diff --git a/DESCRIPTION b/DESCRIPTION
index 6880f72..13bf9e1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: clustree
 Type: Package
 Title: Visualise Clusterings at Different Resolutions
-Version: 0.5.0
-Date: 2022-06-24
+Version: 0.5.0.9001
+Date: 2023-10-24
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
              email = "luke@lazappi.id.au",
@@ -33,7 +33,7 @@ Imports: checkmate,
     igraph,
     dplyr,
     grid,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     viridis,
     methods,
     rlang,
@@ -50,5 +50,5 @@ Suggests:
     pkgdown,
     spelling
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Language: en-GB
diff --git a/NEWS.md b/NEWS.md
index a8244fc..698e895 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,15 @@
+# clustree (development version)
+
+### _clustree_ 0.5.0.9001 (2023-10-24)
+
+* Avoid warnings due to deprecated functionality in _ggplot2_ and
+  _tidyselect_. Includes increasing the _ggplot2_ requirement to >= 3.4.0.
+  (Fixes #35)
+
+### _clustree_ 0.5.0.9000 (2023-10-24)
+
+* Minor updates for compatibility with upcoming _Seurat_ v5 release (Fixes #93)
+
 # _clustree_ 0.5.0 (2022-06-24)
 
 ## Minor changes
diff --git a/R/checks.R b/R/checks.R
index 928f274..9ecf134 100644
--- a/R/checks.R
+++ b/R/checks.R
@@ -9,6 +9,8 @@
 #' @param node_aes value of the node aesthetic to check
 #' @param node_aes_aggr aggregation function associated with the node aesthetic
 #'
+#' @keywords internal
+#'
 #' @importFrom utils head
 assert_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
                             node_aes_aggr) {
@@ -58,6 +60,8 @@ assert_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
 #' @param node_aes_aggr aggregation function associated with the node aesthetic
 #' @param min minimum numeric value allowed
 #' @param max maximum numeric value allowed
+#'
+#' @keywords internal
 assert_numeric_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
                                     node_aes_aggr, min, max) {
 
@@ -87,6 +91,8 @@ assert_numeric_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
 #' @param min minimum numeric value allowed
 #' @param max maximum numeric value allowed
 #'
+#' @keywords internal
+#'
 #' @importFrom grDevices col2rgb
 assert_colour_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
                                    node_aes_aggr, min, max) {
@@ -120,6 +126,8 @@ assert_colour_node_aes <- function(node_aes_name, prefix, metadata, node_aes,
 #'
 #' @param node_aes_list List of node aesthetics
 #'
+#' @keywords internal
+#'
 #' @return Corrected node aesthetics list
 check_node_aes_list <- function(node_aes_list) {
     for (aes in names(node_aes_list)) {
diff --git a/R/clustree.R b/R/clustree.R
index 63cfcff..7d33824 100644
--- a/R/clustree.R
+++ b/R/clustree.R
@@ -284,13 +284,14 @@ clustree.matrix <- function(x, prefix,
                                                 ends = edge_arrow_ends),
                                   end_cap = circle(circle_size_end, "points"),
                                   start_cap = circle(circle_size_start, "points"),
-                                  aes_(colour = ~count,
-                                       alpha = ~in_prop,
-                                       edge_width = ~is_core))
+                                  aes(colour = .data$count,
+                                      alpha = .data$in_prop,
+                                      edge_width = .data$is_core))
 
     } else {
-        gg <- gg + geom_edge_link(aes_(colour = ~count, alpha = ~in_prop,
-                                       edge_width = ~is_core))
+        gg <- gg + geom_edge_link(aes(colour = .data$count,
+                                      alpha = .data$in_prop,
+                                      edge_width = .data$is_core))
     }
 
     if (highlight_core) {
@@ -311,17 +312,17 @@ clustree.matrix <- function(x, prefix,
 
     # Plot node text
     if (scale_node_text && !is.numeric(node_size)) {
-        gg <- gg + geom_node_text(aes_(label = ~cluster,
-                                       size = as.name(graph_attr$node_size)),
+        gg <- gg + geom_node_text(aes(label = .data$cluster,
+                                      size = .data[[graph_attr$node_size]]),
                                   colour = node_text_colour,
                                   angle = node_text_angle
                                   )
     } else {
-        gg <- gg + geom_node_text(aes_(label = ~cluster),
+        gg <- gg + geom_node_text(aes(label = .data$cluster),
                                   size = node_text_size,
                                   colour = node_text_colour,
                                   angle = node_text_angle
-                                  )
+                                 )
     }
 
