diff --git a/.Rbuildignore b/.Rbuildignore
index dd8c5a4..4cb7506 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,7 +2,7 @@
^\.Rproj\.user$
^playground$
^LICENSE\.md$
-^README\.Rmd$
+^README\.qmd$
^docs$
^docker$
^\.travis\.yml$
diff --git a/.gitignore b/.gitignore
index 16e3c0f..1f97331 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,5 @@
/doc/
/Meta/
+
+/.quarto/
diff --git a/NEWS.md b/NEWS.md
index 2240524..492616b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,33 +1,33 @@
# netplot 0.2-9999
-* Invalid arguments passed to `nplot()` now raise an error.
+* Invalid arguments passed to `nplot()` now raise an error.
-* Figures with legends are not drawn twice.
+* Figures with legends are not drawn twice.
-* Values supported by `nplot()` are now included in all methods (helps with
- argument completion).
+* Values supported by `nplot()` are now included in all methods (helps with
+ argument completion).
# netplot 0.2-0
-* The arguments `skip.vertex`, `skip.edges`, and `skip.arrows` now work as
- documented.
-
-* New function `nplot_legend()` helps adding legends to the figure.
+* The arguments `skip.vertex`, `skip.edges`, and `skip.arrows` now work as
+ documented.
-* New `nplot()` method for matrices.
+* New function `nplot_legend()` helps to add legends to the figure.
-* New feature: Gradients.
+* New `nplot()` method for matrices.
-* The argument `sample.edges` now works as expected.
+* New feature: Gradients.
-* `vertex.color`, `vertex.size`, and `vertex.nsides` now accepts formulas.
+* The argument `sample.edges` now work as expected.
-* `edge.width` now accepts formulas.
+* `vertex.color`, `vertex.size`, and `vertex.nsides` now accepts formulas.
-* New function: `locate_vertex()`.
+* `edge.width` now accepts formulas.
+
+* New function: `locate_vertex()`.
# netplot 0.1-0
-* First CRAN release.
+* First CRAN release.
diff --git a/R/netplot.R b/R/netplot.R
index 28bc77f..3f0a831 100644
--- a/R/netplot.R
+++ b/R/netplot.R
@@ -122,18 +122,9 @@ nplot <- function(
skip.arrows = skip.edges,
add = FALSE,
zero.margins = TRUE,
- ...,
edgelist
) {
- # Checking if the passed arguments match the default class
- res <- sapply(
- ...names(),
- match.arg,
- choices = methods::formalArgs(nplot.default),
- several.ok = FALSE
- )
-
UseMethod("nplot")
}
@@ -171,7 +162,6 @@ nplot.igraph <- function(
skip.arrows = !igraph::is_directed(x),
add = FALSE,
zero.margins = TRUE,
- ...,
edgelist
) {
@@ -179,14 +169,37 @@ nplot.igraph <- function(
edge.width <- 1L
nplot.default(
- x = x,
- edgelist = igraph::as_edgelist(x, names = FALSE),
- layout = layout,
- vertex.size = vertex.size,
+ x = x,
+ layout = layout,
+ vertex.size = vertex.size,
+ bg.col = bg.col,
+ vertex.nsides = vertex.nsides,
+ vertex.color = vertex.color,
+ vertex.size.range = vertex.size.range,
+ vertex.frame.color = vertex.frame.color,
+ vertex.rot = vertex.rot,
+ vertex.frame.prop = vertex.frame.prop,
vertex.label = vertex.label,
- edge.width = edge.width,
+ vertex.label.fontsize = vertex.label.fontsize,
+ vertex.label.color = vertex.label.color,
+ vertex.label.fontfamily = vertex.label.fontfamily,
+ vertex.label.fontface = vertex.label.fontface,
+ vertex.label.show = vertex.label.show,
+ vertex.label.range = vertex.label.range,
+ edge.width = edge.width,
+ edge.width.range = edge.width.range,
+ edge.arrow.size = edge.arrow.size,
+ edge.color = edge.color,
+ edge.curvature = edge.curvature,
+ edge.line.lty = edge.line.lty,
+ edge.line.breaks = edge.line.breaks,
+ sample.edges = sample.edges,
+ skip.vertex = skip.vertex,
+ skip.edges = skip.edges,
skip.arrows = skip.arrows,
- ...
