v0.6.0

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",

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)

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

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))

R/graph_edges.R

@@ -16,20 +16,20 @@ 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){
     p <- p + ggraph::scale_edge_colour_manual(values = getOption("snet_highlight", default = c("grey","black")),
                                               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
 }
 

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(),

R/graph_layout.R

@@ -23,15 +23,50 @@ 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$data[,c("x","y")] <- depth_first_recursive_search(p)
   }
   # Add background ----
   if(getOption("snet_background", default = "#FFFFFF")!="#FFFFFF")
     p <- p + ggplot2::theme(panel.background = ggplot2::element_rect(fill = getOption("snet_background", 
                                                                                       default = "#FFFFFF")))
   p
 }
+
+# Helper functions ----
+
+.rotate_layout <- function(layout, angle) {
+  rot <- matrix(c(cos(angle), -sin(angle),
+                  sin(angle),  cos(angle)), ncol = 2)
+  coords <- as.matrix(layout[, c("x", "y")])
+  newcoords <- coords %*% rot
+  layout$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)
+}
+
+
+
+

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 )))
+}

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
 }