diff --git a/DESCRIPTION b/DESCRIPTION
index c8e12f8..2c6984a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: autograph
 Title: Automatic Plotting and Theming of Many Graphs
-Version: 0.5.1
-Date: 2025-12-08
+Version: 0.6.0
+Date: 2026-02-27
 Description: Visual exploration and presentation of networks should not be difficult.
    This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
    It includes 'ggplot2'-based plot methods for many popular network package classes.
@@ -25,7 +25,6 @@ Imports:
     patchwork,
     tidygraph
 Suggests:
-    BiocManager,
     gganimate,
     ggforce (>= 0.5.0),
     gifski,
@@ -34,7 +33,6 @@ Suggests:
     testthat (>= 3.0.0)
 Enhances:
     ergm,
-    Rgraphviz,
     RSiena
 Authors@R: 
     c(person(given = "James",
diff --git a/NAMESPACE b/NAMESPACE
index 54b5a6d..4b35911 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -79,37 +79,7 @@ export(layout_tetrad)
 export(layout_triad)
 export(layout_valence)
 export(match_color)
-export(scale_color_centres)
-export(scale_color_ethz)
-export(scale_color_iheid)
-export(scale_color_rug)
-export(scale_color_sdgs)
-export(scale_color_uzh)
-export(scale_colour_centres)
-export(scale_colour_ethz)
 export(scale_colour_hue)
-export(scale_colour_iheid)
-export(scale_colour_rug)
-export(scale_colour_sdgs)
-export(scale_colour_uzh)
-export(scale_edge_color_centres)
-export(scale_edge_color_ethz)
-export(scale_edge_color_iheid)
-export(scale_edge_color_rug)
-export(scale_edge_color_sdgs)
-export(scale_edge_color_uzh)
-export(scale_edge_colour_centres)
-export(scale_edge_colour_ethz)
-export(scale_edge_colour_iheid)
-export(scale_edge_colour_rug)
-export(scale_edge_colour_sdgs)
-export(scale_edge_colour_uzh)
-export(scale_fill_centres)
-export(scale_fill_ethz)
-export(scale_fill_iheid)
-export(scale_fill_rug)
-export(scale_fill_sdgs)
-export(scale_fill_uzh)
 export(scale_size)
 export(scale_x_continuous)
 export(set_stocnet_theme)
diff --git a/NEWS.md b/NEWS.md
index fe24692..47a7fdf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,34 @@
+# autograph 0.6.0
+
+## Package
+
+- Updated logo
+
+## Graphing
+
+- `graphr()` now auto-dispatches to `graphs()` when passed a list of graphs
+- `graphs()` no longer requires `{patchwork}` to be loaded separately
+- Closed #12 by changing node aesthetics from `color` to `fill` using fillable shape codes (21–25) for nodes to support fill-based colour scales
+- Consolidated legend modifications into internal `graph_legends()` helper
+- Improved legend labelling:
+  - edge sign legend now labelled "Sign"
+  - edge weight/width now labelled "Weight"/"Width"
+  - node mode/shape legend now labelled "Mode"/"Shape"
+- Closed #8 by adding "isolates" argument to `graphr()`:
+  - `"legend"` (default) removes isolates from the graph but notes them in the legend
+  - `"caption"` removes isolates from the graph but notes them in the caption
+  - `"keep"` retains isolates in the graph as-is (closes #12)
+  
+## Theming
+
+- Removed `scale_*()` functions as redundant with better theme support and `match_color()`
+
+## Layouts
+
+- Replaced `{Rgraphviz}` (Bioconductor) with `igraph::layout_with_sugiyama` for Sugiyama/hierarchy layouts, removing the Bioconductor dependency
+- Improved Sugiyama layout with dummy node insertion and barycenter crossing minimisation for better edge routing
+- Fixed #18 for lattice layout snapping by rotating the layout to optimise edge verticality and horizontality
+
 # autograph 0.5.1
 
 ## Plotting
diff --git a/R/autograph_utilities.R b/R/autograph_utilities.R
index 90612d0..0d50324 100644
--- a/R/autograph_utilities.R
+++ b/R/autograph_utilities.R
@@ -1,3 +1,4 @@
+# nocov start
 # Helper function for checking and downloading packages
 thisRequires <- function(pkgname){
   if (!requireNamespace(pkgname, quietly = TRUE) & interactive()) {
@@ -9,15 +10,7 @@ thisRequires <- function(pkgname){
     }
   }
 }
-
-thisRequiresBio <- function(pkgname) {
-  if (!requireNamespace(pkgname, quietly = TRUE) & interactive()) {
-    if(utils::askYesNo(msg = paste("The", pkgname, 
-                                   "package is required to run this function. Would you like to install", pkgname, "from BioConductor?"))) {
-      thisRequires("BiocManager")
-      BiocManager::install(pkgname)
-    }}
-}
+# nocov end
 
 seq_nodes <- function(.data){
   seq.int(manynet::net_nodes(.data))
diff --git a/R/graph_edges.R b/R/graph_edges.R
index b116077..5c3a6ac 100644
--- a/R/graph_edges.R
+++ b/R/graph_edges.R
@@ -16,7 +16,7 @@ graph_edges <- function(p, g, edge_color, edge_size, node_size) {
                                                       guide = ggplot2::guide_legend(
                                                         ifelse(is.null(edge_size) &
                                                                  manynet::is_weighted(g),
-                                                               "Edge Weight", "Edge Size")))
+                                                               "Weight", "Width")))
   if (length(unique(out[["ecolor"]])) == 1) {
     p <- p + ggplot2::guides(edge_colour = "none")
   } else if (length(unique(out[["ecolor"]])) == 2){
@@ -24,12 +24,12 @@ graph_edges <- function(p, g, edge_color, edge_size, node_size) {
                                               guide = ggplot2::guide_legend(
                                                 ifelse(is.null(edge_color) &
                                                          manynet::is_signed(g),
-                                                       "Edge Sign", edge_color)))
+                                                       "Sign", edge_color)))
   } else p <- p + ggraph::scale_edge_colour_manual(values = ag_qualitative(length(unique(out[["ecolor"]]))),
                                                    guide = ggplot2::guide_legend(
                                                      ifelse(is.null(edge_color) &
                                                               manynet::is_signed(g),
-                                                            "Edge Sign", edge_color)))
+                                                            "Sign", edge_color)))
   p
 }
 
