diff --git a/NEWS.md b/NEWS.md
index 32462021..c2fc49f8 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 ## MOSuite development version
 
 - Harmonize Volcano Plot output dimensions as physical inches with 300 DPI defaults for Enhanced and Summary plots. (#274, @TJoshMeyer)
+- Build Venn and Intersection plots directly from per-contrast differential expression results, with configurable strict significance and fold-change thresholds and optional contrast selection. (#278, @TJoshMeyer)
 
 ## MOSuite 0.4.2
 
diff --git a/R/plot_venn_diagram.R b/R/plot_venn_diagram.R
index 3a176fe2..3bf5c1e0 100644
--- a/R/plot_venn_diagram.R
+++ b/R/plot_venn_diagram.R
@@ -4,9 +4,18 @@
 #' tested contrasts). This Venn diagram is available for up to five sets; Intersection plot is available for any number
 #' of sets. Specific sets can be selected for the visualizations and the returned dataset may include all (default) or
 #' specified intersections.
-#' An S7 generic with methods for `multiOmicDataSet` and `data.frame`.
+#' An S7 generic for `multiOmicDataSet` inputs.
 #'
-#' @param moo_diff_summary_dat multiOmicDataSet or summarized differential expression analysis data frame.
+#' @param moo_diff_summary_dat multiOmicDataSet containing per-contrast differential expression results.
+#' @param feature_id_colname Feature identifier column in each contrast result. Defaults to the first column.
+#' @param signif_colname Significance column in each contrast result. Default: `"adjpval"`.
+#' @param signif_threshold Features pass the significance threshold when their value is less than this cutoff
+#'   (exclusive). Default: `0.05`.
+#' @param change_colname Log fold-change column in each contrast result. Default: `"logFC"`.
+#' @param change_threshold Features pass the fold-change threshold when their absolute value is greater than this
+#'   cutoff (exclusive). Default: `1.0`.
+#' @param select_contrasts Contrast names to include. If empty, all available contrasts are used.
+#' @inheritParams plot_venn_sets
 #'
 #' @export
 plot_venn_diagram <- S7::new_generic(
@@ -15,7 +24,10 @@ plot_venn_diagram <- S7::new_generic(
   function(
     moo_diff_summary_dat,
     feature_id_colname = NULL,
-    contrasts_colname = "Contrast",
+    signif_colname = "adjpval",
+    signif_threshold = 0.05,
+    change_colname = "logFC",
+    change_threshold = 1.0,
     select_contrasts = c(),
     plot_type = "Venn diagram",
     intersection_ids = c(),
@@ -60,7 +72,10 @@ plot_venn_diagram <- S7::new_generic(
 S7::method(plot_venn_diagram, multiOmicDataSet) <- function(
   moo_diff_summary_dat,
   feature_id_colname = NULL,
-  contrasts_colname = "Contrast",
+  signif_colname = "adjpval",
+  signif_threshold = 0.05,
+  change_colname = "logFC",
+  change_threshold = 1.0,
   select_contrasts = c(),
   plot_type = "Venn diagram",
   intersection_ids = c(),
@@ -97,55 +112,80 @@ S7::method(plot_venn_diagram, multiOmicDataSet) <- function(
   save_plots = options::opt("save_plots"),
   plots_subdir = "diff"
 ) {
+  diff_results <- moo_diff_summary_dat@analyses$diff
+  if (!is.list(diff_results) || length(diff_results) == 0) {
+    stop(
+      "No per-contrast differential expression results found in moo@analyses$diff"
+    )
+  }
+  if (length(select_contrasts) > 0) {
+    missing_contrasts <- setdiff(select_contrasts, names(diff_results))
+    if (length(missing_contrasts) > 0) {
+      stop(glue::glue(
+        "Selected contrasts not found: {paste(missing_contrasts, collapse = ', ')}"
+      ))
+    }
+    diff_results <- diff_results[select_contrasts]
+  }
+  if (is.null(feature_id_colname)) {
+    feature_id_colname <- names(diff_results[[1]])[1]
+  }
+
+  venn_sets <- lapply(diff_results, function(diff_result) {
+    required_columns <- c(feature_id_colname, signif_colname, change_colname)
+    missing_columns <- setdiff(required_columns, names(diff_result))
+    if (length(missing_columns) > 0) {
+      stop(glue::glue(
+        "Required DEG columns not found: {paste(missing_columns, collapse = ', ')}"
+      ))
+    }
+    is_significant <- !is.na(diff_result[[signif_colname]]) &
+      diff_result[[signif_colname]] < signif_threshold
+    has_change <- !is.na(diff_result[[change_colname]]) &
+      abs(diff_result[[change_colname]]) > change_threshold
+    return(unique(diff_result[[feature_id_colname]][
+      is_significant & has_change
+    ]))
+  })
+
   return(
-    moo_diff_summary_dat@analyses$diff |>
-      join_dfs_wide() |>
-      plot_volcano_summary(print_plots = FALSE, save_plots = FALSE) |>
-      plot_venn_diagram(
-        feature_id_colname,
-        contrasts_colname,
-        select_contrasts,
-        plot_type,
-        intersection_ids,
-        venn_force_unique,
-        venn_numbers_format,
-        venn_significant_digits,
-        venn_fill_colors,
-        venn_fill_transparency,
-        venn_border_colors,
-        venn_font_size_for_category_names,
-        venn_category_names_distance,
-        venn_category_names_position,
-        venn_font_size_for_counts,
-        venn_outer_margin,
-        intersections_order,
-        display_empty_intersections,
-        intersection_bar_color,
-        intersection_point_size,
-        intersection_line_width,
-        table_font_size,
-        table_content,
-        graphics_device,
-        dpi,
-        image_width,
-        image_height,
-        plot_filename,
-        print_plots,
-        save_plots,
-        plots_subdir,
-      )
+    plot_venn_sets(
+      venn_sets = venn_sets,
+      plot_type = plot_type,
+      intersection_ids = intersection_ids,
+      venn_force_unique = venn_force_unique,
+      venn_numbers_format = venn_numbers_format,
+      venn_significant_digits = venn_significant_digits,
+      venn_fill_colors = venn_fill_colors,
+      venn_fill_transparency = venn_fill_transparency,
+      venn_border_colors = venn_border_colors,
+      venn_font_size_for_category_names = venn_font_size_for_category_names,
+      venn_category_names_distance = venn_category_names_distance,
+      venn_category_names_position = venn_category_names_position,
+      venn_font_size_for_counts = venn_font_size_for_counts,
+      venn_outer_margin = venn_outer_margin,
+      intersections_order = intersections_order,
+      display_empty_intersections = display_empty_intersections,
+      intersection_bar_color = intersection_bar_color,
+      intersection_point_size = intersection_point_size,
+      intersection_line_width = intersection_line_width,
+      table_font_size = table_font_size,
+      table_content = table_content,
+      graphics_device = graphics_device,
+      dpi = dpi,
+      image_width = image_width,
+      image_height = image_height,
+      plot_filename = plot_filename,
+      print_plots = print_plots,
+      save_plots = save_plots,
+      plots_subdir = plots_subdir
+    )
   )
 }
 
