Fix edge.width not applied to drawn line widths in nplot

.Rbuildignore

@@ -14,3 +14,6 @@ netplot\._.*\.tar\.gz
 ^Rplots\.pdf$
 ^doc$
 ^Meta$
+^AGENTS\.md$
+^\.devcontainer$
+^\.vscode$

.devcontainer/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "r.plot.useHttpgd": true,
+    "r.alwaysUseActiveTerminal": true
+}

.devcontainer/Containerfile

@@ -0,0 +1,19 @@
+FROM ghcr.io/rocker-org/devcontainer/r-ver:4.5
+
+# Architecture-specific variable (built in Docker BuildKit)
+ARG TARGETARCH
+
+# Install quarto-cli and the orange-book extension
+RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.9.35/quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    dpkg -i quarto-1.9.35-linux-${TARGETARCH}.deb && \
+    rm quarto-1.9.35-linux-${TARGETARCH}.deb
+
+# Adding R packages
+RUN install2.r --error knitr rmarkdown markdown igraphdata intergraph \
+  ggraph gridGraphics ggplot2 gridExtra gridBase magrittr tinytest \
+  sna igraph network
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+  libglpk-dev
+
+CMD ["bash"]

.devcontainer/devcontainer-lock.json

@@ -0,0 +1,9 @@
+{
+  "features": {
+    "ghcr.io/devcontainers/features/github-cli:1": {
+      "version": "1.1.0",
+      "resolved": "ghcr.io/devcontainers/features/github-cli@sha256:d22f50b70ed75339b4eed1ba9ecde3a1791f90e88d37936517e3bace0bbad671",
+      "integrity": "sha256:d22f50b70ed75339b4eed1ba9ecde3a1791f90e88d37936517e3bace0bbad671"
+    }
+  }
+}

.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "netplot",
+	"build": {
+		"dockerfile": "Containerfile"
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"reditorsupport.r",
+				"rdebugger.r-debugger",
+				"quarto.quarto",
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions",
+				"ms-vscode.live-server"
+			]
+		}
+	},
+	"mounts": [
+        // Mount the .vscode configuration into the container
+        "source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
+    ],
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	"features": {
+		"ghcr.io/devcontainers/features/github-cli:1": {
+			"version": "1.1.0"
+		}
+	},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	"remoteUser": "root"
+}

AGENTS.md

@@ -0,0 +1,11 @@
+# What is this project about
+
+This is an R package that uses the `grid` package to create network plots. The package is focused on aesthetics and tries to provide an interface that has a lower footprint in dependencies than other packages, leveraging existing base R packages.
+
+## Development workflow and preferences
+
+- We follow the tinyverse style for code (so minimal dependencies, but still using `roxygen2` for documentation).
+
+- For testing the package, we use `tinytest`.
+
+- For checking the R package, we use `devtools::check()`, and for documenting we call `devtools::document()`.

DESCRIPTION

@@ -17,7 +17,7 @@ Depends:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 Imports: 
     graphics,

Makefile

@@ -1,50 +1,16 @@
-VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Vers", x)]))')
-PKGNAME:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Package", x)]))')
+README.md: README.qmd
+	quarto render README.qmd
 
-install: build
-	cd ../ && \
-		R CMD INSTALL $(PKGNAME)_$(VERSION).tar.gz
-
-$(PKGNAME)_$(VERSION).tar.gz: 
-	cd ../ && R CMD build $(PKGNAME)/
+.PHONY: build check install checkfull checkv clean man docker checkd
 
-build: $(PKGNAME)_$(VERSION).tar.gz
+build: docs
+	R CMD build .
 
-inst/NEWS: NEWS.md
-	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
-	head -n 80 inst/NEWS
+check: docs
+	Rscript -e "devtools::check()"
 
-README.md: README.Rmd
-	Rscript -e 'rmarkdown::render("README.Rmd")'
+install: docs
+	Rscript -e "devtools::install()"
 
-.PHONY: checfull checkv clean
-
-check: $(PKGNAME)_$(VERSION).tar.gz
-	R CMD check --no-vignettes --no-manual $(PKGNAME)_$(VERSION).tar.gz
-
-checkfull: R/*.R inst/NEWS README.md
-	R CMD build . \&& 
-		R CMD check --as-cran $(PKGNAME)_$(VERSION).tar.gz
-
-checkv: $(PKGNAME)_$(VERSION).tar.gz
-	R CMD check --as-cran --use-valgrind $(PKGNAME)_$(VERSION).tar.gz
-
-clean:
-	cd ../ && \
-		rm -rf $(PKGNAME).Rcheck $(PKGNAME)_$(VERSION).tar.gz
-
-.PHONY: man docker
-man: R/* 
-	Rscript --vanilla -e 'roxygen2::roxygenize()'
-
-docker:
-	docker run -v$(pwd):/pkg/ -w/pkg --rm -i uscbiostats/fmcmc:latest make check
-
-checkd:
-	apt update && \
-		tlmgr install amsmath && \
-		install2.r igraph gridGraphics gridBase gridExtra magrittr tinytest sna \
-		ggraph rmarkdown knitr intergraph igraphdata pkgdown markdown && \
-		apt install libglpk-dev --no-install-recommends -y && \
-		R CMD build . && \
-		R CMD check --no-manual $(PKGNAME)_$(VERSION).tar.gz
+docs:
+	Rscript -e "devtools::document()"

NEWS.md

@@ -1,5 +1,9 @@
 # netplot 0.3-0
 
+* `edge.width` now correctly reflected in the drawn line widths. Previously,
+  the width was computed but not consistently applied via the graphical
+  parameters of each edge grob. Closes #17.
+
 * Invalid arguments passed to `nplot()` now raise an error.
 
