wrapped up omics-tests

Author: agusinac

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: OmicFlow
 Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
-Version: 1.6.0.9003
+Version: 1.6.0.9004
 Date: 2026-08-03
 Authors@R: c(
     person(

NEWS.md

@@ -11,6 +11,9 @@
         - test-omics-ordination.R
         - test-omics-feature_merge.R
         - test-omics-composition.R
+        - test-omics-alpha_diversity.R
+        - test-omics-autoFlow.R [SKIP, finish later with issue #43]
+        - test-omics-foldchange.R [SKIP, finish later with issue #43]
         - test-metagenomics.R
         - test-metagenomics-write_biom.R
         - test-proteomics.R

R/omics-class.R

@@ -839,12 +839,12 @@ omics <- R6::R6Class(
     #' @description
     #' Alpha diversity based on \link{diversity}
     #' @param col_name A character variable from the `metaData`.
-    #' @param metric An alpha diversity metric as input to \link{diversity}.
-    #' @param group_by A column name to perform grouped statistical test in \link{diversity_plot} (default: NULL).
+    #' @param metric An alpha diversity metric as input to \link{diversity} (default: \code{"shannon"}).
+    #' @param group_by A column name to perform grouped statistical test in \link{diversity_plot} (default: \code{NULL}).
     #' @param Brewer.palID A character name for the palette set to be applied, see \link[RColorBrewer]{brewer.pal} or \link{colormap}.
     #' @param evenness A boolean wether to divide diversity by number of species, see \link[vegan]{specnumber}.
     #' @param paired A boolean value to perform paired analysis in \link[stats]{wilcox.test} and samplepair subsetting via [`samplepair_subset()`](#method-samplepair_subset)
-    #' @param p.adjust.method A character variable to specify the p.adjust.method to be used, default is 'fdr'.
+    #' @param p.adjust.method A character variable to specify the p.adjust.method to be used (default: \code{'fdr'}).
     #' @examples
     #' library("OmicFlow")
     #'
@@ -868,7 +868,7 @@ omics <- R6::R6Class(
     #' }
     #' @seealso \link{diversity_plot}
     alpha_diversity = function(col_name,
-                               metric = c("shannon", "invsimpson", "simpson"),
+                               metric = "shannon",
                                Brewer.palID = "Set2",
                                group_by = NULL,
                                evenness = FALSE,
@@ -884,6 +884,21 @@ omics <- R6::R6Class(
         cli::cli_abort("The specified {.val {col_name}} does not exist in the {.field metaData}.")
       }
 
+      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")
+        } else if (!column_exists(group_by, private$.metaData)) {
+          cli::cli_abort("The specified {.val {group_by}} does not exist in the {.field metaData}.")
+        }
+        combined_cols <- c(col_name, group_by)
+      } else combined_cols <- col_name
+
+      if (!is.logical(evenness))
+        cli::cli_abort("{.val evenness} can only be a `TRUE` or `FALSE`.")
+      
+      if (!is.logical(paired))
+        cli::cli_abort("{.val paired} can only be a `TRUE` or `FALSE`.")
+
       if (!c(p.adjust.method %in% stats::p.adjust.methods))
         cli::cli_abort("Specified {.val {p.adjust.method}} is not valid. \nValid options: {.val {p.adjust.methods}}")
 
@@ -907,15 +922,8 @@ omics <- R6::R6Class(
         private$.treeData <- .treeData
       }, add = TRUE)
 
-      # Remove NAs when col_name is specified
-      if (!is.null(col_name))
-        self$removeNAs(col_name)
-
-      if (!is.null(group_by)) {
-        combined_cols <- c(col_name, group_by)
-      } else {
-        combined_cols <- col_name
-      }
+      # Remove NAs from `col_name`
+      self$removeNAs(col_name)
 
       # Subset by samplepair completion
       if ( paired && column_exists(private$.samplepair_id, private$.metaData) )
@@ -1702,13 +1710,6 @@ omics <- R6::R6Class(
       cli::cli_abort("{.val {feature_contrast}} does not exist in {.field featureData}!")
     }
 