-#' @inheritParams option_params
-#' @inheritParams filter_counts
-#' @inheritParams plot_volcano_enhanced
-#' @inheritParams plot_volcano_summary
+#' Build Venn or UpSet intersections from feature sets
 #'
-#' @param moo_diff_summary_dat Summarized differential expression analysis
-#' @param contrasts_colname Name of the column in `moo_diff_summary_dat` that contains the contrast names (default:
-#'   "Contrast")
-#' @param select_contrasts A vector of contrast names to select for the plot. If empty, all contrasts are used.
+#' @param venn_sets Named list of feature identifier vectors, one per contrast.
 #' @param plot_type Type of plot to generate: "Venn diagram" or "Intersection plot". Default: "Venn diagram"
 #' @param intersection_ids A vector of intersection IDs to select for the plot. If empty, all intersections are used.
 #' @param venn_force_unique If TRUE, forces unique elements in the Venn diagram. Default: TRUE
@@ -169,18 +209,19 @@ S7::method(plot_venn_diagram, multiOmicDataSet) <- function(
 #' @param intersection_line_width Width of the lines in the intersection plot. Default: 0.5
 #' @param table_font_size Font size for the table in the plot. Default: 3
 #' @param table_content Content of the table in the plot. Default: NULL
+#' @param graphics_device Graphics device used to save the plot. Default: `grDevices::png`
+#' @param dpi Dots per inch of the saved plot. Default: 300
+#' @param image_width Saved plot width in pixels. Default: 4000
+#' @param image_height Saved plot height in pixels. Default: 3000
+#' @param plot_filename Filename for the saved plot. Default: `"venn_diagram.png"`
+#' @param print_plots Whether to print plots. Default: `options::opt("print_plots")`
+#' @param save_plots Whether to save plots. Default: `options::opt("save_plots")`
+#' @param plots_subdir Subdirectory for saved plots. Default: `"diff"`
 #'
-#' @keywords plotters
-#'
-#' @examples
-#' plot_venn_diagram(nidap_volcano_summary_dat, print_plots = TRUE)
+#' @keywords internal
 #'
-#' @rdname plot_venn_diagram
-S7::method(plot_venn_diagram, S7::class_data.frame) <- function(
-  moo_diff_summary_dat,
-  feature_id_colname = NULL,
-  contrasts_colname = "Contrast",
-  select_contrasts = c(),
+plot_venn_sets <- function(
+  venn_sets,
   plot_type = "Venn diagram",
   intersection_ids = c(),
   venn_force_unique = TRUE,
@@ -224,34 +265,12 @@ S7::method(plot_venn_diagram, S7::class_data.frame) <- function(
     "UpSetR"
   ))
 