+ add = add,
+ zero.margins = zero.margins,
+ edgelist = igraph::as_edgelist(x, names = FALSE)
)
}
@@ -226,18 +239,41 @@ nplot.network <- function(
skip.arrows = !network::is.directed(x),
add = FALSE,
zero.margins = TRUE,
- ...,
edgelist
) {
nplot.default(
- x = x,
- layout = layout,
- vertex.size = vertex.size,
+ x = x,
+ layout = layout,
+ vertex.size = vertex.size,
+ bg.col = bg.col,
+ vertex.nsides = vertex.nsides,
+ vertex.color = vertex.color,
+ vertex.size.range = vertex.size.range,
+ vertex.frame.color = vertex.frame.color,
+ vertex.rot = vertex.rot,
+ vertex.frame.prop = vertex.frame.prop,
vertex.label = vertex.label,
- skip.arrows = skip.arrows,
- ...,
- edgelist = network::as.edgelist(x)
+ vertex.label.fontsize = vertex.label.fontsize,
+ vertex.label.color = vertex.label.color,
+ vertex.label.fontfamily = vertex.label.fontfamily,
+ vertex.label.fontface = vertex.label.fontface,
+ vertex.label.show = vertex.label.show,
+ vertex.label.range = vertex.label.range,
+ edge.width = edge.width,
+ edge.width.range = edge.width.range,
+ edge.arrow.size = edge.arrow.size,
+ edge.color = edge.color,
+ edge.curvature = edge.curvature,
+ edge.line.lty = edge.line.lty,
+ edge.line.breaks = edge.line.breaks,
+ sample.edges = sample.edges,
+ skip.vertex = skip.vertex,
+ skip.edges = skip.edges,
+ skip.arrows = skip.arrows,
+ add = add,
+ zero.margins = zero.margins,
+ edgelist = network::as.edgelist(x)
)
}
@@ -276,13 +312,40 @@ nplot.matrix <- function(
skip.arrows = skip.edges,
add = FALSE,
zero.margins = TRUE,
- ...,
edgelist
) {
nplot.igraph(
x = igraph::graph_from_adjacency_matrix(x),
- ...,
+ layout = layout,
+ vertex.size = vertex.size,
+ bg.col = bg.col,
+ vertex.nsides = vertex.nsides,
+ vertex.color = vertex.color,
+ vertex.size.range = vertex.size.range,
+ vertex.frame.color = vertex.frame.color,
+ vertex.rot = vertex.rot,
+ vertex.frame.prop = vertex.frame.prop,
+ vertex.label = vertex.label,
+ vertex.label.fontsize = vertex.label.fontsize,
+ vertex.label.color = vertex.label.color,
+ vertex.label.fontfamily = vertex.label.fontfamily,
+ vertex.label.fontface = vertex.label.fontface,
+ vertex.label.show = vertex.label.show,
+ vertex.label.range = vertex.label.range,
+ edge.width = edge.width,
+ edge.width.range = edge.width.range,
+ edge.arrow.size = edge.arrow.size,
+ edge.color = edge.color,
+ edge.curvature = edge.curvature,
+ edge.line.lty = edge.line.lty,
+ edge.line.breaks = edge.line.breaks,
+ sample.edges = sample.edges,
+ skip.vertex = skip.vertex,
+ skip.edges = skip.edges,
+ skip.arrows = skip.arrows,
+ add = add,
+ zero.margins = zero.margins,
edgelist = NULL
)
diff --git a/README.md b/README.md
deleted file mode 100644
index 5106cfc..0000000
--- a/README.md
+++ /dev/null
@@ -1,180 +0,0 @@
-
-
-
-[](https://cran.r-project.org/package=netplot)
-[](https://cran.r-project.org/package=netplot)
-[](https://github.com/USCCANA/netplot/actions/workflows/ci.yml)
-[](https://ci.appveyor.com/project/gvegayon/netplot)
-[](https://preventivemedicine.usc.edu)
-
-# netplot
-
-An alternative graph visualization tool that emphasizes aesthetics,
-providing default parameters that deliver out-of-the-box lovely
-visualizations.