-    if (!is.null(distmat) && !is.character(distmat) || length(distmat) != 1) {
-      cli::cli_abort("{.arg distmat} needs to be a character with a length of 1")
-    
-      if (!file.exists(distmat))
-        cli::cli_abort("{.arg distmat} does not exists!")
-    }
-
     ## MAIN
     #--------------------------------------------------------------------#
     is_empty = function(obj) {

man/omics.Rd

@@ -18,7 +18,7 @@ counts_dense_file <- system.file("extdata", "counts_dense.tsv", package = "OmicF
 features_file <- system.file("extdata", "features.tsv", package = "OmicFlow")
 
 ## Start tests per section
-# test_check("OmicFlow", filter = "omics")
+test_check("OmicFlow", filter = "omics")
 test_check("OmicFlow", filter = "metagenomics")
 test_check("OmicFlow", filter = "proteomics")
 # test_check("OmicFlow", filter = "metrics")

tests/testthat.R

@@ -14,11 +14,3 @@
       Error in `taxa$write_biom()`:
       ! file1.biom and file2.biom Needs to contain characters and be length of 1.
 
----
-
-    Code
-      taxa$write_biom(filename = output_file)
-    Condition
-      Error in `taxa$write_biom()`:
-      ! C:\Users\Z289224\AppData\Local\Temp\Rtmp0MhSOc/test.biom Already exists!
-

tests/testthat/_snaps/metagenomics-write_biom.md

@@ -0,0 +1,130 @@
+# `omics$alpha_diversity()` -- Argument checks
+
+    Code
+      taxa$alpha_diversity(col_name = 1)
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! 1 must be a character and of length 1
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "1")
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! The specified "1" does not exist in the metaData.
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = c("1", "2"))
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! "1" and "2" must be a character and of length 1
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", group_by = 1)
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! 1 must be a character and of length 1
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", group_by = "1")
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! The specified "1" does not exist in the metaData.
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", group_by = c("1", "2"))
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! "1" and "2" must be a character and of length 1
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", evenness = "FALSE")
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! "evenness" can only be a `TRUE` or `FALSE`.
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", paired = "FALSE")
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! "paired" can only be a `TRUE` or `FALSE`.
+
+---
+
+    Code
+      taxa$alpha_diversity(col_name = "CONTRAST_sex", p.adjust.method = "nothing")
+    Condition
+      Error in `taxa$alpha_diversity()`:
+      ! Specified "nothing" is not valid.  Valid options: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none"
+
+# `omics$alpha_diversity()` -- Behavioral checks
+
+    Code
+      adiv$data
+    Output
+               V1 CONTRAST_sex
+            <num>       <char>
+      1: 3.403898         male
+      2: 3.776849       female
+      3: 3.682609       female
+      4: 3.686005         male
+
+---
+
+    Code
+      adiv$stats
+    Output
+        .y. group1 group2 n1 n2 statistic         p     p.adj p.adj.signif y.position
+      1  V1 female   male  2  2         3 0.6666667 0.6666667           ns    3.78792
+              groups xmin xmax
+      1 female, male    1    2
+
+---
+
+    Code
+      taxa
+    Message
+      
+      -- <metagenomics> object 
+      metaData: 9 variables x 4 samples
+      countData: 4 samples x 242 features
+      featureData: 7 attributes x 242 features
+      treeData: 242 tips x 241 nodes
+
+---
+
+    Code
+      adiv$data
+    Output
+               V1 CONTRAST_sex group_col
+            <num>       <char>    <char>
+      1: 3.403898         male     tumor
+      2: 3.776849       female     tumor
+      3: 3.682609       female   healthy
+      4: 3.686005         male   healthy
+
+---
+
+    Code
+      adiv$stats
+    Output
+        treatment .y. group1 group2 n1 n2 statistic p p.adj p.adj.signif y.position
+      1     tumor  V1 female   male  1  1         1 1     1           ns    3.82176
+      2   healthy  V1 female   male  1  1         0 1     1           ns    3.68636
+              groups xmin xmax
+      1 female, male   NA   NA
+      2 female, male   NA   NA
+