diff --git a/R/graph_labels.R b/R/graph_labels.R
index a0b8913..6776397 100644
--- a/R/graph_labels.R
+++ b/R/graph_labels.R
@@ -2,17 +2,20 @@ graph_labels <- function(p, g, layout) {
   if (layout == "circle" | layout == "concentric") {
     angles <- as.data.frame(.cart2pol(as.matrix(p[["data"]][,1:2])))
     angles$degree <- angles$phi * 180/pi
-    angles <- dplyr::case_when(p[["data"]][,2] == 0 & p[["data"]][,1] == 0 ~ 0.1,
-                               p[["data"]][,2] >= 0 & p[["data"]][,1] > 0 ~ angles$degree,
-                               p[["data"]][,2] < 0 & p[["data"]][,1] > 0 ~ angles$degree,
-                               p[["data"]][,1] == 1 ~ angles$degree,
+    # Extract x and y as vectors for case_when
+    x_coord <- p[["data"]][[1]]
+    y_coord <- p[["data"]][[2]]
+    angles <- dplyr::case_when(y_coord == 0 & x_coord == 0 ~ 0.1,
+                               y_coord >= 0 & x_coord > 0 ~ angles$degree,
+                               y_coord < 0 & x_coord > 0 ~ angles$degree,
+                               x_coord == 1 ~ angles$degree,
                                TRUE ~ angles$degree - 180)
     if (manynet::net_nodes(g) < 10) {
-      hj <- ifelse(p[["data"]][,1] >= 0, -0.8, 1.8)
+      hj <- ifelse(x_coord >= 0, -0.8, 1.8)
     } else if (manynet::net_nodes(g) < 20) {
-      hj <- ifelse(p[["data"]][,1] >= 0, -0.4, 1.4)
+      hj <- ifelse(x_coord >= 0, -0.4, 1.4)
     } else {
-      hj <- ifelse(p[["data"]][,1] >= 0, -0.2, 1.2)
+      hj <- ifelse(x_coord >= 0, -0.2, 1.2)
     }
     p <- p + ggraph::geom_node_text(ggplot2::aes(label = name), repel = TRUE,
                                     family = ag_font(),
diff --git a/R/graph_layout.R b/R/graph_layout.R
index 5b0993e..4ff2c5a 100644
--- a/R/graph_layout.R
+++ b/R/graph_layout.R
@@ -23,11 +23,19 @@ graph_layout <- function(g, layout, labels, node_group, snap, ...) {
   }
   if(snap){
     manynet::snet_info("Snapping layout coordinates to grid.")
-    if(grepl("lattice", 
-             igraph::graph_attr(attr(p$data, "graph"), "grand")$name, 
-             ignore.case = TRUE))
-      p$data[,c("x","y")] <- round(p$data[,c("x","y")])
-    else p$data[,c("x","y")] <- depth_first_recursive_search(p)
+    if(grepl("lattice", manynet::net_name(g), ignore.case = TRUE)){
+      
+      angles <- seq(0, pi/2, length.out = 180)
+      scores <- sapply(angles, function(a) {
+        lay2 <- .rotate_layout(lo, a)
+        .edge_angle_deviation(lay2, g)
+      })
+      
+      best_angle <- angles[which.min(scores)]
+      rotated_coords <- .rotate_layout(lo, best_angle)
+      # Make sure that the coordinates, if rounded to integers, are still unique
+      p$data[,c("x","y")] <- round(rotated_coords[,c("x","y")])
+    } else p$data[,c("x","y")] <- depth_first_recursive_search(p)
   }
   # Add background ----
   if(getOption("snet_background", default = "#FFFFFF")!="#FFFFFF")
@@ -35,3 +43,30 @@ graph_layout <- function(g, layout, labels, node_group, snap, ...) {
                                                                                       default = "#FFFFFF")))
   p
 }
+
+# Helper functions ----
+
+.rotate_layout <- function(layout, angle) {
+  rot <- matrix(c(cos(angle), -sin(angle),
+                  sin(angle),  cos(angle)), ncol = 2)
+  coords <- as.matrix(layout[, c("x", "y")])
+  newcoords <- coords %*% rot
+  layout$x <- newcoords[,1]
+  layout$y <- newcoords[,2]
+  layout
+}
+
+.edge_angle_deviation <- function(layout, graph) {
+  ed <- igraph::as_edgelist(graph)
+  dx <- layout$x[ed[,2]] - layout$x[ed[,1]]
+  dy <- layout$y[ed[,2]] - layout$y[ed[,1]]
+  ang <- atan2(dy, dx)
+  
+  # deviation from nearest multiple of 90°
+  dev <- abs((ang %% (pi/2)) - pi/4)
+  mean(dev)
+}
+
+
+
+
diff --git a/R/graph_legends.R b/R/graph_legends.R
new file mode 100644
index 0000000..0684d0f
--- /dev/null
+++ b/R/graph_legends.R
@@ -0,0 +1,28 @@
+
+graph_legends <- function(p, g, 
+                          node_color = NULL, node_shape = NULL, node_size = NULL,
+                          edge_color = NULL, edge_size = NULL) {
+  p +
+    ggplot2::guides(fill = ggplot2::guide_legend(order = 1,
+                                                 title = ifelse(is.null(node_color), 
+                                                                "Color", node_color)),
+                    color = ggplot2::guide_legend(order = 2), 
+                    shape = ggplot2::guide_legend(order = 3,
+                                                  title = ifelse(is.null(node_shape),
+                                                                 ifelse(manynet::is_twomode(g), "Mode", "Shape"),
+                                                                 node_shape)),
+                    size = ggplot2::guide_legend(order = 4,
+                                                 title = ifelse(is.null(node_size),
+                                                                "Size", node_size)),
+                    linetype = ggplot2::guide_legend(order = 5),
+                    edge_colour = ggplot2::guide_legend(order = 6,
+                                                        title = ifelse(is.null(edge_color),
+                                                                       ifelse(manynet::is_signed(g), "Sign", "Color"),
+                                                                       edge_color)),
+                    edge_size = ggplot2::guide_legend(order = 7,
+                                                      title = ifelse(is.null(edge_size),
+                                                                     ifelse(manynet::is_weighted(g), "Weight", "Size"),
+                                                                     edge_size)),
+                    alpha = ggplot2::guide_legend(order = 99,
+                                                  override.aes = list( alpha = 0, size = 0, shape = NA )))
+}
\ No newline at end of file
diff --git a/R/graph_nodes.R b/R/graph_nodes.R
index 3d9ae70..76b6580 100644
--- a/R/graph_nodes.R
+++ b/R/graph_nodes.R
@@ -11,19 +11,22 @@ graph_nodes <- function(p, g, node_color, node_shape, node_size) {
       p <- p + ggplot2::guides(size = ggplot2::guide_legend(title = node_size))
     if (length(unique(out[["nshape"]])) > 1) 
       p <- p + ggplot2::guides(shape = ggplot2::guide_legend(
-        title = ifelse(manynet::is_twomode(g) & is.null(node_shape), "Node Mode", "Node Shape")))
+        title = ifelse(manynet::is_twomode(g) & is.null(node_shape), 
+                       "Mode", node_shape)))
     if (length(unique(out[["ncolor"]])) > 1){
       if(length(unique(out[["ncolor"]])) == 2){
-        p <- p + ggplot2::scale_colour_manual(values = getOption("snet_highlight", default = c("grey","black")),
+        p <- p + ggplot2::scale_fill_manual(values = getOption("snet_highlight", 
+                                                               default = c("grey","black")),
                                               guide = ggplot2::guide_legend(node_color))
       } else {
-        p <- p + ggplot2::scale_colour_manual(values = ag_qualitative(length(unique(out[["ncolor"]]))),
+        p <- p + ggplot2::scale_fill_manual(values = ag_qualitative(length(unique(out[["ncolor"]]))),
                                               guide = ggplot2::guide_legend(node_color))
       }
     }
   }
   # Consider rescaling nodes
-  p <- p + ggplot2::scale_size(range = c(1/manynet::net_nodes(g)*50, 1/manynet::net_nodes(g)*100))
+  p <- p + ggplot2::scale_size(range = c(1/manynet::net_nodes(g)*50, 
+                                         1/manynet::net_nodes(g)*100))
   p
 }
 
@@ -56,7 +59,7 @@ graph_nodes <- function(p, g, node_color, node_shape, node_size) {
   } else if (is_twomode(g) & is.null(node_shape)) {
     out <- ifelse(igraph::V(g)$type, "One", "Two")
   } else {
-    out <- "circle"
+    out <- 21  # Use fillable circle shape (was "circle")
   }
   out
 }
@@ -104,9 +107,9 @@ graph_nodes <- function(p, g, node_color, node_shape, node_size) {
                                  "R" ~ "Recovered",
                                  "S" ~ "Susceptible")
   cols <- match_color(c("#d73027", "#4575b4", "#E6AB02", "#66A61E"))
-  p + ggraph::geom_node_point(ggplot2::aes(color = node_color),
+  p + ggraph::geom_node_point(ggplot2::aes(fill = node_color),
                               size = out[["nsize"]], shape = out[["nshape"]]) +
-    ggplot2::scale_color_manual(name = NULL, guide = ggplot2::guide_legend(""),
+    ggplot2::scale_fill_manual(name = NULL, guide = ggplot2::guide_legend(""),
                                 values = c("Infected" = cols[1],
                                            "Susceptible" = cols[2],
                                            "Exposed" = cols[3],
@@ -121,9 +124,9 @@ graph_nodes <- function(p, g, node_color, node_shape, node_size) {
   node_color <- ifelse(is.infinite(node_adopts), 
                        max(node_adopts[!is.infinite(node_adopts)]) + 1, 
                        node_adopts)
-  p + ggraph::geom_node_point(ggplot2::aes(shape = nshape, color = node_color),
+  p + ggraph::geom_node_point(ggplot2::aes(shape = nshape, fill = node_color),
                               size = out[["nsize"]]) +
-    ggplot2::scale_color_gradient(low = match_color("#d73027"), high = match_color("#4575b4"),
+    ggplot2::scale_fill_gradient(low = match_color("#d73027"), high = match_color("#4575b4"),
                                   breaks=c(min(node_color)+1, 
                                            ifelse(any(nshape=="Non-Adopter"),
                                                   max(node_color)-1,
@@ -132,40 +135,51 @@ graph_nodes <- function(p, g, node_color, node_shape, node_size) {
                                   name = "Time of\nAdoption\n") +
     ggplot2::scale_shape_manual(name = "",
                                 breaks = c("Seed(s)", "Adopter", "Non-Adopter"),
-                                values = c("Seed(s)" = "triangle",
-                                           "Adopter" = "circle",
-                                           "Non-Adopter" = "square")) +
-    ggplot2::guides(color = ggplot2::guide_colorbar(order = 1, reverse = TRUE),
+                                values = c("Seed(s)" = 24,    # triangle
+                                           "Adopter" = 21,     # circle
+                                           "Non-Adopter" = 22)) +  # square
+    ggplot2::guides(fill = ggplot2::guide_colorbar(order = 1, reverse = TRUE),
                     shape = ggplot2::guide_legend(order = 2))
 }
 