     if (!(is.null(node_label))) {
@@ -516,8 +517,13 @@ clustree.Seurat <- function(x, prefix = paste0(assay, "_snn_res."),
                 )
             }
             aes_name <- paste0(exprs, "_", node_aes_name)
-            x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
-                                               slot = exprs)
+            if (packageVersion("SeuratObject") >= package_version("5.0.0")) {
+                x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
+                                                   layer = exprs)
+            } else {
+                x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
+                                                   slot = exprs)
+            }
             args[[node_aes]] <- aes_name
         }
     }
@@ -541,6 +547,8 @@ clustree.Seurat <- function(x, prefix = paste0(assay, "_snn_res."),
 #' name of a metadata column to use for node transparency
 #' @param allowed vector of allowed node attributes to use as aesthetics
 #'
+#' @keywords internal
+#'
 #' @importFrom ggraph geom_node_point
 #' @importFrom ggplot2 aes_
 add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
@@ -555,25 +563,25 @@ add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
     }
 
     switch(aes_allowed,
-           col_size_alpha = geom_node_point(aes_(colour = as.name(node_colour),
-                                                 size = as.name(node_size),
-                                                 alpha = as.name(node_alpha))),
-           col_alpha      = geom_node_point(aes_(colour = as.name(node_colour),
-                                                 alpha = as.name(node_alpha)),
+           col_size_alpha = geom_node_point(aes(colour = .data[[node_colour]],
+                                                size = .data[[node_size]],
+                                                alpha = .data[[node_alpha]])),
+           col_alpha      = geom_node_point(aes(colour = .data[[node_colour]],
+                                                alpha = .data[[node_alpha]]),
                                             size = node_size),
-           col_size       = geom_node_point(aes_(colour = as.name(node_colour),
-                                                 size = as.name(node_size)),
+           col_size       = geom_node_point(aes(colour = .data[[node_colour]],
+                                                size = .data[[node_size]]),
                                             alpha = node_alpha),
-           col            = geom_node_point(aes_(colour = as.name(node_colour)),
+           col            = geom_node_point(aes(colour = .data[[node_colour]]),
                                             size = node_size,
                                             alpha = node_alpha),
-           size_alpha     = geom_node_point(aes_(size = as.name(node_size),
-                                                 alpha = as.name(node_alpha)),
+           size_alpha     = geom_node_point(aes(size = .data[[node_size]],
+                                                alpha = .data[[node_alpha]]),
                                             colour = node_colour),
-           size           = geom_node_point(aes_(size = as.name(node_size)),
+           size           = geom_node_point(aes(size = .data[[node_size]]),
                                             colour = node_colour,
                                             alpha = node_alpha),
-           alpha          = geom_node_point(aes_(alpha = as.name(node_alpha)),
+           alpha          = geom_node_point(aes(alpha = .data[[node_alpha]]),
                                             colour = node_colour,
                                             size = node_size),
            none           = geom_node_point(colour = node_colour,
@@ -597,6 +605,8 @@ add_node_points <- function(node_colour, node_size, node_alpha, allowed) {
 #' labels
 #' @param allowed vector of allowed node attributes to use as aesthetics
 #'
+#' @keywords internal
+#'
 #' @importFrom ggraph geom_node_label
 #' @importFrom ggplot2 aes_
 add_node_labels <- function(node_label, node_colour, node_label_size,
@@ -605,13 +615,13 @@ add_node_labels <- function(node_label, node_colour, node_label_size,
     is_allowed <- c(node_colour) %in% allowed
 
     if (is_allowed) {
-        geom_node_label(aes_(label = as.name(node_label),
-                             fill = as.name(node_colour)),
+        geom_node_label(aes(label = .data[[node_label]],
+                            fill = .data[[node_colour]]),
                         size = node_label_size,
                         colour = node_label_colour,
                         nudge_y = node_label_nudge)
     } else {
-        geom_node_label(aes_(label = as.name(node_label)),
+        geom_node_label(aes(label = .data[[node_label]]),
                         fill = node_colour,
                         size = node_label_size,
                         colour = node_label_colour,
diff --git a/R/clustree_overlay.R b/R/clustree_overlay.R
index 9b53f64..46a1bd4 100644
--- a/R/clustree_overlay.R
+++ b/R/clustree_overlay.R
@@ -259,12 +259,12 @@ clustree_overlay.matrix <- function(x, prefix, metadata, x_value, y_value,
     levels(edges[[paste0("from_", prefix)]]) <- levels(nodes[[prefix]])
 