-
-Some features:
-
-1. Auto-scaling of vertices using sizes relative to the plotting
- device.
-2. Embedded edge color mixer.
-3. True curved edges drawing.
-4. User-defined edge curvature.
-5. Nicer vertex frame color.
-6. Better use of space-filling the plotting device.
-
-The package uses the `grid` plotting system (just like `ggplot2`).
-
-## Installation
-
-You can install the released version of netplot from
-[CRAN](https://CRAN.R-project.org) with:
-
-``` r
-install.packages("netplot")
-```
-
-And the development version from [GitHub](https://github.com/) with:
-
-``` r
-# install.packages("devtools")
-devtools::install_github("USCCANA/netplot")
-```
-
-## Example
-
-This is a basic example which shows you how to solve a common problem:
-
-``` r
-library(igraph)
-#>
-#> Attaching package: 'igraph'
-#> The following objects are masked from 'package:stats':
-#>
-#> decompose, spectrum
-#> The following object is masked from 'package:base':
-#>
-#> union
-library(netplot)
-#> Loading required package: grid
-#>
-#> Attaching package: 'netplot'
-#> The following object is masked from 'package:igraph':
-#>
-#> ego
-set.seed(1)
-data("UKfaculty", package = "igraphdata")
-l <- layout_with_fr(UKfaculty)
-#> This graph was created by an old(er) igraph version.
-#> Call upgrade_graph() on it to use with the current igraph version
-#> For now we convert it on the fly...
-
-plot(UKfaculty, layout = l) # ala igraph
-```
-
-
-
-``` r
-
-V(UKfaculty)$ss <- runif(vcount(UKfaculty))
-nplot(UKfaculty, layout = l) # ala netplot
-```
-
-
-
-``` r
-sna::gplot(intergraph::asNetwork(UKfaculty), coord=l)
-```
-
-
-
-### UKfaculty
-
-``` r
-# Random names
-set.seed(1)
-nam <- sample(babynames::babynames$name, vcount(UKfaculty))
-
-ans <- nplot(
- UKfaculty,
- layout = l,
- vertex.color = ~ Group,
- vertex.nsides = ~ Group,
- vertex.label = nam,
- vertex.size.range = c(.01, .04, 4),
- vertex.label.col = "black",
- vertex.label.fontface = "bold",
- bg.col = "transparent",
- vertex.label.show = .5,
- vertex.label.range = c(10, 25),
- edge.width.range = c(1, 4, 5)
- )
-
-
-# Plot it!
-ans
-```
-
-
-
-Starting version 0.2-0, we can use gradients!
-
-``` r
-ans |>
- set_vertex_gpar(
- element = "core",
- fill = lapply(get_vertex_gpar(ans, "frame", "col")$col, \(i) {
- radialGradient(c("white", i), cx1=.8, cy1=.8, r1=0)
- }))
-```
-
-
-
-### USairports
-
-``` r
-# Loading the data
-data(USairports, package="igraphdata")
-
-# Generating a layout naively
-layout <- V(USairports)$Position
-#> This graph was created by an old(er) igraph version.
-#> Call upgrade_graph() on it to use with the current igraph version
-#> For now we convert it on the fly...