 .map_nodes <- function(p, out) {
-  if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) == 1 & length(out[["nshape"]]) == 1) {
-    p <- p + ggraph::geom_node_point(colour = out[["ncolor"]], size = out[["nsize"]],
+  if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) == 1 & 
+      length(out[["nshape"]]) == 1) {
+    p <- p + ggraph::geom_node_point(fill = out[["ncolor"]], size = out[["nsize"]],
                                      shape = out[["nshape"]])
-  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) == 1 & length(out[["nshape"]]) == 1) {
-    p <- p + ggraph::geom_node_point(ggplot2::aes(colour = out[["ncolor"]]), 
+  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) == 1 & 
+             length(out[["nshape"]]) == 1) {
+    p <- p + ggraph::geom_node_point(ggplot2::aes(fill = out[["ncolor"]]), 
                                      size = out[["nsize"]], shape = out[["nshape"]])
-  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) > 1 & length(out[["nshape"]]) == 1) {
+  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) > 1 & 
+             length(out[["nshape"]]) == 1) {
     p <- p + ggraph::geom_node_point(ggplot2::aes(size = out[["nsize"]]),
-                                     colour = out[["ncolor"]], shape = out[["nshape"]])
-  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) == 1 & length(out[["nshape"]]) > 1) {
+                                     fill = out[["ncolor"]], shape = out[["nshape"]])
+  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) == 1 & 
+             length(out[["nshape"]]) > 1) {
     p <- p + ggraph::geom_node_point(ggplot2::aes(shape = out[["nshape"]]),
-                                     colour = out[["ncolor"]], size = out[["nsize"]])
-  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) > 1 & length(out[["nshape"]]) == 1) {
-    p <- p + ggraph::geom_node_point(ggplot2::aes(colour = out[["ncolor"]], size = out[["nsize"]]),
+                                     fill = out[["ncolor"]], size = out[["nsize"]])
+  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) > 1 & 
+             length(out[["nshape"]]) == 1) {
+    p <- p + ggraph::geom_node_point(ggplot2::aes(fill = out[["ncolor"]], 
+                                                  size = out[["nsize"]]),
                                      shape = out[["nshape"]])
-  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) == 1 & length(out[["nshape"]]) > 1) {
-    p <- p + ggraph::geom_node_point(ggplot2::aes(colour = out[["ncolor"]], shape = out[["nshape"]]),
+  } else if (length(out[["ncolor"]]) > 1 & length(out[["nsize"]]) == 1 & 
+             length(out[["nshape"]]) > 1) {
+    p <- p + ggraph::geom_node_point(ggplot2::aes(fill = out[["ncolor"]], 
+                                                  shape = out[["nshape"]]),
                                      size = out[["nsize"]])
-  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) > 1 & length(out[["nshape"]]) > 1) {
-    p <- p + ggraph::geom_node_point(ggplot2::aes(size = out[["nsize"]], shape = out[["nshape"]]),
-                                     colour = out[["ncolor"]])
+  } else if (length(out[["ncolor"]]) == 1 & length(out[["nsize"]]) > 1 & 
+             length(out[["nshape"]]) > 1) {
+    p <- p + ggraph::geom_node_point(ggplot2::aes(size = out[["nsize"]], 
+                                                  shape = out[["nshape"]]),
+                                     fill = out[["ncolor"]])
   } else {
-    p <- p + ggraph::geom_node_point(ggplot2::aes(colour = out[["ncolor"]],
+    p <- p + ggraph::geom_node_point(ggplot2::aes(fill = out[["ncolor"]],
                                                   shape = out[["nshape"]],
                                                   size = out[["nsize"]]))
   }
+  p <- p + ggplot2::scale_shape_manual(values = c(21, 22, 24, 23, 25))
   p
 }
 
diff --git a/R/graphr.R b/R/graphr.R
index 63ef8f2..742d887 100644
--- a/R/graphr.R
+++ b/R/graphr.R
@@ -5,12 +5,9 @@
 #'   (m)any network data for exploration, investigation, inspiration, 
 #'   and communication.
 #'   
-#'   It builds upon `{ggplot2}` and `{ggraph}` to offer
-#'   pretty and extensible graphing solutions.
-#'   However, compared to those solutions, 
-#'   `graphr()` contains various algorithms to provide better looking
-#'   graphs by default.
-#'   This means that just passing the function some network data
+#'   `graphr()` builds upon `{ggplot2}` and `{ggraph}` to offer
+#'   pretty, easy, and extensible graphing solutions.
+#'   Just passing the function some network data
 #'   will often be sufficient to return a reasonable-looking graph.
 #'   
 #'   The function also makes it easy to modify many of the most
@@ -84,6 +81,14 @@
 #'   it is recommended to calculate all edge-related statistics prior
 #'   to using this function.
 #'   Edges can also be sized by declaring a numeric size or vector instead.
+#' @param isolates Character scalar, how to treat isolates.
+#'   "keep"  will keep isolates in the graph as they are.
+#'   "legend" (default) will remove isolates from the graph but note them in the legend.
+#'   "caption" will remove isolates from the graph but note them in the caption.
+#'   If there are no isolates, this argument will be ignored.
+#'   If the default layout ("stress") is used, 
+#'   we recommend that the "legend" option is used to avoid isolates crowding
+#'   out the giant component.
 #' @param snap Logical scalar, whether the layout should be snapped to a grid.
 #' @param ... Extra arguments to pass on to the layout algorithm, if necessary.
 #' @return A `ggplot2::ggplot()` object.
@@ -103,9 +108,27 @@
 #' @export
 graphr <- function(.data, layout = NULL, labels = TRUE,
                    node_color, node_shape, node_size, node_group,
-                   edge_color, edge_size, snap = FALSE, ...,
+                   edge_color, edge_size, 
+                   isolates = c("legend","caption","keep"), snap = FALSE, ...,
                    node_colour, edge_colour) {
+  if(manynet::is_list(.data)) return(graphs(.data, layout = layout, labels = labels,
+                             node_color = node_color, node_shape = node_shape, node_size = node_size, node_group = node_group,
+                             edge_color = edge_color, edge_size = edge_size, 
+                             isolates = isolates, snap = snap, ...,
+                             node_colour = node_colour, edge_colour = edge_colour))
   g <- manynet::as_tidygraph(.data)
+  
+  # Separate isolates ----
+  isolates <- .infer_isolates(g, match.arg(isolates))
+  if(isolates != "keep"){
+    if(manynet::is_labelled(g)){
+      isos <- manynet::node_names(g)[manynet::node_is_isolate(g)]
+    } else {
+      isos <- which(manynet::node_is_isolate(g))
+    }
+    g <- manynet::to_no_isolates(g)
+  } 
+  
   layout <- .infer_layout(g, layout)
   if (missing(node_color) && missing(node_colour)) {
     node_color <- NULL
@@ -144,11 +167,36 @@ graphr <- function(.data, layout = NULL, labels = TRUE,
   if (isTRUE(labels) & manynet::is_labelled(g)) {
     p <- graph_labels(p, g, layout)
   }
+  
+  # Note isolates ----
+  if(isolates == "legend"){
+    if (length(isos) > 3) label_text <- paste(c(utils::head(isos, 3),"..."), collapse = "\n") else 
+      label_text <- paste(isos, collapse = "\n")
+    p <- p + ggplot2::geom_point(aes(x=rep(0, manynet::net_nodes(g)), y=0, 
+                                     alpha = "Isolates"), 
+                                 size = 0) +
+      ggplot2::scale_alpha_manual(name = "+ Isolates", 
+                                  values = c("Isolates" = 0.5), 
+                                  labels = label_text)
+  } else if(isolates == "caption"){
+    p <- p + ggplot2::labs(caption = paste("Isolates:", paste(isos, collapse = ", ")))
+  }
+  
+  # Add legends ----
+  p <- graph_legends(p, g, 
+                     node_color, node_shape, node_size,
+                     edge_color, edge_size)
+  
   # assign("last.warning", NULL, envir = baseenv()) # to avoid persistent ggrepel
   p
 }
 