 * Figures with legends are not drawn twice.

R/geometry.R

@@ -2,13 +2,17 @@
 #' @param size Numeric vector. Size of the node (radious).
 #' @param rel Numeric vector of length 3. Relative size for the minimum and maximum
 #' of the plot, and curvature of the scale. The third number is used as `size^rel[3]`.
+#' If `NULL`, scaling is suppressed.
 #'
 #' @details
 #' This function is to be called after [plot.new], as it takes the parameter `usr`
 #' from the
 #' @noRd
 rescale_size <- function(size, rel=c(.01, .05, 1)) {
 
+  if (is.null(rel))
+    return(size)
+
   # Checking the rel size
   if (length(rel) == 2)
     rel <- c(rel, 1)
@@ -204,4 +208,3 @@ map_attribute_to_shape <- function(x) {
   names(sides_lookup)[as.numeric(factor(x))]
 
 }
-

R/grob_vertex.R

@@ -1,7 +1,7 @@
   sides_lookup <- list(
     line     = list(sides = 2, rot = 0),    # 1
     triangle = list(sides = 3, rot = 0),    # 2
-    square   = list(sides = 4, rot = pi/2), # 3
+    square   = list(sides = 4, rot = pi/4), # 3
     diamond  = list(sides = 4, rot = 0),    # 4
     pentagon = list(sides = 5, rot = 0),    # 5
     hexagon  = list(sides = 6, rot = 0),    # 6
@@ -10,6 +10,31 @@
     circle   = list(sides = 25, rot = 0)    # 9
   )
 
+resolve_vertex_shape <- function(nsides, rot) {
+
+  if (!is.numeric(nsides) & !is.character(nsides)) {
+    stop("vertex.nsides must be numeric or character")
+  }
+
+  rot <- as.numeric(rot)
+
+  if (is.character(nsides)) {
+
+    shape <- nsides
+
+    if (shape %in% names(sides_lookup)) {
+      info <- sides_lookup[[shape]]
+      return(list(sides = info$sides, rot = info$rot + rot))
+    } else {
+      stop("Invalid shape name: ", shape)
+    }
+
+  }
+
+  list(sides = nsides, rot = rot)
+
+}
+
 #' Functions to calculate graph polygons coordinates
 #' @param netenv An object of class network environment.
 #' @param v,e Integer scalars. vertex or edge index.
@@ -25,27 +50,10 @@ grob_vertex <- function(netenv, v) {
   #   netenv$vertex.nsides <- eval(netenv$vertex.nsides, envir = data)
   # }
 
-  # Relax vertex.nsides validation
-  if(!is.numeric(netenv$vertex.nsides[v]) & !is.character(netenv$vertex.nsides[v])) {
-    stop("vertex.nsides must be numeric or character")
-  }
-
-  # Handle shape names
-  if(is.character(netenv$vertex.nsides[v])) {
-
-    shape <- netenv$vertex.nsides[v]
-
-    if(shape %in% names(sides_lookup)) {
-      info <- sides_lookup[[shape]]
-      netenv$vertex.nsides[v] <- info$sides
-      netenv$vertex.rot[v] <- info$rot
-    } else {
-      stop("Invalid shape name: ", shape)
-    }
-
-  }
-
-
+  vertex_shape <- resolve_vertex_shape(
+    nsides = netenv$vertex.nsides[v],
+    rot    = netenv$vertex.rot[v]
+  )
 
   if (netenv$skip.vertex)
     return(
@@ -63,18 +71,18 @@ grob_vertex <- function(netenv, v) {
   coords <- npolygon(
     x = netenv$layout[v, 1],
     y = netenv$layout[v, 2],
-    n = as.integer(netenv$vertex.nsides[v]),
+    n = as.integer(vertex_shape$sides),
     r = netenv$vertex.size[v]*(1 - netenv$vertex.frame.prop[v]),
-    d = as.integer(netenv$vertex.rot[v])
+    d = vertex_shape$rot
   )
 
   # Frame coordinates
   framecoords <- npolygon(
     x = netenv$layout[v, 1],
     y = netenv$layout[v, 2],
-    n = as.integer(netenv$vertex.nsides[v]),
+    n = as.integer(vertex_shape$sides),
     r = netenv$vertex.size[v],
-    d = as.integer(netenv$vertex.rot[v])
+    d = vertex_shape$rot
   )
 
   # Create color palette