector(x))
-        cli::cli_abort("Input must a matrix of class matrix or Matrix, not a vector.")
-
+        cli::cli_abort("{.val x} must be a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}, not a {.cls vector}.")
+    
     if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
         x <- methods::as(x, "CsparseMatrix")
-    } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
-
+    } else cli::cli_abort("{.val x} isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
+    
     if (!is.numeric(x@x))
-        cli::cli_abort("Input data must be numeric.")
+        cli::cli_abort("{.val x} must be numeric.")
+
+    if (!is.logical(weighted))
+        cli::cli_abort("{.val weighted} needs to be either `TRUE` or `FALSE`.")
 
-    if (!is.wholenumber(threads))
-        cli::cli_abort("{.val {threads}} must be a whole number.")
+    if (length(threads) != 1) {
+        cli::cli_abort("{.val threads} must be a single whole number.")
+    } else if (!is.wholenumber(threads)) {
+        cli::cli_abort("{.val threads} must be a whole number.")
+    }
 
     ## MAIN
     #--------------------------------------------------------------------#

R/colormap.R

@@ -1,7 +1,7 @@
 #' Color map of a variable
 #'
 #' @description Creates an object of hexcode colors with names given a vector of characters.
-#' This function is built into the \code{ordination} method from the abstract class \link{omics} and inherited by other omics classes, such as;
+#' This function is built into the \code{composition} method from the abstract class \link{omics} and inherited by other omics classes, such as;
 #' \link{metagenomics} and \link{proteomics}.
 #'
 #' @param data A \link[base]{data.frame} or \link[data.table]{data.table}.
@@ -29,18 +29,18 @@ colormap <- function(data,
   OPTIONS <- rownames(RColorBrewer::brewer.pal.info)
 
   if (!inherits(data, "data.frame") && !inherits(data, "data.table"))
-    cli::cli_abort("Data must be a {.cls data.frame} or {.cls data.table}.")
+    cli::cli_abort("{.val data} must be a {.cls data.frame} or {.cls data.table}.")
 
-  if (!is.character(col_name) && length(col_name) != 1) {
-    cli::cli_abort("{.val {col_name}} needs to contain characters with length of 1.")
+  if (!is.character(col_name) || length(col_name) != 1) {
+    cli::cli_abort("{.val col_name} needs to contain characters with length of 1.")
   } else if (!column_exists(col_name, data)) {
-    cli::cli_abort("The {.val {col_name}} column does not exist in the provided data.")
+    cli::cli_abort("The {.val col_name} column does not exist in the provided data.")
   }
 
-  if (!is.character(Brewer.palID) && length(Brewer.palID) != 1) {
-    cli::cli_abort("The {.val {Brewer.palID}} needs to contain characters with length of 1.")
+  if (!is.character(Brewer.palID) || length(Brewer.palID) != 1) {
+    cli::cli_abort("The {.val Brewer.palID} needs to contain characters with length of 1.")
   } else if (!c(Brewer.palID %in% OPTIONS)) {
-    cli::cli_abort("{.val {Brewer.palID}} is not a valid Brewer pal ID. \nValid options: {.val {OPTIONS}}.")
+    cli::cli_abort("{.val Brewer.palID} is not a valid Brewer pal ID. \nValid options: {.val {OPTIONS}}.")
   }
 
   ## MAIN

R/composition_plot.R

@@ -4,10 +4,10 @@
 #' The function is compatible with the class \link{omics} method \code{composition()}.
 #'
 #' @param data A \link[base]{data.frame} or \link[data.table]{data.table}.
-#' @param palette An object with names and hexcode or color names, see \link{colormap}.
-#' @param feature_rank A character variable of the feature column.
-#' @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).
+#' @param palette A \link[stats]{setNames}, see \link{colormap}.
+#' @param feature_rank A column name containing the feature names.
+#' @param title_name A character to set the \code{ggtitle} of the \link[ggplot2]{ggplot}, (default: \code{NULL}).
+#' @param group_by A character variable to aggregate the stacked bars by group (default: \code{NULL}).
 #' @return A \link[ggplot2]{ggplot2} object to be further modified
 #' 
 #' @examples
@@ -75,30 +75,33 @@ composition_plot <- function(data,
   #--------------------------------------------------------------------#
 
   if (!inherits(data, "data.frame") && !inherits(data, "data.table"))
-    cli::cli_abort("Data must be a {.cls data.frame} or {.cls data.table}.")
+    cli::cli_abort("{.val data} must be a {.cls data.frame} or {.cls data.table}.")
 
   if (!is.character(palette))
-    cli::cli_abort("{.val {palette}} needs to contain characters.")
+    cli::cli_abort("{.val palette} needs to contain characters.")
 