-# Helper functions for graphr()
+# Helper functions for graphr() ----
+.infer_isolates <- function(g, isolates){
+  if(!any(manynet::node_is_isolate(g))) isolates <- "keep"
+  isolates
+}
+
 .infer_layout <- function(g, layout) {
   if (is.null(layout)) {
     if(manynet::is_list(g))
diff --git a/R/graphs.R b/R/graphs.R
index a808cfe..4fcdacd 100644
--- a/R/graphs.R
+++ b/R/graphs.R
@@ -41,7 +41,6 @@
 #' @export
 graphs <- function(netlist, waves,
                    based_on = c("first", "last", "both"), ...) {
-  thisRequires("patchwork")
   based_on <- match.arg(based_on)
   if (manynet::is_manynet(netlist) && manynet::is_changing(netlist)){
     if (manynet::is_list(attr(netlist, "network"))) netlist <- attr(netlist, "network") else
diff --git a/R/grapht.R b/R/grapht.R
index 9359c36..3683a2b 100644
--- a/R/grapht.R
+++ b/R/grapht.R
@@ -1,3 +1,4 @@
+# nocov start
 # Dynamic networks ####
 
 #' Easily animate dynamic networks with sensible defaults
@@ -195,10 +196,10 @@ grapht <- function(tlist, keep_isolates = TRUE,
     if (node_shape %in% names(nodes_out)) {
       node_shape <- as.factor(nodes_out[[node_shape]])
       if (!any(grepl("circle|square|triangle", node_shape))) {
-        node_shape <- c("circle", "square", "triangle")[node_shape]
+        node_shape <- c(21, 22, 24)[node_shape]  # circle, square, triangle (fillable)
       }
     }
-  } else node_shape <- "circle"
+  } else node_shape <- 21  # fillable circle (was "circle")
   if (!is.null(node_color)) {
     if (node_color %in% names(nodes_out)) {
       node_color <- .check_color(nodes_out[[node_color]])
@@ -228,9 +229,9 @@ grapht <- function(tlist, keep_isolates = TRUE,
   # Plot nodes ####
   if ("diffusion" %in% names(nodes_out)) {
     cols <- match_color(c("#d73027", "#4575b4", "#E6AB02", "#66A61E"))
-    p + ggraph::geom_node_point(ggplot2::aes(color = node_color),
+    p + ggraph::geom_node_point(ggplot2::aes(fill = node_color),
                                 size = node_size, shape = node_shape) +
-      ggplot2::scale_color_manual(name = NULL, guide = ggplot2::guide_legend(""),
+      ggplot2::scale_fill_manual(name = NULL, guide = ggplot2::guide_legend(""),
                                   values = c("Infected" = cols[1],
                                              "Susceptible" = cols[2],
                                              "Exposed" = cols[3],
@@ -240,7 +241,7 @@ grapht <- function(tlist, keep_isolates = TRUE,
   } else {
     p <- p + ggplot2::geom_point(aes(x, y, group = name), alpha = alphad,
                                  size = node_size, data = nodes_out,
-                                 color = node_color, shape = node_shape,
+                                 fill = node_color, shape = node_shape,
                                  show.legend = FALSE) +
       ggplot2::theme_void()
   }
@@ -317,3 +318,4 @@ grapht <- function(tlist, keep_isolates = TRUE,
     dplyr::mutate(status = ifelse(is.na(status), FALSE, TRUE)) %>%
     dplyr::distinct()
 }
+# nocov end
diff --git a/R/layout_partition.R b/R/layout_partition.R
index 57e5f3f..6f2373e 100644
--- a/R/layout_partition.R
+++ b/R/layout_partition.R
@@ -3,11 +3,6 @@
 #' @description
 #'   These algorithms layout networks based on two or more partitions,
 #'   and are recommended for use with `graphr()` or `{ggraph}`.
-#'   Note that these layout algorithms use `{Rgraphviz}`, 
-#'   a package that is only available on Bioconductor.
-#'   It will first need to be downloaded using `BiocManager::install("Rgraphviz")`.
-#'   If it has not already been installed, there is a prompt the first time
-#'   these functions are used though.
 #'
 #'   The "hierarchy" layout layers the first node set along the bottom,
 #'   and the second node set along the top, 
@@ -167,7 +162,6 @@ layout_lineage <- function(.data, rank, circular = FALSE) {
   } else if (length(rank) != length(.data)) {
     rank <- as.numeric(manynet::node_attribute(.data, rank))
   }
-  thisRequiresBio("Rgraphviz")
   out <- layout_tbl_graph_alluvial(
     manynet::as_igraph(mutate(.data, type = ifelse(
       rank > mean(rank), TRUE, FALSE)), twomode = TRUE))
@@ -183,6 +177,119 @@ layout_tbl_graph_lineage <- layout_lineage
   (vector - min(vector)) / (max(vector) - min(vector))
 }
 