     if (use_colour == "points") {
-        gg <- ggplot(points, aes_(x = as.name(x_value), y = as.name(y_value))) +
-            geom_point(aes_(colour = as.name(paste0(hi_res, "_cluster"))),
+        gg <- ggplot(points, aes(x = .data[[x_value]], y = .data[[y_value]])) +
+            geom_point(aes(colour = .data[[paste0(hi_res, "_cluster")]]),
                        size = point_size, alpha = point_alpha,
                        shape = point_shape)
     } else {
-        gg <- ggplot(points, aes_(x = as.name(x_value), y = as.name(y_value))) +
+        gg <- ggplot(points, aes(x = .data[[x_value]], y = .data[[y_value]])) +
             geom_point(colour = alt_colour, size = point_size,
                        alpha = point_alpha, shape = point_shape)
     }
@@ -283,26 +283,26 @@ clustree_overlay.matrix <- function(x, prefix, metadata, x_value, y_value,
         if (use_colour == "edges") {
             gg <- gg +
                 geom_segment(data = edges_res,
-                             aes_(x = as.name(paste0("from_", x_value)),
-                                  y = as.name(paste0("from_", y_value)),
-                                  xend = as.name(paste0("to_", x_value)),
-                                  yend = as.name(paste0("to_", y_value)),
-                                  alpha = ~ in_prop,
-                                  colour = as.name(paste0("from_", prefix))),
+                             aes(x = .data[[paste0("from_", x_value)]],
+                                 y = .data[[paste0("from_", y_value)]],
+                                 xend = .data[[paste0("to_", x_value)]],
+                                 yend = .data[[paste0("to_", y_value)]],
+                                 alpha = .data$in_prop,
+                                 colour = .data[[paste0("from_", prefix)]]),
                              arrow = arrow(length = unit(edge_width * 5,
                                                          "points")),
-                             size = edge_width)
+                             linewidth = edge_width)
         } else {
             gg <- gg +
                 geom_segment(data = edges_res,
-                             aes_(x = as.name(paste0("from_", x_value)),
-                                  y = as.name(paste0("from_", y_value)),
-                                  xend = as.name(paste0("to_", x_value)),
-                                  yend = as.name(paste0("to_", y_value)),
-                                  alpha = ~ in_prop),
+                             aes(x = .data[[paste0("from_", x_value)]],
+                                 y = .data[[paste0("from_", y_value)]],
+                                 xend = .data[[paste0("to_", x_value)]],
+                                 yend = .data[[paste0("to_", y_value)]],
+                                 alpha = .data$in_prop),
                              arrow = arrow(length = unit(edge_width * 5,
                                                          "points")),
-                             size = edge_width,
+                             linewidth = edge_width,
                              colour = alt_colour)
         }
     }
@@ -310,9 +310,9 @@ clustree_overlay.matrix <- function(x, prefix, metadata, x_value, y_value,
     if (label_nodes) {
         gg <- gg +
             ggrepel::geom_label_repel(data = nodes,
-                                      aes_(x = as.name(x_val),
-                                           y = as.name(y_val),
-                                           label = ~ node),
+                                      aes(x = .data[[x_val]],
+                                          y = .data[[y_val]],
+                                          label = .data$node),
                                       size = label_size)
     }
 
@@ -604,8 +604,13 @@ clustree_overlay.Seurat <- function(x, x_value, y_value,
                 )
             }
             aes_name <- paste0(exprs, "_", node_aes_name)
-            x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
-                                               slot = exprs)
+            if (packageVersion("SeuratObject") >= package_version("5.0.0")) {
+                x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
+                                                   layer = exprs)
+            } else {
+                x[[aes_name]] <- Seurat::FetchData(x, vars = node_aes_value,
+                                                   slot = exprs)
+            }
             args[[node_aes]] <- aes_name
         }
     }
@@ -638,6 +643,8 @@ clustree_overlay.Seurat <- function(x, x_value, y_value,
 #' @param node_alpha either a numeric value giving the alpha of all nodes or the
 #' name of a metadata column to use for node transparency
 #'
+#' @keywords internal
+#'
 #' @importFrom ggplot2 aes_ geom_point
 overlay_node_points <- function(nodes, x_value, y_value, node_colour, node_size,
                                 node_alpha) {
@@ -653,57 +660,57 @@ overlay_node_points <- function(nodes, x_value, y_value, node_colour, node_size,
 
