Improved plot dpi

Author: alexanderbates

.Rbuildignore

@@ -5,3 +5,5 @@
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -7,3 +7,4 @@ docs/figs/*.pdf
 tests/testthat/Rplots.pdf
 .httr-oauth
 spare
+docs

DESCRIPTION

@@ -11,10 +11,10 @@ Authors@R:
            comment = c(ORCID = "0000-0002-1195-0445")))
 Description: Functions for creating neuroanatomy plots in the ggplot2 style.
 License: GPL-3 + file LICENSE
-URL: https://github.com/natverse/nat.ggplot, https://natverse.github.io/nat.ggplot/
+URL: https://github.com/natverse/nat.ggplot, https://natverse.github.io/nat.ggplot/, http://natverse.org/nat.ggplot/
 BugReports: https://github.com/natverse/nat.ggplot/issues
 Depends: 
-    R (>= 3.5.0,
+    R (>= 3.5.0)
 Imports: 
     nat,
     ggplot2 (>= 3.5),

NAMESPACE

@@ -15,7 +15,6 @@ S3method(ggplot2_neuron_path,"NULL")
 S3method(ggplot2_neuron_path,mesh3d)
 S3method(ggplot2_neuron_path,neuron)
 S3method(ggplot2_neuron_path,neuronlist)
-S3method(prune_vertices,synapticneuron)
 export(g.anat)
 export(geom_neuron)
 export(ggneuron)

R/data.R

@@ -31,10 +31,10 @@
 #' \dontrun{
 #' library(nat)
 #' library(nat.ggplot)
-#' 
+#'
 #' # Plot the neurons
 #' plot3d(banc.skels)
-#' 
+#'
 #' # Use with ggplot2
 #' library(ggplot2)
 #' ggplot() + geom_neuron(banc.skels, rotation_matrix = banc_view)
@@ -76,7 +76,7 @@
 #' \dontrun{
 #' library(ggplot2)
 #' library(nat.ggplot)
-#' 
+#'
 #' # Plot synapses coloured by type
 #' ggplot(banc.syns, aes(x = X, y = Y)) +
 #'   geom_point(aes(colour = factor(prepost)), alpha = 0.5) +
@@ -124,14 +124,14 @@
 #' \dontrun{
 #' library(nat.ggplot)
 #' library(ggplot2)
-#' 
+#'
 #' # Plot split neurons showing axon/dendrite compartments
-#' ggplot() + geom_neuron(bc.neurons.flow[[1]], rotation_matrix = banc_view)
-#' 
+#' ggplot() + geom_neuron(banc.neurons.flow[[1]], rotation_matrix = banc_view)
+#'
 #' # Plot all split neurons
-#' ggneuron(bc.neurons.flow, rotation_matrix = banc_view)
+#' ggneuron(banc.neurons.flow, rotation_matrix = banc_view)
 #' }
-"bc.neurons.flow"
+"banc.neurons.flow"
 