+# Sugiyama-style layout with dummy nodes and barycenter heuristic
+# for better edge crossing minimization
+.sugiyama_layout <- function(g, layers = NULL, times = 100) {
+  n <- igraph::vcount(g)
+  el <- igraph::as_edgelist(g, names = FALSE)
+  # Layer assignment
+  if (is.null(layers)) {
+    lo <- igraph::layout_with_sugiyama(g, maxiter = times)
+    node_layer <- lo$layout[, 2]
+  } else {
+    node_layer <- layers
+  }
+  layer_vals <- sort(unique(node_layer))
+  n_layers <- length(layer_vals)
+  if (n_layers < 2) {
+    return(cbind(seq_len(n), node_layer))
+  }
+  # Map layers to 0-based indices (used as list keys offset by 1)
+  layer_idx <- match(node_layer, layer_vals) - 1L
+  # Build adjacency between original nodes
+  adj <- vector("list", n)
+  radj <- vector("list", n)
+  for (i in seq_len(n)) { adj[[i]] <- integer(0); radj[[i]] <- integer(0) }
+  if (nrow(el) > 0) {
+    for (i in seq_len(nrow(el))) {
+      u <- el[i, 1]; v <- el[i, 2]
+      adj[[u]] <- c(adj[[u]], v)
+      radj[[v]] <- c(radj[[v]], u)
+    }
+  }
+  # Insert dummy nodes for edges spanning multiple layers
+  dummy_id <- n
+  # For barycenter, we need per-layer node lists and inter-layer edges
+  all_layer <- layer_idx  # will grow with dummies
+  # Build inter-layer edges (only between adjacent layers)
+  inter_edges <- list()
+  if (nrow(el) > 0) {
+    for (i in seq_len(nrow(el))) {
+      u <- el[i, 1]; v <- el[i, 2]
+      lu <- layer_idx[u]; lv <- layer_idx[v]
+      if (lu == lv) next
+      # Ensure direction goes from lower layer to higher
+      if (lu > lv) { tmp <- u; u <- v; v <- tmp; tmp <- lu; lu <- lv; lv <- tmp }
+      if (lv - lu == 1) {
+        inter_edges[[length(inter_edges) + 1]] <- c(u, v)
+      } else {
+        # Insert dummy nodes
+        prev <- u
+        for (k in (lu + 1):(lv - 1)) {
+          dummy_id <- dummy_id + 1
+          all_layer <- c(all_layer, k)
+          inter_edges[[length(inter_edges) + 1]] <- c(prev, dummy_id)
+          prev <- dummy_id
+        }
+        inter_edges[[length(inter_edges) + 1]] <- c(prev, v)
+      }
+    }
+  }
+  total_nodes <- length(all_layer)
+  if (length(inter_edges) == 0) {
+    return(cbind(seq_len(n), node_layer))
+  }
+  inter_edges_mat <- do.call(rbind, inter_edges)
+  # Build per-layer node lists
+  layer_nodes <- lapply(0:(n_layers - 1), function(k) which(all_layer == k))
+  # Initialize x positions: sequential within each layer
+  x_pos <- rep(0, total_nodes)
+  for (k in seq_along(layer_nodes)) {
+    nodes_in_layer <- layer_nodes[[k]]
+    x_pos[nodes_in_layer] <- seq_along(nodes_in_layer)
+  }
+  # Build forward/backward adjacency for the expanded graph
+  fwd_adj <- vector("list", total_nodes)
+  bwd_adj <- vector("list", total_nodes)
+  for (i in seq_len(total_nodes)) { fwd_adj[[i]] <- integer(0); bwd_adj[[i]] <- integer(0) }
+  if (!is.null(inter_edges_mat) && nrow(inter_edges_mat) > 0) {
+    for (i in seq_len(nrow(inter_edges_mat))) {
+      u <- inter_edges_mat[i, 1]; v <- inter_edges_mat[i, 2]
+      fwd_adj[[u]] <- c(fwd_adj[[u]], v)
+      bwd_adj[[v]] <- c(bwd_adj[[v]], u)
+    }
+  }
+  # Barycenter crossing minimization sweeps
+  for (iter in seq_len(times)) {
+    # Forward sweep: layer 1 to n_layers-1
+    for (k in 2:n_layers) {
+      nodes_k <- layer_nodes[[k]]
+      if (length(nodes_k) <= 1) next
+      bc <- sapply(nodes_k, function(nd) {
+        neighbors <- bwd_adj[[nd]]
+        if (length(neighbors) == 0) return(x_pos[nd])
+        mean(x_pos[neighbors])
+      })
+      ord <- order(bc)
+      x_pos[nodes_k[ord]] <- seq_along(nodes_k)
+    }
+    # Backward sweep: layer n_layers-2 to 0
+    for (k in (n_layers - 1):1) {
+      nodes_k <- layer_nodes[[k]]
+      if (length(nodes_k) <= 1) next
+      bc <- sapply(nodes_k, function(nd) {
+        neighbors <- fwd_adj[[nd]]
+        if (length(neighbors) == 0) return(x_pos[nd])
+        mean(x_pos[neighbors])
+      })
+      ord <- order(bc)
+      x_pos[nodes_k[ord]] <- seq_along(nodes_k)
+    }
+  }
+  # Extract coordinates for original nodes only
+  cbind(x_pos[seq_len(n)], node_layer)
+}
+
 #' @rdname layout_partition
 #' @examples
 #' #graphr(ison_southern_women, layout = "hierarchy", center = "events",
@@ -191,24 +298,24 @@ layout_tbl_graph_lineage <- layout_lineage
 layout_hierarchy <- function(.data, center = NULL,
                                        circular = FALSE, times = 1000) {
   if (is.null(center)) {
-    thisRequiresBio("Rgraphviz")
-    prep <- manynet::as_matrix(.data)
-    if (anyDuplicated(rownames(prep))) {
-      rownames(prep) <- seq_len(nrow(prep))
-      colnames(prep) <- seq_len(ncol(prep)) + max(nrow(prep))
+    g <- manynet::as_igraph(.data)
+    if (manynet::is_twomode(.data)) {
+      layers <- ifelse(igraph::V(g)$type, 2, 1)
+    } else {
+      layers <- NULL
     }
-    if (any(prep<0)) prep[prep<0] <- 0
-    out <- manynet::as_graphAM(prep)
-    out <- suppressMessages(Rgraphviz::layoutGraph(out, layoutType = 'dot',
-                                                   attrs = list(graph = list(rankdir = "BT"))))
-    nodeX <- .rescale(out@renderInfo@nodes$nodeX)
-    nodeY <- .rescale(out@renderInfo@nodes$nodeY)
+    lo <- .sugiyama_layout(g, layers = layers, times = times)
+    nodeX <- lo[, 1]
+    nodeY <- lo[, 2]
+    if (length(unique(nodeX)) > 1) nodeX <- .rescale(nodeX)
+    if (length(unique(nodeY)) > 1) nodeY <- .rescale(nodeY)
     if (manynet::is_twomode(.data) & "name" %in% igraph::vertex_attr_names(.data)) {
       names <- igraph::vertex_attr(.data, "name")
+      names(nodeX) <- igraph::vertex_attr(g, "name")
+      names(nodeY) <- igraph::vertex_attr(g, "name")
       nodeX <- nodeX[order(match(names(nodeX), names))]
       nodeY <- nodeY[order(match(names(nodeY), names))]
     }
-    # nodeY <- abs(nodeY - max(nodeY))
     out <- .to_lo(cbind(nodeX, nodeY))
   } else {
     if (!manynet::is_twomode(.data)) manynet::snet_abort("Please declare a two-mode network.")
@@ -259,21 +366,20 @@ layout_tbl_graph_hierarchy <- layout_hierarchy
 #' #graphr(ison_southern_women, layout = "alluvial")
 #' @export
 layout_alluvial <- function(.data,
-                                      circular = FALSE, times = 1000){
-  thisRequiresBio("Rgraphviz")
-  prep <- manynet::as_matrix(.data, twomode = FALSE)
-  if(anyDuplicated(rownames(prep))){
-    rownames(prep) <- seq_len(nrow(prep))
-    colnames(prep) <- seq_len(ncol(prep))
+                            circular = FALSE, times = 1000){
+  g <- manynet::as_igraph(.data)
+  if (manynet::is_twomode(.data)) {
+    layers <- ifelse(igraph::V(g)$type, 2, 1)
+  } else {
+    layers <- NULL
   }
-  if(any(prep<0)) prep[prep<0] <- 0
-  out <- manynet::as_graphAM(prep)
-  out <- suppressMessages(Rgraphviz::layoutGraph(out, layoutType = 'dot',
-                                                 attrs = list(graph = list(rankdir = "LR"))))
-  nodeX <- .rescale(out@renderInfo@nodes$nodeX)
-  nodeY <- .rescale(out@renderInfo@nodes$nodeY)
-  # nodeY <- abs(nodeY - max(nodeY))
-  .to_lo(cbind(nodeX, nodeY))  
+  lo <- .sugiyama_layout(g, layers = layers, times = times)
+  nodeX <- lo[, 1]
+  nodeY <- lo[, 2]
+  # Swap x and y for left-to-right layout (alluvial)
+  if (length(unique(nodeY)) > 1) nodeY <- .rescale(nodeY)
+  if (length(unique(nodeX)) > 1) nodeX <- .rescale(nodeX)
+  .to_lo(cbind(nodeY, nodeX))
 }
 