     switch(aes_allowed,
            col_size_alpha = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            fill = as.name(node_colour),
-                                            size = as.name(node_size),
-                                            alpha = as.name(node_alpha)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           fill = .data[[node_colour]],
+                                           size = .data[[node_size]],
+                                           alpha = .data[[node_alpha]]),
                                        shape = 21),
            col_alpha      = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            fill = as.name(node_colour),
-                                            alpha = as.name(node_alpha)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           fill = .data[[node_colour]],
+                                           alpha = .data[[node_alpha]]),
                                        size = node_size,
                                        shape = 21),
            col_size       = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            fill = as.name(node_colour),
-                                            size = as.name(node_size)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           fill = .data[[node_colour]],
+                                           size = .data[[node_size]]),
                                        alpha = node_alpha,
                                        shape = 21),
            col            = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            fill = as.name(node_colour)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           fill = .data[[node_colour]]),
                                         size = node_size,
                                         alpha = node_alpha,
                                         shape = 21),
            size_alpha     = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            fill = as.name(node_size),
-                                            alpha = as.name(node_alpha)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           fill = .data[[node_size]],
+                                           alpha = .data[[node_alpha]]),
                                        colour = node_colour,
                                        shape = 21),
            size           = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            size = as.name(node_size)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           size = .data[[node_size]]),
                                        fill = node_colour,
                                        alpha = node_alpha,
                                        shape = 21),
            alpha          = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value),
-                                            alpha = as.name(node_alpha)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]],
+                                           alpha = .data[[node_alpha]]),
                                        fill = node_colour,
                                        size = node_size,
                                        shape = 21),
            none           = geom_point(data = nodes,
-                                       aes_(x = as.name(x_value),
-                                            y = as.name(y_value)),
+                                       aes(x = .data[[x_value]],
+                                           y = .data[[y_value]]),
                                        fill = node_colour,
                                        size = node_size,
                                        alpha = node_alpha,
@@ -746,6 +753,8 @@ overlay_node_points <- function(nodes, x_value, y_value, node_colour, node_size,
 #'
 #' @return ggplot object
 #'
+#' @keywords internal
+#'
 #' @importFrom ggplot2 scale_colour_hue geom_jitter scale_y_reverse scale_alpha
 #' ylab theme
 #' element_line element_blank
@@ -771,14 +780,13 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
                                     !!as.name(paste0("to_", prefix)))))
 
     if (use_colour == "points") {
-
-        gg <- ggplot(points, aes_(x = as.name(side_value), y = point_y)) +
-            geom_jitter(aes_(colour = as.name(colnames(points)[3])),
+        gg <- ggplot(points, aes(x = .data[[side_value]], y = point_y)) +
+            geom_jitter(aes(colour = .data[[colnames(points)[3]]]),
                         height = y_jitter * median(y_diffs), width = 0,
                         size = point_size, alpha = point_alpha,
                         shape = point_shape)
     } else {
-        gg <- ggplot(points, aes_(x = as.name(side_value), y = point_y)) +
+        gg <- ggplot(points, aes(x = .data[[side_value]], y = point_y)) +
             geom_jitter(height = y_jitter * median(y_diffs), width = 0,
                         colour = alt_colour, size = point_size,
                         alpha = point_alpha, shape = point_shape)
@@ -797,26 +805,26 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
         if (use_colour == "edges") {
             gg <- gg +
                 geom_segment(data = edges_res,
-                             aes_(x = as.name(paste0("from_", side_value)),
-                                  y = ~ from_y,
-                                  xend = as.name(paste0("to_", side_value)),
-                                  yend = ~ to_y,
-                                  alpha = ~ in_prop,
-                                  colour = as.name(paste0("from_", prefix))),
+                             aes(x = .data[[paste0("from_", side_value)]],
+                                 y = .data$from_y,
+                                 xend = .data[[paste0("to_", side_value)]],
+                                 yend = .data$to_y,
+                                 alpha = .data$in_prop,
+                                 colour = .data[[paste0("from_", prefix)]]),
                              arrow = arrow(length = unit(edge_width * 5,
                                                          "points")),
-                             size = edge_width)
+                             linewidth = edge_width)
         } else {
             gg <- gg +
                 geom_segment(data = edges_res,
-                             aes_(x = as.name(paste0("from_", side_value)),
-                                  y = ~ from_y,
-                                  xend = as.name(paste0("to_", side_value)),
-                                  yend = ~ to_y,
-                                  alpha = ~ in_prop),
+                             aes(x = .data[[paste0("from_", side_value)]],
+                                 y = .data$from_y,
+                                 xend = .data[[paste0("to_", side_value)]],
+                                 yend = .data$to_y,
+                                 alpha = .data$in_prop),
                              arrow = arrow(length = unit(edge_width * 5,
                                                          "points")),
-                             size = edge_width,
+                             linewidth = edge_width,
                              colour = alt_colour)
         }
     }
@@ -824,10 +832,10 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
     if (label_nodes) {
         gg <- gg +
             ggrepel::geom_label_repel(data = nodes,
-                                      aes_(x = as.name(paste0("mean_",
-                                                              side_value)),
-                                           y = ~ y,
-                                           label = ~ node),
+                                      aes(x = .data[[paste0("mean_",
+                                                            side_value)]],
+                                          y = .data$y,
+                                          label = .data$node),
                                       size = label_size)
     }
 