-  if (nrow(moo_diff_summary_dat) == 0) {
-    stop("Dataframe is empty")
-  }
-
-  ### PH:
-  # Input - DEG table from Volcano Summary, I think we need to make this function more generic.
-  #    The input should be the Limma DEG table and maybe be used with the DEG Gene List Template
-  # Output - Venn Diagram Figure + Venn table
-  # Purpose - compare DEGS from different Comparisons
-
-  input_dataset <- as.data.frame(moo_diff_summary_dat)
-  if (is.null(feature_id_colname)) {
-    feature_id_colname <- colnames(moo_diff_summary_dat)[1]
-  }
-
-  ### PH: Create venn Table from DEG table
-
-  # SET INPUT ====
-
-  # select required columns
-  set_elements <- input_dataset[, feature_id_colname]
-  set_names <- input_dataset[, contrasts_colname]
-
-  # prepare format - R list
-  vlist <- split(set_elements, set_names)
-  if (!is.null(select_contrasts)) {
-    vlist <- vlist[select_contrasts]
+  if (
+    !is.list(venn_sets) || length(venn_sets) == 0 || is.null(names(venn_sets))
+  ) {
+    stop("venn_sets must be a non-empty named list")
   }
+  vlist <- venn_sets
   num_categories <- length(vlist)
   if (num_categories == 0) {
     stop("Zero categories found")
@@ -279,11 +298,7 @@ S7::method(plot_venn_diagram, S7::class_data.frame) <- function(
   if (num_categories > 1) {
     sets <- fromList(vlist)
 
-    if (!is.null(select_contrasts)) {
-      Intersection <- sets[, match(select_contrasts, colnames(sets))]
-    } else {
-      Intersection <- sets
-    }
+    Intersection <- sets
 
     # generate intersection frequency table and gene list (all intersections for the output dataset/table not the plot)
     intersection_matrix <- Intersection
@@ -334,7 +349,7 @@ S7::method(plot_venn_diagram, S7::class_data.frame) <- function(
 