 #' @rdname layout_partition
diff --git a/R/theme_palettes.R b/R/theme_palettes.R
index c08a0be..d504106 100644
--- a/R/theme_palettes.R
+++ b/R/theme_palettes.R
@@ -118,3 +118,4 @@ ggpizza <- function(colors, init.angle = 105, cex = 4, labcol = NULL) {
     ggplot2::coord_equal() +
     ggplot2::theme_void()
 }
+
diff --git a/R/theme_scales.R b/R/theme_scales.R
deleted file mode 100644
index 5a574aa..0000000
--- a/R/theme_scales.R
+++ /dev/null
@@ -1,297 +0,0 @@
-#' Themed scales for further customization
-#' 
-#' @description These functions enable to add color scales to be graphs.
-#' @name theme_scales
-#' @param direction Direction for using palette colors.
-#' @param ... Extra arguments passed to `ggplot2::discrete_scale()`.
-#' @examples
-#' #ison_brandes %>%
-#' #mutate(core = migraph::node_is_core(ison_brandes)) %>%
-#' #graphr(node_color = "core") +
-#' #scale_color_iheid()
-#' #graphr(ison_physicians[[1]], edge_color = "type") +
-#' #scale_edge_color_ethz()
-NULL
-
-#' @rdname theme_scales
-#' @export
-scale_fill_iheid <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "IHEID", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_iheid <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "IHEID", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_iheid <- scale_colour_iheid
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_iheid <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "IHEID", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_iheid <- scale_edge_colour_iheid
-
-#' Centres color scales
-#' 
-#' @rdname theme_scales
-#' @export
-scale_fill_centres <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "Centres", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_centres <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "Centres", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_centres <- scale_colour_centres
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_centres <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "Centres", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_centres <- scale_edge_colour_centres
-
-#' SDGs color scales
-#' 
-#' @rdname theme_scales
-#' @export
-scale_fill_sdgs <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "SDGs", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_sdgs <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "SDGs", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_sdgs <- scale_colour_sdgs
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_sdgs <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "SDGs", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_sdgs <- scale_edge_colour_sdgs
-
-#' ETHZ color scales
-#' 
-#' @rdname theme_scales
-#' @export
-scale_fill_ethz <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "ETHZ", direction), 
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_ethz <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "ETHZ", direction), 
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_ethz <- scale_colour_ethz
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_ethz <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "ETHZ", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_ethz <- scale_edge_colour_ethz
-
-#' UZH color scales
-#' 
-#' @rdname theme_scales
-#' @export
-scale_fill_uzh <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "UZH", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_uzh <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "UZH", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_uzh <- scale_colour_uzh
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_uzh <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "UZH", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_uzh <- scale_edge_colour_uzh
-
-#' RUG color scales
-#' 
-#' @rdname theme_scales
-#' @export
-scale_fill_rug <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("fill",
-                          palette = palette_gen(palette = "RUG", direction),
-                          na.value = "grey", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_colour_rug <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("colour",
-                          palette = palette_gen(palette = "RUG", direction),
-                          na.value = "grey", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_color_rug <- scale_colour_rug
-
-#' @rdname theme_scales
-#' @export
-scale_edge_colour_rug <- function(direction = 1, ...) {
-  ggplot2::discrete_scale("edge_colour",
-                          palette = palette_gen(palette = "RUG", direction),
-                          na.value = "black", name = "", ...)
-}
-
-#' @rdname theme_scales
-#' @export
-scale_edge_color_rug <- scale_edge_colour_rug
-
-# Helper functions
-corp_color <- function(...) {
-  corp_colors <- c(`IHEIDRed` = "#E20020", `IHEIDBlack` = "#000010",
-                   `IHEIDGrey` = "#6f7072", `AHCD` = "#622550",
-                   `CFFD` = "#0094D8", `CIES` = "#268D2B",
-                   `CTEI` = "#008F92", `CGEN` = "#820C2B",
-                   `CCDP` = "#3E2682", `GLGC` = "#006564",
-                   `GLHC` = "#A8086E", `GLMC` = "#006EAA",
-                   `NoPoverty` = "#e5243b", `ZeroHunger` = "#DDA63A",
-                   `GoodHealth` = "#4C9F38",
-                   `QualityEducation` = "#C5192D",
-                   `GenderEquality` = "#FF3A21", `CleanWater` = "#26BDE2",
-                   `CleanEnergy` = "#FCC30B",
-                   `EconomicGrowth` = "#A21942",
-                   `Innovation` = "#FD6925",
-                   `ReducedInequalities` = "#DD1367",
-                   `SustainableCities` = "#FD9D24", 
-                   `ResponsibleConsumption` = "#BF8B2E",
-                   `ClimateAction` = "#3F7E44", `BelowWater` = "#0A97D9",
-                   `OnLand` = "#56C02B", `StrongInstitutions` = "#00689D",
-                   `GoalPartnerships` = "#19486A",
-                   `ETHZ_Blue` = "#215CAF", `ETHZ_Petrol` = "#007894",
-                   `ETHZ_Green` = "#627313", `ETHZ_Bronze` = "#8E6713",
-                   `ETHZ_Red`=	"#B7352D", `ETHZ_Purple` = "#A7117A",
-                   `ETHZ_Grey`	= "#6F6F6F", `UZH_Blue` = "#0028a5",
-                   `UZH_Grey` = "#a3adb7", `UZH_Orange` = "#dc6027",
-                   `RUG_Red` = "#dc002d", `RUG_Black` = "#000000")
-  cols <- c(...)
-  if (is.null(cols))
-    return (corp_colors)
-  corp_colors[cols]
-}
-
-corp_palette <- function(palette, ...) {
-  corp_palettes <- list(`IHEID` = corp_color("IHEIDRed",
-                                             "IHEIDBlack",
-                                             "IHEIDGrey"),
-                        `Centres` = corp_color("AHCD", "CFFD", 
-                                               "CIES", "CTEI",
-                                               "CGEN", "CCDP",
-                                               "GLGC", "GLHC",
-                                               "GLMC"),
-                        `SDGs` = corp_color("NoPoverty",
-                                            "ZeroHunger",
-                                            "GoodHealth", 
-                                            "QualityEducation",
-                                            "GenderEquality", 
-                                            "CleanWater",
-                                            "CleanEnergy",
-                                            "EconomicGrowth",
-                                            "Innovation", 
-                                            "ReducedInequalities",
-                                            "SustainableCities",
-                                            "ResponsibleConsumption",
-                                            "ClimateAction", 
-                                            "BelowWater", 
-                                            "OnLand",
-                                            "StrongInstitutions",
-                                            "GoalPartnerships"),
-                        `ETHZ` = corp_color("ETHZ_Blue", "ETHZ_Petrol",
-                                           "ETHZ_Green", "ETHZ_Bronze",
-                                           "ETHZ_Red", "ETHZ_Purple", "ETHZ_Grey"),
-                        `UZH` = corp_color("UZH_Blue", "UZH_Grey", "UZH_Orange"),
-                        `RUG` = corp_color("RUG_Red", "RUG_Black"))
-  unlist(unname(corp_palettes[c(palette)]))
-}
-
-palette_gen <- function(palette, direction = 1) {
-  function(n) {
-    if (n > length(corp_palette(palette)))
-      warning("Not enough colors in this palette!")
-    else {
-      all_colors <- corp_palette(palette)
-      all_colors <- unname(unlist(all_colors))
-      all_colors <- if (direction >= 0) all_colors else rev(all_colors)
-      color_list <- all_colors[1:n]
-    }
-  }
-}
-
diff --git a/R/zzz.R b/R/zzz.R
index 6a7a3c2..ac4ca01 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,3 +1,4 @@
+# nocov start
 .onAttach <- function(...) {
 
   # suppressMessages(suppressPackageStartupMessages(library("manynet", warn.conflicts = FALSE)))
@@ -42,5 +43,6 @@
   }
 
 }
+# nocov end
 
 
diff --git a/man/figures/logo-old.png b/man/figures/logo-old.png
new file mode 100644
index 0000000..bbaaaa0
Binary files /dev/null and b/man/figures/logo-old.png differ
diff --git a/man/figures/logo.png b/man/figures/logo.png
index bbaaaa0..f5a84fb 100644
Binary files a/man/figures/logo.png and b/man/figures/logo.png differ
diff --git a/man/layout_partition.Rd b/man/layout_partition.Rd
index bc57921..3bfa1f6 100644
--- a/man/layout_partition.Rd
+++ b/man/layout_partition.Rd
@@ -107,11 +107,6 @@ Defaults to NULL.}
 \description{
 These algorithms layout networks based on two or more partitions,
 and are recommended for use with \code{graphr()} or \code{{ggraph}}.
-Note that these layout algorithms use \code{{Rgraphviz}},
-a package that is only available on Bioconductor.
-It will first need to be downloaded using \code{BiocManager::install("Rgraphviz")}.
-If it has not already been installed, there is a prompt the first time
-these functions are used though.
 
 The "hierarchy" layout layers the first node set along the bottom,
 and the second node set along the top,
diff --git a/man/plot_graphr.Rd b/man/plot_graphr.Rd
index 23af626..83add13 100644
--- a/man/plot_graphr.Rd
+++ b/man/plot_graphr.Rd
@@ -15,6 +15,7 @@ graphr(
   node_group,
   edge_color,
   edge_size,
+  isolates = c("legend", "caption", "keep"),
   snap = FALSE,
   ...,
   node_colour,
@@ -87,6 +88,15 @@ it is recommended to calculate all edge-related statistics prior
 to using this function.
 Edges can also be sized by declaring a numeric size or vector instead.}
 
+\item{isolates}{Character scalar, how to treat isolates.
+"keep"  will keep isolates in the graph as they are.
+"legend" (default) will remove isolates from the graph but note them in the legend.
+"caption" will remove isolates from the graph but note them in the caption.
+If there are no isolates, this argument will be ignored.
+If the default layout ("stress") is used,
+we recommend that the "legend" option is used to avoid isolates crowding
+out the giant component.}
+
 \item{snap}{Logical scalar, whether the layout should be snapped to a grid.}
 
 \item{...}{Extra arguments to pass on to the layout algorithm, if necessary.}
@@ -100,12 +110,9 @@ This function provides users with an easy way to graph
 (m)any network data for exploration, investigation, inspiration,
 and communication.
 
-It builds upon \code{{ggplot2}} and \code{{ggraph}} to offer
-pretty and extensible graphing solutions.
-However, compared to those solutions,
-\code{graphr()} contains various algorithms to provide better looking
-graphs by default.
-This means that just passing the function some network data
+\code{graphr()} builds upon \code{{ggplot2}} and \code{{ggraph}} to offer
+pretty, easy, and extensible graphing solutions.
+Just passing the function some network data
 will often be sufficient to return a reasonable-looking graph.
 