@@ -838,8 +846,8 @@ plot_overlay_side <- function(nodes, edges, points, prefix, side_value,
         scale_colour_hue(drop = FALSE) +
         ylab(prefix) +
         theme_minimal() +
-        theme(axis.line.x = element_line(size = 1, colour = "grey50"),
-              axis.ticks.x = element_line(size = 0.6, colour = "grey50"),
+        theme(axis.line.x = element_line(linewidth = 1, colour = "grey50"),
+              axis.ticks.x = element_line(linewidth = 0.6, colour = "grey50"),
               panel.grid.major.x = element_blank(),
               panel.grid.minor.x = element_blank(),
               panel.grid.minor.y = element_blank())
diff --git a/R/graph.R b/R/graph.R
index f4aab99..f647eb6 100644
--- a/R/graph.R
+++ b/R/graph.R
@@ -16,6 +16,8 @@
 #'
 #' @return [tidygraph::tbl_graph] object containing the tree graph
 #'
+#' @keywords internal
+#'
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data
 build_tree_graph <- function(clusterings, prefix, count_filter, prop_filter,
@@ -60,6 +62,8 @@ build_tree_graph <- function(clusterings, prefix, count_filter, prop_filter,
 #' @param prefix string indicating columns containing clustering information
 #' @param node_aes_list nested list containing node aesthetics
 #'
+#' @keywords internal
+#'
 #' @return data.frame containing node information
 get_tree_nodes <- function(clusterings, prefix, metadata, node_aes_list) {
 
@@ -110,6 +114,8 @@ get_tree_nodes <- function(clusterings, prefix, metadata, node_aes_list) {
 #'
 #' @return data.frame containing edge information
 #'
+#' @keywords internal
+#'
 #' @importFrom dplyr %>%
 #' @importFrom rlang .data :=
 get_tree_edges <- function(clusterings, prefix) {
@@ -152,13 +158,13 @@ get_tree_edges <- function(clusterings, prefix) {
     })
 
     edges <- dplyr::bind_rows(edges) %>%
-        dplyr::mutate(from_node = paste0(prefix, .data$from_res,
-                                         "C", .data$from_clust)) %>%
-        dplyr::mutate(to_node = paste0(prefix, .data$to_res,
-                                       "C", .data$to_clust)) %>%
-        dplyr::select(.data$from_node, .data$to_node, dplyr::everything()) %>%
-        dplyr::rename(!!as.name(paste0("from_", prefix)) := .data$from_res,
-                      !!as.name(paste0("to_", prefix)) := .data$to_res)
+        dplyr::mutate(from_node = paste0(prefix, !!as.name("from_res"),
+                                         "C", !!as.name("from_clust"))) %>%
+        dplyr::mutate(to_node = paste0(prefix, !!as.name("to_res"),
+                                       "C", !!as.name("to_clust"))) %>%
+        dplyr::select("from_node", "to_node", dplyr::everything()) %>%
+        dplyr::rename(!!as.name(paste0("from_", prefix)) := !!as.name("from_res"),
+                      !!as.name(paste0("to_", prefix)) := !!as.name("to_res"))
 
     return(edges)
 
@@ -177,6 +183,8 @@ get_tree_edges <- function(clusterings, prefix) {
 #' @param is_cluster logical vector indicating which rows of metadata are in the
 #' node to be summarized
 #'
+#' @keywords internal
+#'
 #' @return data.frame with aggregated data
 aggr_metadata <- function(node_data, col_name, col_aggr, metadata,
                           is_cluster) {
@@ -200,6 +208,8 @@ aggr_metadata <- function(node_data, col_name, col_aggr, metadata,
 #' @param node_aes_list nested list containing node aesthetics
 #' @param metadata data.frame containing metadata that can be used as aesthetics
 #'
+#' @keywords internal
+#'
 #' @return graph with additional attributes
 store_node_aes <- function(graph, node_aes_list, metadata) {
 
diff --git a/R/stability.R b/R/stability.R
index b7038b1..300026e 100644
--- a/R/stability.R
+++ b/R/stability.R
@@ -8,6 +8,8 @@
 #' @param clusterings numeric matrix containing clustering information, each
 #' column contains clustering at a separate resolution
 #'
+#' @keywords internal
+#'
 #' @return matrix with stability score for each cluster
 calc_sc3_stability <- function(clusterings) {
 
