Merge pull request #28 from agusinac/dev

v1.5

Author: agusinac

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

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main]
+    branches: [dev]
   pull_request:
-    branches: [main]
+    branches: [dev]
 
 name: R-CMD-check.yaml
 
@@ -22,9 +22,7 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docker-build-push.yaml

@@ -3,6 +3,31 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.5.0 - [2026-01-26]
+
+### `Added`
+- [#23](https://github.com/agusinac/OmicFlow/issues/23) active bindings on data types, in place modification and automatic synchronisation between other data types by default via private function `sync`.
+- [#23](https://github.com/agusinac/OmicFlow/issues/23) `featureData` is now always created as placeholder.
+
+### `Changed`
+- [#23](https://github.com/agusinac/OmicFlow/issues/23) omics classes are now cloneable.
+- [#23](https://github.com/agusinac/OmicFlow/issues/23) `removeZeros()` function is now private.
+- [#26](https://github.com/agusinac/OmicFlow/issues/26) clarified `initialize` and field tags.
+- [#27](https://github.com/agusinac/OmicFlow/issues/27) Both `denseMatrix` as `sparseMatrix` are converted to `CsparseMatrix`, compatible to `omics$normalize`, `omics$feature_merge`, `diversity`, `hill_taxa` and `C-functions`. 
+- Replaced `tmp_link` and `tmp_restore` with inline code. Seems like `private$.countData` doesn't work with a private function.
+- Improved the `cli` formatting and visualisation of different arguments.
+- `print()` inherited for each sub-class from `omics` and uses `cli::cli_inform` instead of `cat`
+- [#21](https://github.com/agusinac/OmicFlow/issues/21) introduced custom half boxplot/point in `diversity_plot`, now also added `group_by` to perform grouped statistical tests.
+- Replaced `read_rarefraction_qiime` by `check_table` from private function of class `omics.`
+- `autoFlow` compatible to denseMatrix formats, applies fdr correction in other omics layers, report can be set to False, removed `nmds`.
+
+### `Fixed`
+- [#25](https://github.com/agusinac/OmicFlow/issues/25) changed default value of `initialize` function.
+
+### `Deprecated`
+- Removed `tmp_restore` and `tmp_link`
+- Utils function `read_rarefraction_qiime`
+
 ## v1.4.2 - [2025-11-30]
 
 ### `Fixed`
@@ -17,7 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#22](https://github.com/agusinac/OmicFlow/issues/22) `private$check_matrix` checks if any zero's are present before creating a `sparseMatrix`.
 - [#20](https://github.com/agusinac/OmicFlow/issues/20) `omics$compositon` Doesn't show `Others` when there are none.
 - [#24](https://github.com/agusinac/OmicFlow/issues/24) `volcano_plot` only sizes the points if there are significant features found.
-
+ 
 ### `Deprecated`
 - [#21](https://github.com/agusinac/OmicFlow/issues/21) Removed `gghalves` in `diversity_plot`
 

CHANGELOG.md

@@ -1,7 +1,7 @@
 Package: OmicFlow
 Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
-Version: 1.4.2
-Date: 2025-11-30
+Version: 1.5.0
+Date: 2026-01-26
 Authors@R: c(
     person(
         "Alem", "Gusinac",
@@ -52,12 +52,12 @@ Imports:
     tools,
     utils,
     vegan,
-    yyjsonr
+    yyjsonr,
+    cli
 Suggests: 
     DT,
     downloadthis,
     rmarkdown,
-    cli,
     testthat (>= 3.0.0)
 LinkingTo:
     Rcpp,

DESCRIPTION

@@ -13,15 +13,14 @@ export(hill_taxa)
 export(jaccard)
 export(jsd)
 export(manhattan)
+export(matrix_to_dtable)
 export(metagenomics)
 export(omics)
 export(ordination_plot)
 export(pairwise_adonis)
 export(pairwise_anosim)
 export(plot_pairwise_stats)
 export(proteomics)
-export(read_rarefraction_qiime)
-export(sparse_to_dtable)
 export(unifrac)
 export(volcano_plot)
 import(Matrix)
@@ -39,19 +38,23 @@ 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_nudge)
 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)
@@ -64,9 +67,12 @@ 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,validate_json_file)
 useDynLib(OmicFlow, .registration = TRUE)

NAMESPACE

@@ -7,5 +7,8 @@
 #' @importFrom stats na.omit p.adjust
 #' @useDynLib OmicFlow, .registration = TRUE
 #' @importFrom Rcpp sourceCpp
+#' @importFrom utils globalVariables
 ## usethis namespace: end
+
+utils::globalVariables(c(".", "group_col"))
 NULL

R/OmicFlow-package.R

@@ -1,7 +1,7 @@
-#' Compute Bray-Curtis Dissimilarity from a Sparse Matrix.
+#' Compute Bray-Curtis Dissimilarity from a Dense or Sparse Matrix.
 #'
 #' @description 
-#' Calculates the Bray-Curtis dissimilarity of a \link[Matrix]{sparseMatrix} pairwise for each column. 
+#' Calculates the Bray-Curtis dissimilarity of a Matrix pairwise for each column.
 #' 
 #' @details
 #' The Bray-Curtis dissimilarity between two samples \eqn{A} and \eqn{B}, each of length \eqn{n}, is defined as:
@@ -11,7 +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. 
 #' When weighted is set to FALSE, counts are replaced by presence/absence data.
 #'
-#' @param x A \link[Matrix]{sparseMatrix}.
+#' @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).
 #' @return A column x column \link[stats]{dist} object.
@@ -45,15 +45,15 @@ bray <- 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.")
+    if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
+        x <- as(x, "CsparseMatrix")
+    } else cli::cli_abort("Input isn't a {.cls matrix}, {.cls denseMatrix} or {.cls sparseMatrix}.")
 