   # returned intersections
 
-  if (!is.null(intersection_ids)) {
+  if (length(intersection_ids) > 0) {
     intersection_ids <- sort(as.numeric(intersection_ids))
     tabsel <- tab[tab$Id %in% intersection_ids, ]
     Intersectionsel <- Intersection[Intersection$Id %in% intersection_ids, ]
@@ -397,7 +412,7 @@ S7::method(plot_venn_diagram, S7::class_data.frame) <- function(
     pSet <- UpSetR::upset(
       sets,
       nsets = num_categories,
-      sets = select_contrasts,
+      sets = names(vlist),
       order.by = intersections_order,
       nintersects = NA,
       text.scale = 2,
diff --git a/inst/quarto/report.qmd b/inst/quarto/report.qmd
index d5090eef..fbee2392 100644
--- a/inst/quarto/report.qmd
+++ b/inst/quarto/report.qmd
@@ -160,6 +160,6 @@ dat_volcano_enhanced <- moo@analyses$diff |>
 ### Venn Diagram
 
 ```{r venn_diagram}
-venn_dat <- dat_volcano_summary |> plot_venn_diagram()
+venn_dat <- moo |> plot_venn_diagram()
 head(venn_dat)
 ```
diff --git a/man/plot_venn_diagram.Rd b/man/plot_venn_diagram.Rd
index 228ea032..fe499203 100644
--- a/man/plot_venn_diagram.Rd
+++ b/man/plot_venn_diagram.Rd
@@ -3,13 +3,15 @@
 \name{plot_venn_diagram}
 \alias{plot_venn_diagram}
 \alias{plot_venn_diagram,MOSuite::multiOmicDataSet-method}
-\alias{plot_venn_diagram,data.frame-method}
 \title{Plot a venn diagram, UpSet plot, or table of intersections}
 \usage{
 plot_venn_diagram(
   moo_diff_summary_dat,
   feature_id_colname = NULL,
-  contrasts_colname = "Contrast",
+  signif_colname = "adjpval",
+  signif_threshold = 0.05,
+  change_colname = "logFC",
+  change_threshold = 1,
   select_contrasts = c(),
   plot_type = "Venn diagram",
   intersection_ids = c(),
@@ -46,44 +48,10 @@ plot_venn_diagram(
 plot_venn_diagram(
   moo_diff_summary_dat,
   feature_id_colname = NULL,
-  contrasts_colname = "Contrast",
-  select_contrasts = c(),
-  plot_type = "Venn diagram",
-  intersection_ids = c(),
-  venn_force_unique = TRUE,
-  venn_numbers_format = "raw",
-  venn_significant_digits = 2,
-  venn_fill_colors = c("darkgoldenrod2", "darkolivegreen2", "mediumpurple3",
-    "darkorange2", "lightgreen"),
-  venn_fill_transparency = 0.2,
-  venn_border_colors = "fill colors",
-  venn_font_size_for_category_names = 3,
-  venn_category_names_distance = c(),
-  venn_category_names_position = c(),
-  venn_font_size_for_counts = 6,
-  venn_outer_margin = 0,
-  intersections_order = "degree",
-  display_empty_intersections = FALSE,
-  intersection_bar_color = "steelblue4",
-  intersection_point_size = 2.2,
-  intersection_line_width = 0.7,
-  table_font_size = 0.7,
-  table_content = "all intersections",
-  graphics_device = grDevices::png,
-  dpi = 300,
-  image_width = 4000,
-  image_height = 3000,
-  plot_filename = "venn_diagram.png",
-  print_plots = options::opt("print_plots"),
-  save_plots = options::opt("save_plots"),
-  plots_subdir = "diff"
-)
-
-## S7 method for class <data.frame>
-plot_venn_diagram(
-  moo_diff_summary_dat,
-  feature_id_colname = NULL,
-  contrasts_colname = "Contrast",
+  signif_colname = "adjpval",
+  signif_threshold = 0.05,
+  change_colname = "logFC",
+  change_threshold = 1,
   select_contrasts = c(),
   plot_type = "Venn diagram",
   intersection_ids = c(),
@@ -117,17 +85,21 @@ plot_venn_diagram(
 )
 }
 \arguments{
-\item{moo_diff_summary_dat}{Summarized differential expression analysis}
+\item{moo_diff_summary_dat}{multiOmicDataSet containing per-contrast differential expression results.}
 