 The function also makes it easy to modify many of the most
diff --git a/man/theme_scales.Rd b/man/theme_scales.Rd
deleted file mode 100644
index aa9b978..0000000
--- a/man/theme_scales.Rd
+++ /dev/null
@@ -1,112 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/theme_scales.R
-\name{theme_scales}
-\alias{theme_scales}
-\alias{scale_fill_iheid}
-\alias{scale_colour_iheid}
-\alias{scale_color_iheid}
-\alias{scale_edge_colour_iheid}
-\alias{scale_edge_color_iheid}
-\alias{scale_fill_centres}
-\alias{scale_colour_centres}
-\alias{scale_color_centres}
-\alias{scale_edge_colour_centres}
-\alias{scale_edge_color_centres}
-\alias{scale_fill_sdgs}
-\alias{scale_colour_sdgs}
-\alias{scale_color_sdgs}
-\alias{scale_edge_colour_sdgs}
-\alias{scale_edge_color_sdgs}
-\alias{scale_fill_ethz}
-\alias{scale_colour_ethz}
-\alias{scale_color_ethz}
-\alias{scale_edge_colour_ethz}
-\alias{scale_edge_color_ethz}
-\alias{scale_fill_uzh}
-\alias{scale_colour_uzh}
-\alias{scale_color_uzh}
-\alias{scale_edge_colour_uzh}
-\alias{scale_edge_color_uzh}
-\alias{scale_fill_rug}
-\alias{scale_colour_rug}
-\alias{scale_color_rug}
-\alias{scale_edge_colour_rug}
-\alias{scale_edge_color_rug}
-\title{Themed scales for further customization}
-\usage{
-scale_fill_iheid(direction = 1, ...)
-
-scale_colour_iheid(direction = 1, ...)
-
-scale_color_iheid(direction = 1, ...)
-
-scale_edge_colour_iheid(direction = 1, ...)
-
-scale_edge_color_iheid(direction = 1, ...)
-
-scale_fill_centres(direction = 1, ...)
-
-scale_colour_centres(direction = 1, ...)
-
-scale_color_centres(direction = 1, ...)
-
-scale_edge_colour_centres(direction = 1, ...)
-
-scale_edge_color_centres(direction = 1, ...)
-
-scale_fill_sdgs(direction = 1, ...)
-
-scale_colour_sdgs(direction = 1, ...)
-
-scale_color_sdgs(direction = 1, ...)
-
-scale_edge_colour_sdgs(direction = 1, ...)
-
-scale_edge_color_sdgs(direction = 1, ...)
-
-scale_fill_ethz(direction = 1, ...)
-
-scale_colour_ethz(direction = 1, ...)
-
-scale_color_ethz(direction = 1, ...)
-
-scale_edge_colour_ethz(direction = 1, ...)
-
-scale_edge_color_ethz(direction = 1, ...)
-
-scale_fill_uzh(direction = 1, ...)
-
-scale_colour_uzh(direction = 1, ...)
-
-scale_color_uzh(direction = 1, ...)
-
-scale_edge_colour_uzh(direction = 1, ...)
-
-scale_edge_color_uzh(direction = 1, ...)
-
-scale_fill_rug(direction = 1, ...)
-
-scale_colour_rug(direction = 1, ...)
-
-scale_color_rug(direction = 1, ...)
-
-scale_edge_colour_rug(direction = 1, ...)
-
-scale_edge_color_rug(direction = 1, ...)
-}
-\arguments{
-\item{direction}{Direction for using palette colors.}
-
-\item{...}{Extra arguments passed to \code{ggplot2::discrete_scale()}.}
-}
-\description{
-These functions enable to add color scales to be graphs.
-}
-\examples{
-#ison_brandes \%>\%
-#mutate(core = migraph::node_is_core(ison_brandes)) \%>\%
-#graphr(node_color = "core") +
-#scale_color_iheid()
-#graphr(ison_physicians[[1]], edge_color = "type") +
-#scale_edge_color_ethz()
-}
diff --git a/tests/testthat/test-graphr.R b/tests/testthat/test-graphr.R
index 3be6c8e..2c18a83 100644
--- a/tests/testthat/test-graphr.R
+++ b/tests/testthat/test-graphr.R
@@ -1,3 +1,15 @@
+data_objs <- mget(ls("package:manynet"), inherits = TRUE)
+# Filter to relevant objects 
+data_objs <- data_objs[grepl("ison_|fict_|irps_|mpn_", names(data_objs))]
+# data_objs <- data_objs[!grepl("starwars|physicians|potter", names(data_objs))]
+for (nm in names(data_objs)) { 
+  test_that(paste("graphr() works on", nm), {
+    skip_if(grepl("starwars|physicians|potter|marvel", nm))
+    expect_error(graphr(data_objs[[nm]]), NA) }) 
+}
+
+fmrg <- to_giant(to_uniplex(fict_marvel, "relationship"))
+
 test_that("unweighted, unsigned, undirected networks graph correctly", {
   skip_on_cran()
   # Unweighted, unsigned, undirected network
@@ -10,13 +22,13 @@ test_that("unweighted, unsigned, undirected networks graph correctly", {
   expect_equal(test_brandes[["layers"]][[1]][["aes_params"]][["edge_linetype"]], "solid")
   # Node parameters
   expect_equal(round(test_brandes[["layers"]][[2]][["aes_params"]][["size"]]), 11)
-  expect_equal(as.character(test_brandes[["layers"]][[2]][["aes_params"]][["shape"]]), "circle")
+  expect_equal(test_brandes[["layers"]][[2]][["aes_params"]][["shape"]], 21)  # fillable circle
 })
 
 test_that("unweighted, signed, undirected networks graph correctly", {
   skip_on_cran()
   # Unweighted, signed, undirected network
-  test_marvel <- graphr(to_giant(ison_marvel_relationships))
+  test_marvel <- graphr(fmrg)
   # Node position
   expect_equal(round(test_marvel[["data"]][["x"]][[1]]), -1)
   expect_equal(round(test_marvel[["data"]][["y"]][[1]]), 1)
@@ -40,7 +52,7 @@ test_that("unweighted, unsigned, directed networks graph correctly", {
   #expect_equal(test_algebra[["layers"]][[1]][["mapping"]][["edge_colour"]], "black")
   # Node parameters
   expect_equal(round(test_algebra[["layers"]][[2]][["aes_params"]][["size"]]), 8)
-  expect_equal(test_algebra[["layers"]][[2]][["aes_params"]][["shape"]], "circle")
+  expect_equal(test_algebra[["layers"]][[2]][["aes_params"]][["shape"]], 21)  # fillable circle
 })
 
 test_that("weighted, unsigned, directed networks graph correctly", {
@@ -65,15 +77,13 @@ test_that("fancy node mods graph correctly", {
   skip_on_cran()
   skip_on_ci()
   # one-mode network
-  ison_marvel_relationships <- dplyr::mutate(ison_marvel_relationships,
-                                             nodesize = Appearances/1000)
-  testcolnodes <- graphr(ison_marvel_relationships, node_color = "Gender",
-                         node_size = "nodesize", node_shape = "Attractive")
+  fmrg <- dplyr::mutate(fmrg, nodesize = Appearances/1000)
+  testcolnodes <- graphr(fmrg, node_color = "Gender",
+                         node_size = "Appearances", 
+                         node_shape = "Attractive")
   expect_s3_class(testcolnodes, c("ggraph","gg","ggplot"))
-  expect_equal(round(testcolnodes$data$x[1]), 4)
-  expect_equal(round(testcolnodes$data$y[1]), 3)
   expect_equal(nrow(testcolnodes[["plot_env"]][["lo"]]),
-               c(net_nodes(ison_marvel_relationships)))
+               c(net_nodes(fmrg)))
   # two-mode network
   ison_southern_women <- add_node_attribute(ison_southern_women, "group",
                                             c(sample(c("a", "b"),
@@ -121,3 +131,52 @@ test_that("unquoted arguments plot correctly", {
                graphr(ison_lawfirm, node_color = gender))
 })
 