@@ -70,6 +72,8 @@ calc_sc3_stability <- function(clusterings) {
 #' @seealso The documentation for the `calculate_stability` function in the
 #' SC3 package
 #'
+#' @keywords internal
+#'
 #' @return SC3 stability index
 calc_sc3_stability_cluster <- function(clusterings, res, cluster) {
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index fb4be72..1165dfc 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,15 +1,15 @@
 url: https://lazappi.github.io/clustree/
 template:
   bootstrap: 5
-  params:
-    bootswatch: cosmo
-    ganalytics: UA-52309538-5
-reference:
-    - title: clustree functions
-      contents:
-        - clustree
-        - clustree_overlay
-    - title: Example datasets
-      contents:
-        - nba_clusts
-        - sc_example
+  bootswatch: cosmo
+  includes:
+    in_header: |
+      <!-- Google tag (gtag.js) -->
+      <script async src="https://www.googletagmanager.com/gtag/js?id=G-6GT3P9FP6F"></script>
+      <script>
+        window.dataLayer = window.dataLayer || [];
+        function gtag(){dataLayer.push(arguments);}
+        gtag('js', new Date());
+
+        gtag('config', 'G-6GT3P9FP6F');
+      </script>
diff --git a/man/add_node_labels.Rd b/man/add_node_labels.Rd
index 83539d4..1946075 100644
--- a/man/add_node_labels.Rd
+++ b/man/add_node_labels.Rd
@@ -31,3 +31,4 @@ labels}
 \description{
 Add node labels to a clustering tree plot with the specified aesthetics.
 }
+\keyword{internal}
diff --git a/man/add_node_points.Rd b/man/add_node_points.Rd
index 72b488e..5bfd64b 100644
--- a/man/add_node_points.Rd
+++ b/man/add_node_points.Rd
@@ -21,3 +21,4 @@ name of a metadata column to use for node transparency}
 \description{
 Add node points to a clustering tree plot with the specified aesthetics.
 }
+\keyword{internal}
diff --git a/man/aggr_metadata.Rd b/man/aggr_metadata.Rd
index be7be73..b0d6c95 100644
--- a/man/aggr_metadata.Rd
+++ b/man/aggr_metadata.Rd
@@ -25,3 +25,4 @@ data.frame with aggregated data
 \description{
 Aggregate a metadata column to get a summarized value for a cluster node
 }
+\keyword{internal}
diff --git a/man/assert_colour_node_aes.Rd b/man/assert_colour_node_aes.Rd
index 2a59724..2d085f9 100644
--- a/man/assert_colour_node_aes.Rd
+++ b/man/assert_colour_node_aes.Rd
@@ -33,3 +33,4 @@ used as node aesthetics}
 \description{
 Raise error if an incorrect set of colour node parameters has been supplied.
 }
+\keyword{internal}
diff --git a/man/assert_node_aes.Rd b/man/assert_node_aes.Rd
index af58058..80e1049 100644
--- a/man/assert_node_aes.Rd
+++ b/man/assert_node_aes.Rd
@@ -21,3 +21,4 @@ used as node aesthetics}
 \description{
 Raise error if an incorrect set of node parameters has been supplied.
 }
+\keyword{internal}
diff --git a/man/assert_numeric_node_aes.Rd b/man/assert_numeric_node_aes.Rd
index 24d6403..70068f3 100644
--- a/man/assert_numeric_node_aes.Rd
+++ b/man/assert_numeric_node_aes.Rd
@@ -33,3 +33,4 @@ used as node aesthetics}
 \description{
 Raise error if an incorrect set of numeric node parameters has been supplied.
 }
+\keyword{internal}
diff --git a/man/build_tree_graph.Rd b/man/build_tree_graph.Rd
index 0090362..318a12c 100644
--- a/man/build_tree_graph.Rd
+++ b/man/build_tree_graph.Rd
@@ -37,3 +37,4 @@ used as node aesthetics}
 Build a tree graph from a set of clusterings, metadata and associated
 aesthetics
 }
+\keyword{internal}
diff --git a/man/calc_sc3_stability.Rd b/man/calc_sc3_stability.Rd
index da32f91..2500b5a 100644
--- a/man/calc_sc3_stability.Rd
+++ b/man/calc_sc3_stability.Rd
@@ -19,3 +19,4 @@ set of clusterings. The index varies from 0 to 1, where 1 suggests that a
 cluster is more stable across resolutions. See \code{\link[=calc_sc3_stability_cluster]{calc_sc3_stability_cluster()}}
 for more details.
 }
+\keyword{internal}
diff --git a/man/calc_sc3_stability_cluster.Rd b/man/calc_sc3_stability_cluster.Rd
index f7f9923..453cc9e 100644
--- a/man/calc_sc3_stability_cluster.Rd
+++ b/man/calc_sc3_stability_cluster.Rd
@@ -56,3 +56,4 @@ Where:
 The documentation for the \code{calculate_stability} function in the
 SC3 package
 }
+\keyword{internal}
diff --git a/man/check_node_aes_list.Rd b/man/check_node_aes_list.Rd
index f04e06e..965bf33 100644
--- a/man/check_node_aes_list.Rd
+++ b/man/check_node_aes_list.Rd
@@ -15,3 +15,4 @@ Corrected node aesthetics list
 \description{
 Warn if node aesthetic names are incorrect
 }
+\keyword{internal}
diff --git a/man/get_tree_edges.Rd b/man/get_tree_edges.Rd
index 4a6ff4b..630636c 100644
--- a/man/get_tree_edges.Rd
+++ b/man/get_tree_edges.Rd
@@ -18,3 +18,4 @@ data.frame containing edge information
 \description{
 Extract the edges from a set of clusterings
 }
+\keyword{internal}
diff --git a/man/get_tree_nodes.Rd b/man/get_tree_nodes.Rd
index 3e765ca..1dfc045 100644
--- a/man/get_tree_nodes.Rd
+++ b/man/get_tree_nodes.Rd
@@ -23,3 +23,4 @@ data.frame containing node information
 \description{
 Extract the nodes from a set of clusterings and add relevant attributes
 }
+\keyword{internal}
diff --git a/man/overlay_node_points.Rd b/man/overlay_node_points.Rd
index 4481433..cfd4981 100644
--- a/man/overlay_node_points.Rd
+++ b/man/overlay_node_points.Rd
@@ -33,3 +33,4 @@ name of a metadata column to use for node transparency}
 Overlay clustering tree nodes on a scatter plot with the specified
 aesthetics.
 }
+\keyword{internal}
diff --git a/man/plot_overlay_side.Rd b/man/plot_overlay_side.Rd
index 1101c9a..35cee99 100644
--- a/man/plot_overlay_side.Rd
+++ b/man/plot_overlay_side.Rd
@@ -74,3 +74,4 @@ Plot the side view of a clustree overlay plot. If the ordinary plot shows the
 tree from above this plot shows it from the side, highlighting either the
 x or y dimension and the clustering resolution.
 }
+\keyword{internal}
diff --git a/man/store_node_aes.Rd b/man/store_node_aes.Rd
index 419002a..6deaa3d 100644
--- a/man/store_node_aes.Rd
+++ b/man/store_node_aes.Rd
@@ -19,3 +19,4 @@ graph with additional attributes
 \description{
 Store the names of node attributes to use as aesthetics as graph attributes
 }
+\keyword{internal}
diff --git a/tests/testthat/test-clustree-overlay.R b/tests/testthat/test-clustree-overlay.R
index dfe96dd..79c6863 100644
--- a/tests/testthat/test-clustree-overlay.R
+++ b/tests/testthat/test-clustree-overlay.R
@@ -32,25 +32,37 @@ seurat_clusters2$resX <- "X"
 seurat_clusters2$TSNE1 <- sc_example$tsne[, 1]
 seurat_clusters2$TSNE2 <- sc_example$tsne[, 2]
 