-\item{feature_id_colname}{The column from the counts data containing the Feature IDs (Usually Gene or Protein ID).
-This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts
-Matrix will be available to select for this parameter. (Default: \code{NULL} - first column in the counts matrix will be
-used.)}
+\item{feature_id_colname}{Feature identifier column in each contrast result. Defaults to the first column.}
 
-\item{contrasts_colname}{Name of the column in \code{moo_diff_summary_dat} that contains the contrast names (default:
-"Contrast")}
+\item{signif_colname}{Significance column in each contrast result. Default: \code{"adjpval"}.}
 
-\item{select_contrasts}{A vector of contrast names to select for the plot. If empty, all contrasts are used.}
+\item{signif_threshold}{Features pass the significance threshold when their value is less than this cutoff
+(exclusive). Default: \code{0.05}.}
+
+\item{change_colname}{Log fold-change column in each contrast result. Default: \code{"logFC"}.}
+
+\item{change_threshold}{Features pass the fold-change threshold when their absolute value is greater than this
+cutoff (exclusive). Default: \code{1.0}.}
+
+\item{select_contrasts}{Contrast names to include. If empty, all available contrasts are used.}
 
 \item{plot_type}{Type of plot to generate: "Venn diagram" or "Intersection plot". Default: "Venn diagram"}
 
@@ -172,32 +144,26 @@ same colors as \code{venn_fill_colors})}
 
 \item{table_content}{Content of the table in the plot. Default: NULL}
 
-\item{graphics_device}{passed to \code{ggsave(device)}. Default: \code{grDevices::png}}
+\item{graphics_device}{Graphics device used to save the plot. Default: \code{grDevices::png}}
 
-\item{dpi}{dots-per-inch of the output image (see \code{ggsave()}) - only used if save_plots is TRUE}
+\item{dpi}{Dots per inch of the saved plot. Default: 300}
 
-\item{image_width}{output image width in inches - only used if save_plots is TRUE. Default: 10}
+\item{image_width}{Saved plot width in pixels. Default: 4000}
 
-\item{image_height}{output image height in inches - only used if save_plots is TRUE. Default: 10}
+\item{image_height}{Saved plot height in pixels. Default: 3000}
 
-\item{plot_filename}{plot output filename - only used if save_plots is TRUE. When multiple comparisons are saved
-separately, the comparison name is appended before the file extension.}
+\item{plot_filename}{Filename for the saved plot. Default: \code{"venn_diagram.png"}}
 
-\item{print_plots}{Whether to print plots during analysis (Defaults to \code{FALSE}, overwritable using option 'moo_print_plots' or environment variable 'MOO_PRINT_PLOTS')}
+\item{print_plots}{Whether to print plots. Default: \code{options::opt("print_plots")}}
 
-\item{save_plots}{Whether to save plots to files during analysis (Defaults to \code{TRUE}, overwritable using option 'moo_save_plots' or environment variable 'MOO_SAVE_PLOTS')}
+\item{save_plots}{Whether to save plots. Default: \code{options::opt("save_plots")}}
 