-  if (!is.character(feature_rank) && length(feature_rank) != 1) {
-    cli::cli_abort("{.val {feature_rank}} needs to contain characters with length of 1.")
+  if (!is.character(feature_rank) || length(feature_rank) != 1) {
+    cli::cli_abort("{.val feature_rank} needs to contain characters with length of 1.")
   } else if (!column_exists(feature_rank, data)) {
-    cli::cli_abort("The {.val {feature_rank}} column does not exist in the provided {.arg data}.")
+    cli::cli_abort("The {.val {feature_rank}} column does not exist in the provided {.val data}.")
   }
 
-  if (!is.null(title_name) && !is.character(title_name))
-    cli::cli_abort("{.val {title_name}} needs to be of type character.")
+  if (!is.null(title_name)) {
+    if (!is.character(title_name) || length(title_name) != 1) {
+      cli::cli_abort("{.val title_name} must be a character and of length 1")
+    }
+  }
 
   if (!is.null(group_by)) {
-    if (!is.character(group_by) && length(group_by) != 1) {
-      cli::cli_abort("{.val {group_by}} must be a character and of length 1")
+    if (!is.character(group_by) || length(group_by) != 1) {
+      cli::cli_abort("{.val group_by} must be a character and of length 1")
     } else if (!column_exists(group_by, data)) {
-      cli::cli_abort("The specified {.val {group_by}} does not exist in the provided {.arg data}.")
+      cli::cli_abort("The specified {.val {group_by}} does not exist in the provided {.val data}.")
     }
   }
 
   if (!column_exists("SAMPLE_ID", data))
-    cli::cli_abort("{.arg SAMPLE_ID} needs to exist within the provided {.arg data}.")
+    cli::cli_abort("{.arg SAMPLE_ID} needs to exist within the provided {.val data}.")
 
   ## MAIN
   #--------------------------------------------------------------------#

R/cosine.R

@@ -41,15 +41,24 @@ cosine <- function(x, weighted = TRUE, threads = 1) {
 
     ## Error handling
     #--------------------------------------------------------------------#
+    if (is.vector(x))
+        cli::cli_abort("{.val x} must be a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}, not a {.cls vector}.")
+    
     if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
         x <- methods::as(x, "CsparseMatrix")
-    } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
-
+    } else cli::cli_abort("{.val x} isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
+    
     if (!is.numeric(x@x))
-        cli::cli_abort("Input data must be numeric.")
+        cli::cli_abort("{.val x} must be numeric.")
+    
+    if (!is.logical(weighted))
+        cli::cli_abort("{.val weighted} needs to be either `TRUE` or `FALSE`.")
 
-    if (!is.wholenumber(threads))
-        cli::cli_abort("{.val {threads}} must be a whole number.")
+    if (length(threads) != 1) {
+        cli::cli_abort("{.val threads} must be a single whole number.")
+    } else if (!is.wholenumber(threads)) {
+        cli::cli_abort("{.val threads} must be a whole number.")
+    }
 
     ## MAIN
     #--------------------------------------------------------------------#

R/diversity.R

@@ -42,31 +42,33 @@
 #' @export
 
 diversity <- function(x,
-                      metric = c("shannon", "simpson", "invsimpson"),
+                      metric = "shannon",
                       normalize = TRUE,
                       base = exp(1)) {
 
   ## Error handling
   #--------------------------------------------------------------------#
-
+  if (is.vector(x))
+      cli::cli_abort("{.val x} must be a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}, not a {.cls vector}.")
+  
   if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
     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))
-    cli::cli_abort("Input data must be {.cls numeric} type")
+  } else cli::cli_abort("{.val x} isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
 
   if (any(x@x < 0, na.rm = TRUE))
-    cli::cli_abort("Input data must be non-negative")
+    cli::cli_abort("{.val x} must be non-negative.")
 
-  if (!is.numeric(base))
-    cli::cli_abort("{.val {base}} needs to be a {.cls numeric} type.")
+  if (!is.logical(normalize))
+    cli::cli_abort("{.val normalize} needs to be either `TRUE` or `FALSE`.")
+
+  if (!is.numeric(base) || length(base) != 1)
+    cli::cli_abort("{.val base} needs to be a {.cls numeric} type with length of 1.")
 
   OPTIONS <- c("shannon", "simpson", "invsimpson")
-  if (!is.character(metric) && length(metric) != 1) {
-    cli::cli_abort("{.val {metric}} needs to contain characters with length of 1.")
+  if (!is.character(metric) || length(metric) != 1) {
+    cli::cli_abort("{.val metric} needs to contain characters with length of 1.")
   } else if (!metric %in% OPTIONS) {
-    cli::cli_abort("{.val {metric}} is not a valid metric. Valid options: <{.val {OPTIONS}}>")
+    cli::cli_abort("{.val {metric}} is not a valid {.arg metric}.\nValid options: <{.val {OPTIONS}}>")
   }
 
   ## MAIN