 #' Low Resolution BANC Brain Neuropil Mesh
 #'
@@ -156,18 +156,18 @@
 #' \dontrun{
 #' library(nat.ggplot)
 #' library(ggplot2)
-#' 
+#'
 #' # Plot brain neuropil with default view
-#' ggplot() + 
-#'   geom_neuron(banc.brain_neuropil, 
-#'               cols = c("grey75", "grey50"), 
+#' ggplot() +
+#'   geom_neuron(banc.brain_neuropil,
+#'               cols = c("grey75", "grey50"),
 #'               alpha = 0.3)
-#' 
+#'
 #' # Plot with frontal view
-#' ggplot() + 
-#'   geom_neuron(banc.brain_neuropil, 
+#' ggplot() +
+#'   geom_neuron(banc.brain_neuropil,
 #'               rotation_matrix = banc_view,
-#'               cols = c("grey75", "grey50"), 
+#'               cols = c("grey75", "grey50"),
 #'               alpha = 0.3)
 #' }
 "banc.brain_neuropil"
@@ -176,9 +176,7 @@
 #'
 #' @description
 #' A list of simplified mesh3d objects representing the 3D surface reconstructions
-#' of 5 LHPD2a1 neurons from the BANC connectome dataset. These meshes have been
-#' decimated to approximately 20% of their original face count for efficient
-#' visualisation whilst preserving morphological features.
+#' of 4 LHPD2a1 neurons from the BANC connectome dataset.
 #'
 #' @format A list of 5 mesh3d objects, each containing vertices and faces defining
 #' the 3D surface of a neuron.
@@ -204,15 +202,15 @@
 #' \dontrun{
 #' library(nat.ggplot)
 #' library(ggplot2)
-#' 
+#'
 #' # Plot first neuron mesh
-#' ggplot() + 
-#'   geom_neuron(banc.meshes[[1]], 
+#' ggplot() +
+#'   geom_neuron(banc.meshes[[1]],
 #'               rotation_matrix = banc_view,
 #'               cols = c("purple", "magenta"))
-#' 
+#'
 #' # Plot all neuron meshes
-#' ggneuron(banc.meshes, 
+#' ggneuron(banc.meshes,
 #'          rotation_matrix = banc_view,
 #'          cols = c("purple", "magenta"))
 #' }
@@ -223,7 +221,7 @@
 #' @description
 #' A 4x4 rotation matrix for displaying BANC connectome data in a frontal view.
 #' This matrix can be applied to any 3D neuroanatomy data to rotate it into a
-#' standard frontal viewing orientation.
+#' standard frontal viewing orientation. Provded as an example for the user.
 #'
 #' @format A 4x4 numeric matrix representing a 3D rotation transformation.
 #'
@@ -239,17 +237,17 @@
 #' library(nat.ggplot)
 #' library(nat)
 #' library(ggplot2)
-#' 
+#'
 #' # Use the frontal view for plotting
-#' ggplot() + 
+#' ggplot() +
 #'   geom_neuron(banc.skels, rotation_matrix = banc_view)
-#' 
+#'
 #' # Create a custom view interactively
 #' plot3d(banc.brain_neuropil)
 #' # Rotate to desired angle with mouse
 #' my_view <- rgl_view()$userMatrix
 #' # Use custom view
-#' ggplot() + 
+#' ggplot() +
 #'   geom_neuron(banc.brain_neuropil, rotation_matrix = my_view)
 #' }
 "banc_view"

R/ggplot2.R

@@ -178,7 +178,7 @@ ggplot2_neuron_path.NULL <- function(x, rotation_matrix = NULL, ...) {
 #'
 #' # Plot split neurons showing axon/dendrite
 #' g.anat +
-#'   geom_neuron(bc.neurons.flow[[1]],
+#'   geom_neuron(banc.neurons.flow[[1]],
 #'               rotation_matrix = banc_view)
 #'
 #' # Plot synapses as points
@@ -247,7 +247,7 @@ geom_neuron.neuron <- function(x = NULL,
                        ...),
     ggplot2::geom_point(mapping = ggplot2::aes(x = .data$X, y = .data$Y),
                         data = soma,
-                        color = cols[1],
+                        color = "black", #cols[1],
                         size = root,
                         ...),
     ggplot2::scale_color_gradient(low = cols[1],
@@ -689,7 +689,9 @@ geom_neuron.splitneuron <- function(x = NULL,
     # },
     ggplot2::geom_point(mapping = ggplot2::aes(x = .data$X, y = .data$Y),
                         data = soma,
-                        color = cols[1], alpha = 0.75, size = root)
+                        color = "black", #cols[1],
+                        alpha = 0.75,
+                        size = root)
   )
 
   # And synapses?
@@ -764,7 +766,7 @@ geom_neuron.splitneuron <- function(x = NULL,
 #'          cols1 = c("lightblue", "darkblue"))
 #'
 #' # Visualise split neurons with custom colours
-#' ggneuron(bc.neurons.flow,
+#' ggneuron(banc.neurons.flow,
 #'          volume = banc.brain_neuropil,
 #'          rotation_matrix = banc_view,
 #'          info = "LHPD2a1 neurons with axon/dendrite split")
@@ -809,8 +811,7 @@ ggneuron <- function(x,
     ggplot2::labs(title = info)
 }
 
-#' @method prune_vertices synapticneuron
-#' @export
+# hidden
 prune_vertices.synapticneuron <- function (x, verticestoprune, invert = FALSE, ...){
   if(length(verticestoprune)==nrow(x$d)){
     warning('no points left after pruning')