-\item{plots_subdir}{subdirectory in \verb{figures/} where plots will be saved if \code{save_plots} is \code{TRUE}}
+\item{plots_subdir}{Subdirectory for saved plots. Default: \code{"diff"}}
 }
 \description{
 Generates Venn diagram of intersections across a series of sets (e.g., intersections of significant genes across
 tested contrasts). This Venn diagram is available for up to five sets; Intersection plot is available for any number
 of sets. Specific sets can be selected for the visualizations and the returned dataset may include all (default) or
 specified intersections.
-An S7 generic with methods for \code{multiOmicDataSet} and \code{data.frame}.
-}
-\examples{
-plot_venn_diagram(nidap_volcano_summary_dat, print_plots = TRUE)
-
+An S7 generic for \code{multiOmicDataSet} inputs.
 }
-\keyword{plotters}
diff --git a/man/plot_venn_sets.Rd b/man/plot_venn_sets.Rd
new file mode 100644
index 00000000..e5fff535
--- /dev/null
+++ b/man/plot_venn_sets.Rd
@@ -0,0 +1,105 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_venn_diagram.R
+\name{plot_venn_sets}
+\alias{plot_venn_sets}
+\title{Build Venn or UpSet intersections from feature sets}
+\usage{
+plot_venn_sets(
+  venn_sets,
+  plot_type = "Venn diagram",
+  intersection_ids = c(),
+  venn_force_unique = TRUE,
+  venn_numbers_format = "raw",
+  venn_significant_digits = 2,
+  venn_fill_colors = c("darkgoldenrod2", "darkolivegreen2", "mediumpurple3",
+    "darkorange2", "lightgreen"),
+  venn_fill_transparency = 0.2,
+  venn_border_colors = "fill colors",
+  venn_font_size_for_category_names = 3,
+  venn_category_names_distance = c(),
+  venn_category_names_position = c(),
+  venn_font_size_for_counts = 6,
+  venn_outer_margin = 0,
+  intersections_order = "degree",
+  display_empty_intersections = FALSE,
+  intersection_bar_color = "steelblue4",
+  intersection_point_size = 2.2,
+  intersection_line_width = 0.7,
+  table_font_size = 0.7,
+  table_content = "all intersections",
+  graphics_device = grDevices::png,
+  dpi = 300,
+  image_width = 4000,
+  image_height = 3000,
+  plot_filename = "venn_diagram.png",
+  print_plots = options::opt("print_plots"),
+  save_plots = options::opt("save_plots"),
+  plots_subdir = "diff"
+)
+}
+\arguments{
+\item{venn_sets}{Named list of feature identifier vectors, one per contrast.}
+
+\item{plot_type}{Type of plot to generate: "Venn diagram" or "Intersection plot". Default: "Venn diagram"}
+
+\item{intersection_ids}{A vector of intersection IDs to select for the plot. If empty, all intersections are used.}
+
+\item{venn_force_unique}{If TRUE, forces unique elements in the Venn diagram. Default: TRUE}
+
+\item{venn_numbers_format}{Format for the numbers in the Venn diagram. Options: "raw", "percent", "raw-percent",
+"percent-raw". Default: "raw"}
+
+\item{venn_significant_digits}{Number of significant digits for the Venn diagram numbers. Default: 2}
+
+\item{venn_fill_colors}{A vector of colors to fill the Venn diagram categories. Default: c("darkgoldenrod2",
+"darkolivegreen2", "mediumpurple3", "darkorange2", "lightgreen")}
+
+\item{venn_fill_transparency}{Transparency level for the Venn diagram fill colors. Default: 0.2}
+
+\item{venn_border_colors}{Colors for the borders of the Venn diagram categories. Default: "fill colors" (uses the
+same colors as \code{venn_fill_colors})}
+
+\item{venn_font_size_for_category_names}{Font size for the category names in the Venn diagram. Default: 3}
+
+\item{venn_category_names_distance}{Distance of the category names from the Venn diagram circles. Default: c()}
+
+\item{venn_category_names_position}{Position of the category names in the Venn diagram. Default: c()}
+
+\item{venn_font_size_for_counts}{Font size for the counts in the Venn diagram. Default: 6}
+
+\item{venn_outer_margin}{Outer margin for the Venn diagram. Default: 0}
+
+\item{intersections_order}{Order of the intersections in the plot. Default: "by size"}
+
+\item{display_empty_intersections}{If TRUE, displays empty intersections in the plot. Default: FALSE}
+
+\item{intersection_bar_color}{Color for the intersection bars in the plot. Default: "lightgray"}
+
+\item{intersection_point_size}{Size of the points in the intersection plot. Default: 2}
+
