From 2053d782b87bae601f82c562f07a6b262c144ccc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= <szhorvat@gmail.com>
Date: Mon, 7 Jul 2025 11:41:43 +0000
Subject: [PATCH 1/6] feat: `layout_nicely()` now aligns the layout with the
 axes for small graphs

---
 R/layout.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/layout.R b/R/layout.R
index 4915534df6a..c4546a47837 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -957,7 +957,7 @@ layout_nicely <- function(graph, dim = 2, ...) {
     args$dim <- dim
 
     if (vcount(graph) < 1000) {
-      do.call(layout_with_fr, args)
+      layout_align_impl(graph, do.call(layout_with_fr, args))
     } else {
       do.call(layout_with_drl, args)
     }

From ca42aaa1f926a248add1cbeb18f11f082d4f91aa Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 7 Jul 2025 15:03:03 +0200
Subject: [PATCH 2/6] added automatic tree layout

---
 R/layout.R | 37 ++++++++++++++++++++++++++++++++-----
 1 file changed, 32 insertions(+), 5 deletions(-)

diff --git a/R/layout.R b/R/layout.R
index c4546a47837..3887ff1f221 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -877,12 +877,18 @@ layout.circle <- function(..., params = list()) {
 #'
 #' `layout_nicely()` tries to choose an appropriate layout function for the
 #' supplied graph, and uses that to generate the layout. The current
-#' implementation works like this: \enumerate{ \item If the graph has a graph
-#' attribute called \sQuote{layout}, then this is used. If this attribute is an
-#' R function, then it is called, with the graph and any other extra arguments.
+#' implementation works like this:
+#' \enumerate{
+#' \item If the graph has a graph attribute called \sQuote{layout},
+#' then this is used. If this attribute is an R function, then it is called, with the graph and any other extra arguments.
+#'
 #' \item Otherwise, if the graph has vertex attributes called \sQuote{x} and
 #' \sQuote{y}, then these are used as coordinates. If the graph has an
-#' additional \sQuote{z} vertex attribute, that is also used.  \item Otherwise,
+#' additional \sQuote{z} vertex attribute, that is also used.
+#'
+#' \item Otherwise, if the graph is a forest and has less than 30 vertices, `layout_as_tree()` is used.
+#'
+#' \item Otherwise,
 #' if the graph is connected and has less than 1000 vertices, the
 #' Fruchterman-Reingold layout is used, by calling `layout_with_fr()`.
 #' \item Otherwise the DrL layout is used, `layout_with_drl()` is called.  }
@@ -916,6 +922,7 @@ layout_nicely <- function(graph, dim = 2, ...) {
   ## 1. If there is a 'layout' graph attribute, we just use that.
   ## 2. Otherwise, if there are vertex attributes called 'x' and 'y',
   ##    we use those (and the 'z' vertex attribute as well, if present).
+  ## 3. If the graph is a forest and has less than 30 vertices, layout_as_tree is used
   ## 3. Otherwise, if the graph is small (<1000) we use
   ##    the Fruchterman-Reingold layout.
   ## 4. Otherwise we use the DrL layout generator.
@@ -954,10 +961,15 @@ layout_nicely <- function(graph, dim = 2, ...) {
     }
 
     args$graph <- graph
+
+    if (is_forest(graph) && vcount(graph) <= 30) {
+      return(align_layout(graph, do.call(layout_as_tree, args)))
+    }
+
     args$dim <- dim
 
     if (vcount(graph) < 1000) {
-      layout_align_impl(graph, do.call(layout_with_fr, args))
+      align_layout(graph, do.call(layout_with_fr, args))
     } else {
       do.call(layout_with_drl, args)
     }
@@ -3008,3 +3020,18 @@ drl_defaults <- list(
   final = igraph.drl.final,
   refine = igraph.drl.refine
 )
+
+#' Align a vertex layout
+#' This function centers a vertex layout on the coordinate system origin and
+#' rotates the layout to achieve a visually pleasing alignment with the coordinate
+#' axes. Doing this is particularly useful with force-directed layouts such as [layout_with_fr()].
+#' @param graph The graph whose layout is to be aligned.
+#' @param layout A matrix whose rows are the coordinates of vertices.
+#' @return modified layout matrix
+#' @examples
+#' g <- make_lattice(c(3, 3))
+#' l1 <- layout_with_fr(g)
+#' l2 <- align_layout(g,l1)
+#' plot(g, layout = l1)
+#' plot(g, layout = l2)
+align_layout <- layout_align_impl

From 3379805cf0bc96ed23c9a03e372269b40b68ae7f Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 7 Jul 2025 15:03:12 +0200
Subject: [PATCH 3/6] documentation