-if (requireNamespace("Seurat", quietly = TRUE) &&
-    packageVersion(pkg = "Seurat") < package_version(x = "3.0.0")) {
-    library("Seurat")
-    seurat <- CreateSeuratObject(sc_example$counts,
-                                 meta.data = sc_example$seurat_clusters)
-    seurat <- SetDimReduction(seurat, "TSNE", "cell.embeddings",
-                              sc_example$tsne)
-}
-
-if (requireNamespace("Seurat", quietly = TRUE) &&
-    packageVersion(pkg = "Seurat") >= package_version(x = "3.0.0")) {
-    library("Seurat")
-    seurat <- CreateSeuratObject(counts = sc_example$counts,
-                                 meta.data = sc_example$seurat_clusters)
-    seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
-        embeddings = sc_example$tsne,
-        key = "tSNE_",
-        assay = DefaultAssay(seurat)
-    ))
+if (requireNamespace("Seurat", quietly = TRUE)) {
+
+    library(Seurat)
+
+    seurat_version <- packageVersion("Seurat")
+
+    if (seurat_version >= package_version("5.0.0")) {
+        seurat <- CreateSeuratObject(
+            counts = as(sc_example$counts, "sparseMatrix"),
+            data = as(sc_example$logcounts, "sparseMatrix"),
+            meta.data = sc_example$seurat_clusters
+        )
+        seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
+            embeddings = sc_example$tsne,
+            key = "tSNE_",
+            assay = DefaultAssay(seurat)
+        ))
+    } else if (seurat_version >= package_version("3.0.0")) {
+        seurat <- CreateSeuratObject(counts = sc_example$counts,
+                                     meta.data = sc_example$seurat_clusters)
+        seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
+            embeddings = sc_example$tsne,
+            key = "tSNE_",
+            assay = DefaultAssay(seurat)
+        ))
+    } else {
+        seurat <- CreateSeuratObject(sc_example$counts,
+                                     meta.data = sc_example$seurat_clusters)
+        seurat <- SetDimReduction(seurat, "TSNE", "cell.embeddings",
+                                  sc_example$tsne)
+    }
 }
 