+\item{intersection_line_width}{Width of the lines in the intersection plot. Default: 0.5}
+
+\item{table_font_size}{Font size for the table in the plot. Default: 3}
+
+\item{table_content}{Content of the table in the plot. Default: NULL}
+
+\item{graphics_device}{Graphics device used to save the plot. Default: \code{grDevices::png}}
+
+\item{dpi}{Dots per inch of the saved plot. Default: 300}
+
+\item{image_width}{Saved plot width in pixels. Default: 4000}
+
+\item{image_height}{Saved plot height in pixels. Default: 3000}
+
+\item{plot_filename}{Filename for the saved plot. Default: \code{"venn_diagram.png"}}
+
+\item{print_plots}{Whether to print plots. Default: \code{options::opt("print_plots")}}
+
+\item{save_plots}{Whether to save plots. Default: \code{options::opt("save_plots")}}
+
+\item{plots_subdir}{Subdirectory for saved plots. Default: \code{"diff"}}
+}
+\description{
+Build Venn or UpSet intersections from feature sets
+}
+\keyword{internal}
diff --git a/tests/testthat/_snaps/plot_venn_diagram.md b/tests/testthat/_snaps/plot_venn_diagram.md
deleted file mode 100644
index b6e1eb0e..00000000
--- a/tests/testthat/_snaps/plot_venn_diagram.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# plot_venn_diagram works with defaults
-
-    Code
-      p <- plot_venn_diagram(nidap_volcano_summary_dat, print_plots = FALSE,
-        save_plots = TRUE)
-    Message
-      All intersections: 1:7,c(1, 2, 3, 4, 5, 6, 7),c(163, 237, 518, 780, 225, 379, 766),c("Yes", "Yes", "Yes", "Yes", "Yes", "Yes", "Yes")
-      Intersections returned: 1:7,c(1, 2, 3, 4, 5, 6, 7),c(163, 237, 518, 780, 225, 379, 766)
-
diff --git a/tests/testthat/test-plot_venn_diagram.R b/tests/testthat/test-plot_venn_diagram.R
index 9c637156..0136cb97 100644
--- a/tests/testthat/test-plot_venn_diagram.R
+++ b/tests/testthat/test-plot_venn_diagram.R
@@ -1,56 +1,89 @@
-test_that("plot_venn_diagram works with defaults", {
-  expect_snapshot(
-    p <- plot_venn_diagram(
-      nidap_volcano_summary_dat,
-      print_plots = FALSE,
-      save_plots = TRUE
+make_venn_test_moo <- function() {
+  contrast_ba <- data.frame(
+    Gene = c("both", "ba_only", "p_boundary", "fc_boundary"),
+    logFC = c(2, 2, 2, 1),
+    adjpval = c(0.01, 0.01, 0.05, 0.01)
+  )
+  contrast_ca <- data.frame(
+    Gene = c("both", "ca_only", "p_boundary", "fc_boundary"),
+    logFC = c(-2, -2, -2, -1),
+    adjpval = c(0.01, 0.01, 0.05, 0.01)
+  )
+  return(
+    multiOmicDataSet(
+      sample_metadata = data.frame(Sample = "S1"),
+      anno_dat = data.frame(),
+      counts_lst = list(raw = data.frame(Gene = "seed", S1 = 1)),
+      analyses_lst = list(diff = list("B-A" = contrast_ba, "C-A" = contrast_ca))
     )
   )
-  expect_equal(
-    plot_venn_diagram(nidap_volcano_summary_dat),
-    as.data.frame(nidap_venn_diagram_dat)
+}
+
+test_that("plot_venn_diagram builds intersections directly from DEG MOO results", {
+  result <- plot_venn_diagram(
+    make_venn_test_moo(),
+    print_plots = FALSE,
+    save_plots = FALSE
   )
+
+  expect_s3_class(result, "data.frame")
+  expect_setequal(result$Gene, c("both", "ba_only", "ca_only"))
+  expect_false(any(result$Gene %in% c("p_boundary", "fc_boundary")))
+  expect_true("(B-A ∩ C-A)" %in% result$Intersection)
 })
-test_that("plot_venn_diagram raises condition for empty df", {
-  expect_error(
-    plot_venn_diagram(structure(
-      list(
-        GeneName = character(0),
-        Contrast = character(0),
-        FC = numeric(0),
-        logFC = numeric(0),
-        tstat = numeric(0),
-        pval = numeric(0),
-        adjpval = numeric(0)
-      ),
-      class = "data.frame",
-      row.names = integer(0)
-    )),
-    "Dataframe is empty"
+
+test_that("plot_venn_diagram respects a subset of MOO contrasts", {
+  moo <- make_venn_test_moo()
+  moo@analyses$diff[["D-A"]] <- data.frame(
+    Gene = c("both", "da_only"),
+    logFC = c(2, 2),
+    adjpval = c(0.01, 0.01)
+  )
+
+  result <- plot_venn_diagram(
+    moo,
+    select_contrasts = c("B-A", "C-A"),
+    print_plots = FALSE,
+    save_plots = FALSE
   )
+
+  expect_setequal(result$Gene, c("both", "ba_only", "ca_only"))
+  expect_false("da_only" %in% result$Gene)
+  expect_false(any(grepl("D-A", result$Intersection, fixed = TRUE)))
 })
 