---
 man/align_layout.Rd  | 32 ++++++++++++++++++++++++++++++++
 man/layout_nicely.Rd | 14 ++++++++++----
 2 files changed, 42 insertions(+), 4 deletions(-)
 create mode 100644 man/align_layout.Rd

diff --git a/man/align_layout.Rd b/man/align_layout.Rd
new file mode 100644
index 00000000000..5ecdbe4ac9d
--- /dev/null
+++ b/man/align_layout.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/layout.R
+\name{align_layout}
+\alias{align_layout}
+\title{Align a vertex layout
+This function centers a vertex layout on the coordinate system origin and
+rotates the layout to achieve a visually pleasing alignment with the coordinate
+axes. Doing this is particularly useful with force-directed layouts such as \code{\link[=layout_with_fr]{layout_with_fr()}}.}
+\usage{
+align_layout(graph, layout)
+}
+\arguments{
+\item{graph}{The graph whose layout is to be aligned.}
+
+\item{layout}{A matrix whose rows are the coordinates of vertices.}
+}
+\value{
+modified layout matrix
+}
+\description{
+Align a vertex layout
+This function centers a vertex layout on the coordinate system origin and
+rotates the layout to achieve a visually pleasing alignment with the coordinate
+axes. Doing this is particularly useful with force-directed layouts such as \code{\link[=layout_with_fr]{layout_with_fr()}}.
+}
+\examples{
+g <- make_lattice(c(3, 3))
+l1 <- layout_with_fr(g)
+l2 <- align_layout(g,l1)
+plot(g, layout = l1)
+plot(g, layout = l2)
+}
diff --git a/man/layout_nicely.Rd b/man/layout_nicely.Rd
index 6ac67a3e336..a8df0563316 100644
--- a/man/layout_nicely.Rd
+++ b/man/layout_nicely.Rd
@@ -28,12 +28,18 @@ graph, automatically, based on a simple algorithm. See details below.
 \details{
 \code{layout_nicely()} tries to choose an appropriate layout function for the
 supplied graph, and uses that to generate the layout. The current
-implementation works like this: \enumerate{ \item If the graph has a graph
-attribute called \sQuote{layout}, then this is used. If this attribute is an
-R function, then it is called, with the graph and any other extra arguments.
+implementation works like this:
+\enumerate{
+\item If the graph has a graph attribute called \sQuote{layout},
+then this is used. If this attribute is an R function, then it is called, with the graph and any other extra arguments.
+
 \item Otherwise, if the graph has vertex attributes called \sQuote{x} and
 \sQuote{y}, then these are used as coordinates. If the graph has an
-additional \sQuote{z} vertex attribute, that is also used.  \item Otherwise,
+additional \sQuote{z} vertex attribute, that is also used.
+
+\item Otherwise, if the graph is a forest and has less than 30 vertices, \code{layout_as_tree()} is used.
+
+\item Otherwise,
 if the graph is connected and has less than 1000 vertices, the
 Fruchterman-Reingold layout is used, by calling \code{layout_with_fr()}.
 \item Otherwise the DrL layout is used, \code{layout_with_drl()} is called.  }

From c285ab20ca57c561ada2600edbff30b4d5c3a2c1 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 7 Jul 2025 15:18:11 +0200
Subject: [PATCH 4/6] export

---
 NAMESPACE  | 1 +
 R/layout.R | 1 +
 2 files changed, 2 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 4bd16e4bea4..0642cdf4496 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -126,6 +126,7 @@ export(aging.ba.game)
 export(aging.barabasi.game)
 export(aging.prefatt.game)
 export(algorithm)
+export(align_layout)
 export(all_shortest_paths)
 export(all_simple_paths)
 export(alpha.centrality)
diff --git a/R/layout.R b/R/layout.R
index 3887ff1f221..37a9e52ff07 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -3028,6 +3028,7 @@ drl_defaults <- list(
 #' @param graph The graph whose layout is to be aligned.
 #' @param layout A matrix whose rows are the coordinates of vertices.
 #' @return modified layout matrix
+#' @export
 #' @examples
 #' g <- make_lattice(c(3, 3))
 #' l1 <- layout_with_fr(g)

From 42f7161dd0a01bfab4224d7c8e883c0da2e9575e Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 7 Jul 2025 15:24:12 +0200
Subject: [PATCH 5/6] dont align tree layout

---
 R/layout.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/layout.R b/R/layout.R
index 37a9e52ff07..d25fee763f5 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -963,7 +963,7 @@ layout_nicely <- function(graph, dim = 2, ...) {
     args$graph <- graph
 
     if (is_forest(graph) && vcount(graph) <= 30) {
-      return(align_layout(graph, do.call(layout_as_tree, args)))
+      return(do.call(layout_as_tree, args))
     }
 
     args$dim <- dim

From a384af209d19a0d4b8c763dcbcebfeffff8a1e99 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 7 Jul 2025 15:55:19 +0200
Subject: [PATCH 6/6] added align_layout to pkgdown

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 646b86e8fc8..e543b111bf1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -65,6 +65,7 @@ reference:
   - has_concept("plot.common")
   - has_concept("plot.shapes")
   - vertex.shape.pie
+  - align_layout
 - subtitle: Graph coloring
 - contents:
   - has_concept("coloring")