+# Tests for fill aesthetic (color-to-fill change)
+test_that("nodes use fill aesthetic instead of colour", {
+  skip_on_cran()
+  # Default node uses fill parameter
+  p <- graphr(ison_brandes)
+  expect_equal(p[["layers"]][[2]][["aes_params"]][["fill"]], "black")
+  # Mapped node_color uses fill in aes
+  p2 <- ison_brandes %>%
+    dplyr::mutate(color = c(rep(c(1, 2), 5), 1)) %>%
+    graphr(node_color = color)
+  expect_false(is.null(p2[["layers"]][[2]][["mapping"]][["fill"]]))
+})
+
+test_that("node_color with multiple values uses fill scale", {
+  skip_on_cran()
+  # More than 2 colors triggers scale_fill_manual with qualitative palette
+  p <- ison_brandes %>%
+    dplyr::mutate(grp = c(rep(c("a", "b", "c"), 3), "a", "b")) %>%
+    graphr(node_color = grp)
+  expect_s3_class(p, c("ggraph", "gg", "ggplot"))
+  # Check that fill scale is used (not colour)
+  scale_names <- vapply(p[["scales"]][["scales"]], function(s) {
+    paste(s[["aesthetics"]], collapse = ",")
+  }, character(1))
+  expect_true(any(grepl("fill", scale_names)))
+})
+
+test_that("two-mode networks get correct node shapes", {
+  skip_on_cran()
+  p <- graphr(ison_southern_women)
+  expect_s3_class(p, c("ggraph", "gg", "ggplot"))
+  # Two-mode shape mapping should use "One"/"Two" labels
+  node_layer <- p[["layers"]][[2]]
+  expect_false(is.null(node_layer[["mapping"]][["shape"]]))
+})
+
+test_that("node_color with 2 values uses highlight palette", {
+  skip_on_cran()
+  p <- ison_brandes %>%
+    dplyr::mutate(grp = c(rep(c("x", "y"), 5), "x")) %>%
+    graphr(node_color = grp)
+  expect_s3_class(p, c("ggraph", "gg", "ggplot"))
+  # Should use scale_fill_manual with highlight defaults
+  scale_names <- vapply(p[["scales"]][["scales"]], function(s) {
+    paste(s[["aesthetics"]], collapse = ",")
+  }, character(1))
+  expect_true(any(grepl("fill", scale_names)))
+})
+
diff --git a/tests/testthat/test-layout_partition.R b/tests/testthat/test-layout_partition.R
index ff960e2..65a4001 100644
--- a/tests/testthat/test-layout_partition.R
+++ b/tests/testthat/test-layout_partition.R
@@ -1,10 +1,9 @@
 # Layouts
 test_that("concentric and circular layouts graph correctly", {
   skip_on_cran()
-  test_circle <- graphr(to_giant(ison_marvel_relationships),
-                        layout = "circle")
-  test_conc <- graphr(to_giant(ison_marvel_relationships),
-                      layout = "concentric", membership = "Gender")
+  fmrg <- to_giant(to_uniplex(fict_marvel, "relationship"))
+  test_circle <- graphr(fmrg, layout = "circle")
+  test_conc <- graphr(fmrg, layout = "concentric", membership = "Gender")
   expect_equal(test_circle$plot_env$layout, "circle")
   expect_equal(test_conc$plot_env$layout, "concentric")
   expect_equal(eval(quote(pairlist(...)),
@@ -23,7 +22,6 @@ test_that("concentric layout works when node names are missing", {
 
 test_that("hierarchy and lineage layouts graph correctly", {
   skip_on_cran()
-  skip_on_ci()
   test_lin <- ison_adolescents %>% 
     mutate(year = rep(c(1985, 1990, 1995, 2000), times = 2)) %>%
     graphr(layout = "lineage", rank = "year")
@@ -54,10 +52,61 @@ test_that("hierarchy and lineage layouts graph correctly", {
 
 test_that("hierarchy layout works for two mode networks", {
   skip_on_cran()
-  skip_on_ci()
   tm <- ison_brandes %>%
     mutate(type = twomode_type, name = LETTERS[1:11]) %>%
     graphr()
   expect_length(unique(tm$data[tm$data$type == TRUE, "y"]), 1)
   expect_length(unique(tm$data[tm$data$type == FALSE, "y"]), 1)
 })
+
+test_that("default hierarchy layout uses sugiyama for two-mode networks", {
+  skip_on_cran()
+  p <- graphr(ison_southern_women, layout = "hierarchy")
+  expect_s3_class(p, c("ggraph", "gg", "ggplot"))
+  expect_equal(p$plot_env$layout, "hierarchy")
+  # Two-mode should have exactly 2 unique y values (layers)
+  expect_equal(length(unique(round(p$data$y, 6))), 2)
+})
+
+test_that("alluvial layout works", {
+  skip_on_cran()
+  p <- graphr(ison_southern_women, layout = "alluvial")
+  expect_s3_class(p, c("ggraph", "gg", "ggplot"))
+  expect_equal(p$plot_env$layout, "alluvial")
+})
+
+test_that("hierarchy layout minimises edge crossings", {
+  skip_on_cran()
+  # Helper: count bipartite edge crossings given x positions
+  count_crossings <- function(el, x_pos) {
+    crossings <- 0
+    if (nrow(el) < 2) return(0)
+    for (i in 1:(nrow(el) - 1)) {
+      for (j in (i + 1):nrow(el)) {
+        a1 <- x_pos[el[i, 1]]; b1 <- x_pos[el[i, 2]]
+        a2 <- x_pos[el[j, 1]]; b2 <- x_pos[el[j, 2]]
+        if ((a1 - a2) * (b1 - b2) < 0) crossings <- crossings + 1
+      }
+    }
+    crossings
+  }
+  # Test with ison_southern_women (18 women, 14 events, 89 ties)
+  g <- manynet::as_igraph(ison_southern_women)
+  n <- igraph::vcount(g)
+  el <- igraph::as_edgelist(g, names = FALSE)
+  layers <- ifelse(igraph::V(g)$type, 2, 1)
+  lo <- autograph:::.sugiyama_layout(g, layers = layers, times = 100)
+  x_pos <- lo[, 1]
+  # Naive layout: sequential ordering within each layer
+  naive_x <- rep(0, n)
+  naive_x[layers == 1] <- seq_len(sum(layers == 1))
+  naive_x[layers == 2] <- seq_len(sum(layers == 2))
+  optimised_crossings <- count_crossings(el, x_pos)
+  naive_crossings <- count_crossings(el, naive_x)
+  # The optimised layout should have fewer crossings than naive
+  expect_lt(optimised_crossings, naive_crossings)
+  # Verify all nodes got valid positions
+  expect_true(all(is.finite(x_pos)))
+  expect_equal(length(unique(lo[layers == 1, 2])), 1)
+  expect_equal(length(unique(lo[layers == 2, 2])), 1)
+})
diff --git a/tests/testthat/test-theme_scales.R b/tests/testthat/test-theme_scales.R
deleted file mode 100644
index 7ae5ae3..0000000
--- a/tests/testthat/test-theme_scales.R
+++ /dev/null
@@ -1,28 +0,0 @@
-##### test scales
-test_that("scales graph correctly", {
-  test_sdg <- ison_brandes %>%
-    mutate(color = c(rep(c(1,2,3,4,5), 2), 1)) %>%
-    graphr(node_color = color) +
-    scale_color_sdgs()
-  test_iheid <- ison_brandes %>%
-    mutate(color = c(rep(c(1,2), 5), 3)) %>%
-    graphr(node_color = color) +
-    scale_color_iheid()
-  test_ethz <- ison_brandes %>%
-    mutate(color = c(rep(c(1,2,3), 3), 4, 5)) %>%
-    graphr(node_color = color) +
-    scale_color_ethz()
-  test_uzh <- ison_brandes %>%
-    mutate(color = c(rep(c(1,2,3), 3), 1, 2)) %>%
-    graphr(node_color = color) +
-    scale_color_uzh()
-  test_rug <- ison_brandes %>%
-    mutate(color = c(rep(c(1,2), 4), 1, 2, 1)) %>%
-    graphr(node_color = color) +
-    scale_color_rug()
-  expect_equal(as.character(test_sdg[["scales"]][["scales"]][[2]][["call"]]), "scale_color_sdgs")
-  expect_equal(as.character(test_iheid[["scales"]][["scales"]][[2]][["call"]]), "scale_color_iheid")
-  expect_equal(as.character(test_ethz[["scales"]][["scales"]][[2]][["call"]]), "scale_color_ethz")
-  expect_equal(as.character(test_uzh[["scales"]][["scales"]][[2]][["call"]]), "scale_color_uzh")
-  expect_equal(as.character(test_rug[["scales"]][["scales"]][[2]][["call"]]), "scale_color_rug")
-})