-test_that("intersection matrix assignment avoids recursive evaluation error", {
-  # This test demonstrates the fix for the recursive default argument reference error
-  # The error occurred with this pattern:
-  #   Intersection <- sapply(colnames(Intersection), function(x) Intersection[, x])
-  # The fix uses a temporary variable:
-  #   intersection_matrix <- Intersection;
-  #   Intersection <- sapply(colnames(intersection_matrix), ...)
-
-  # Call plot_venn_diagram directly to ensure the fix works in practice
-  expect_no_error({
-    result <- plot_venn_diagram(
-      nidap_volcano_summary_dat,
+test_that("plot_venn_diagram errors for missing contrast DEG columns", {
+  expect_error(
+    plot_venn_diagram(
+      make_venn_test_moo(),
+      signif_colname = "missing_column",
       print_plots = FALSE,
       save_plots = FALSE
+    ),
+    "Required DEG columns not found"
+  )
+})
+
+test_that("plot_venn_diagram uses an Intersection plot for more than five contrasts", {
+  moo <- make_venn_test_moo()
+  moo@analyses$diff <- rep(moo@analyses$diff["B-A"], 6)
+  names(moo@analyses$diff) <- paste0("contrast_", seq_len(6))
+  for (contrast_name in names(moo@analyses$diff)) {
+    moo@analyses$diff[[contrast_name]] <- data.frame(
+      Gene = c("both", contrast_name),
+      logFC = c(2, 2),
+      adjpval = c(0.01, 0.01)
     )
-  })
+  }
 
-  # Verify the result has the expected structure
-  expect_s3_class(result, "data.frame")
-  expect_true("Gene" %in% colnames(result))
-  expect_true("Intersection" %in% colnames(result))
-  expect_true("Id" %in% colnames(result))
-  expect_true("Size" %in% colnames(result))
+  expect_no_error(
+    suppressWarnings(
+      plot_venn_diagram(
+        moo,
+        plot_type = "Venn diagram",
+        print_plots = FALSE,
+        save_plots = FALSE
+      )
+    )
+  )
 })
diff --git a/vignettes/visualization.Rmd b/vignettes/visualization.Rmd
index ffa10732..9352f0f8 100644
--- a/vignettes/visualization.Rmd
+++ b/vignettes/visualization.Rmd
@@ -153,7 +153,7 @@ head(dat_volcano_summary)
 ### Venn Diagram
 
 ```{r venn_diagram, fig.width=7, fig.height=7}
-venn_dat <- dat_volcano_summary |> plot_venn_diagram()
+venn_dat <- moo |> plot_venn_diagram()
 head(venn_dat)
 ```