-    x <- drop(as(x, "sparseMatrix"))
     if (!is.numeric(x@x))
         cli::cli_abort("Input data must be numeric.")
 
     if (!is.wholenumber(threads))
-        cli::cli_abort("{threads} must be a whole number.")
+        cli::cli_abort("{.val {threads}} must be a whole number.")
 
     ## MAIN
     #--------------------------------------------------------------------#

R/bray.R

@@ -1,7 +1,7 @@
-#' Compute Canberra Dissimilarity from a Sparse Matrix.
+#' Compute Canberra Dissimilarity from a from a Dense or Sparse Matrix.
 #'
 #' @description 
-#' Calculates the Canberra dissimilarity of a \link[Matrix]{sparseMatrix} pairwise for each column.
+#' Calculates the Canberra dissimilarity of a Matrix pairwise for each column.
 #' 
 #' @details
 #' The Canberra dissimilarity between two samples \eqn{A} and \eqn{B}, each of length \eqn{n}, is defined as:
@@ -11,7 +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[Matrix]{sparseMatrix}.
+#' @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).
 #' @return A column x column \link[stats]{dist} object.
@@ -48,12 +48,15 @@ canberra <- function(x, weighted = TRUE, threads = 1) {
     if (is.vector(x))
         cli::cli_abort("Input must a matrix of class matrix or Matrix, not a vector.")
 
-    x <- drop(as(x, "sparseMatrix"))
+    if (inherits(x, "denseMatrix") || inherits(x, "matrix") || inherits(x, "sparseMatrix")) {
+        x <- 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 numeric.")
 
     if (!is.wholenumber(threads))
-        cli::cli_abort("{threads} must be a whole number.")
+        cli::cli_abort("{.val {threads}} must be a whole number.")
 
     ## MAIN
     #--------------------------------------------------------------------#

R/canberra.R

@@ -28,22 +28,24 @@ colormap <- function(data,
   #--------------------------------------------------------------------#
 
   if (!inherits(data, "data.frame") && !inherits(data, "data.table"))
-    cli::cli_abort("Data must be a data.frame or data.table.")
+    cli::cli_abort("Data must be a {.cls data.frame} or {.cls data.table}.")
 
   if (!is.character(col_name) && length(col_name) != 1) {
-    cli::cli_abort("Column name: {col_name} needs to contain characters with length of 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 {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 {Brewer.palID} needs to contain characters with length of 1.")
+    cli::cli_abort("The {.val {Brewer.palID}} needs to contain characters with length of 1.")
 
   ## MAIN
   #--------------------------------------------------------------------#
 
   unique_groups <- unique(data[[col_name]])
-  chosen_palette <- RColorBrewer::brewer.pal(length(unique_groups), Brewer.palID)
+  suppressWarnings(
+    chosen_palette <- RColorBrewer::brewer.pal(length(unique_groups), Brewer.palID)
+  )
   colors <- stats::setNames(chosen_palette, unique_groups)
   return(colors)
 }

R/colormap.R

@@ -78,27 +78,27 @@ composition_plot <- function(data,
   #--------------------------------------------------------------------#
 
   if (!inherits(data, "data.frame") && !inherits(data, "data.table"))
-    cli::cli_abort("Data must be a data.frame or data.table.")
+    cli::cli_abort("Data must be a {.cls data.frame} or {.cls data.table}.")
 
   if (!is.character(palette))
-    cli::cli_abort("{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("{feature_rank} needs to contain characters with length of 1.")
+    cli::cli_abort("{.val {feature_rank}} needs to contain characters with length of 1.")
 
   if (!is.null(title_name) && !is.character(title_name))
-    cli::cli_abort("{title_name} needs to be of type character.")
+    cli::cli_abort("{.val {title_name}} needs to be of type character.")
 
   if (!is.null(group_by)) {
     if (!is.character(group_by) && length(group_by) != 1) {
-      cli::cli_abort("{group_by} must be a character and of length 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 {group_by} does not exist in the metaData.")
+      cli::cli_abort("The specified {.val {group_by}} does not exist in the provided {.arg data}.")
     }
   }
 
   if (!column_exists("SAMPLE_ID", data))
-    cli::cli_abort("SAMPLE_ID needs to exist within the provided data.frame/data.table.")
+    cli::cli_abort("{.arg SAMPLE_ID} needs to exist within the provided {.arg data}.")
 
   ## MAIN
   #--------------------------------------------------------------------#