 if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
diff --git a/tests/testthat/test-clustree.R b/tests/testthat/test-clustree.R
index e8cbd8f..aac41a2 100644
--- a/tests/testthat/test-clustree.R
+++ b/tests/testthat/test-clustree.R
@@ -25,25 +25,37 @@ nba_tibble <- dplyr::as_tibble(nba_clusts)
 seurat_clusters2 <- sc_example$seurat_clusters
 seurat_clusters2$resX <- "X"
 
-if (requireNamespace("Seurat", quietly = TRUE) &&
-    packageVersion(pkg = "Seurat") < package_version(x = "3.0.0")) {
-    library("Seurat")
-    seurat <- CreateSeuratObject(sc_example$counts,
-                                 meta.data = sc_example$seurat_clusters)
-    seurat <- SetDimReduction(seurat, "TSNE", "cell.embeddings",
-                              sc_example$tsne)
-}
-
-if (requireNamespace("Seurat", quietly = TRUE) &&
-    packageVersion(pkg = "Seurat") >= package_version(x = "3.0.0")) {
-    library("Seurat")
-    seurat <- CreateSeuratObject(counts = sc_example$counts,
-                                 meta.data = sc_example$seurat_clusters)
-    seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
-        embeddings = sc_example$tsne,
-        key = "tSNE_",
-        assay = DefaultAssay(seurat)
-    ))
+if (requireNamespace("Seurat", quietly = TRUE)) {
+
+    library(Seurat)
+
+    seurat_version <- packageVersion("Seurat")
+
+    if (seurat_version >= package_version("5.0.0")) {
+        seurat <- CreateSeuratObject(
+            counts = as(sc_example$counts, "sparseMatrix"),
+            data = as(sc_example$logcounts, "sparseMatrix"),
+            meta.data = sc_example$seurat_clusters
+        )
+        seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
+            embeddings = sc_example$tsne,
+            key = "tSNE_",
+            assay = DefaultAssay(seurat)
+        ))
+    } else if (seurat_version >= package_version("3.0.0")) {
+        seurat <- CreateSeuratObject(counts = sc_example$counts,
+                                     meta.data = sc_example$seurat_clusters)
+        seurat[["TSNE"]] <- suppressWarnings(CreateDimReducObject(
+            embeddings = sc_example$tsne,
+            key = "tSNE_",
+            assay = DefaultAssay(seurat)
+        ))
+    } else {
+        seurat <- CreateSeuratObject(sc_example$counts,
+                                     meta.data = sc_example$seurat_clusters)
+        seurat <- SetDimReduction(seurat, "TSNE", "cell.embeddings",
+                                  sc_example$tsne)
+    }
 }
 
 if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
diff --git a/vignettes/clustree.Rmd b/vignettes/clustree.Rmd
index bab4c5b..859af90 100644
--- a/vignettes/clustree.Rmd
+++ b/vignettes/clustree.Rmd
@@ -244,11 +244,11 @@ clustree(sce, prefix = "sc3_", suffix = "_clusters")
 
 ```{r seurat-present, echo = FALSE}
 seurat_present <- requireNamespace("Seurat", quietly = TRUE) &&
-    packageVersion("Seurat") >= package_version(x = "3.0.0")
+    packageVersion("Seurat") >= package_version(x = "5.0.0")
 ```
 
 ```{r seurat-not, echo = FALSE, results = 'asis', eval = !seurat_present}
-cat("> **NOTE:** This section requires the Seurat package (>= 3.0.0).",
+cat("> **NOTE:** This section requires the Seurat package (>= 5.0.0).",
     "This package isn't installed so the results won't be shown.")
 ```
 
@@ -258,8 +258,9 @@ convert our `SingleCellExperiment` to `Seurat` format:
 ```{r seurat, eval = seurat_present}
 suppressPackageStartupMessages(library("Seurat"))
 
-# Create the Seurat object
-seurat <- CreateSeuratObject(counts = sc_example$counts,
+# Create the Seurat object, Seurat >= expects a sparse matrix
+seurat <- CreateSeuratObject(counts = as(sc_example$counts, "sparseMatrix"),
+                             data = as(sc_example$logcounts, "sparseMatrix"),
                              meta.data = sc_example$seurat_clusters)
 
 # Add the t-SNE embedding