-layout <- do.call(rbind, lapply(layout, function(x) strsplit(x, " ")[[1]]))
-layout[] <- stringr::str_remove(layout, "^[a-zA-Z]+")
-layout <- matrix(as.numeric(layout[]), ncol=2)
-
-# Some missingness
-layout[which(!complete.cases(layout)), ] <- apply(layout, 2, mean, na.rm=TRUE)
-
-# Have to rotate it (it doesn't matter the origin)
-layout <- netplot:::rotate(layout, c(0,0), pi/2)
-
-# Simplifying the network
-net <- simplify(USairports, edge.attr.comb = list(
- weight = "sum",
- name = "concat",
- Passengers = "sum",
- "ignore"
-))
-
-# Pretty graph
-nplot(
- net,
- layout = layout,
- edge.width = ~ Passengers,
- edge.color =
- ~ ego(col = "white", alpha = 0) + alter(col = "yellow", alpha = .75),
- skip.vertex = TRUE,
- skip.arrows = TRUE,
- edge.width.range = c(.75, 4, 4),
- bg.col = "black",
- edge.line.breaks = 10
- )
-```
-
-
diff --git a/README.Rmd b/README.qmd
similarity index 90%
rename from README.Rmd
rename to README.qmd
index 15f28aa..0957de8 100644
--- a/README.Rmd
+++ b/README.qmd
@@ -1,7 +1,5 @@
---
-output:
- github_document:
- html_preview: false
+format: gfm
---
@@ -18,6 +16,7 @@ knitr::opts_chunk$set(
[](https://cran.r-project.org/package=netplot)
[](https://cran.r-project.org/package=netplot)
+[](https://cran.r-project.org/package=rgexf)
[](https://github.com/USCCANA/netplot/actions/workflows/ci.yml)
[](https://ci.appveyor.com/project/gvegayon/netplot)
[](https://preventivemedicine.usc.edu)
@@ -73,7 +72,10 @@ sna::gplot(intergraph::asNetwork(UKfaculty), coord=l)
### UKfaculty
-```{r, fig.width=14, fig.height=14}
+```{r}
+#| label: fig-uk-faculty
+#| fig-width: 14
+#| fig-height: 14
# Random names
set.seed(1)
nam <- sample(babynames::babynames$name, vcount(UKfaculty))
@@ -100,7 +102,10 @@ ans
Starting version 0.2-0, we can use gradients!
-```{r uk-faculty-gradient, fig.width=14, fig.height=14}
+```{r}
+#| label: fig-uk-faculty-gradient
+#| fig-width: 14
+#| fig-height: 14
ans |>
set_vertex_gpar(
element = "core",
@@ -111,7 +116,8 @@ ans |>
### USairports
-```{r us-airports, cache=FALSE}
+```{r}
+#| label: fig-us-airports
# Loading the data
data(USairports, package="igraphdata")
@@ -140,8 +146,9 @@ nplot(
net,
layout = layout,
edge.width = ~ Passengers,
- edge.color =
- ~ ego(col = "white", alpha = 0) + alter(col = "yellow", alpha = .75),
+ edge.color = ~
+ ego(col = "white", alpha = 0) +
+ alter(col = "yellow", alpha = .75),
skip.vertex = TRUE,
skip.arrows = TRUE,
edge.width.range = c(.75, 4, 4),
diff --git a/man/figures/README-unnamed-chunk-1-2.png b/man/figures/README-fig-uk-faculty-1.png
similarity index 100%
rename from man/figures/README-unnamed-chunk-1-2.png
rename to man/figures/README-fig-uk-faculty-1.png
diff --git a/man/figures/README-fig-uk-faculty-gradient-1.png b/man/figures/README-fig-uk-faculty-gradient-1.png
new file mode 100644
index 0000000..68a9902
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diff --git a/man/figures/README-us-airports-1.png b/man/figures/README-fig-us-airports-1.png
similarity index 100%
rename from man/figures/README-us-airports-1.png
rename to man/figures/README-fig-us-airports-1.png
diff --git a/man/figures/README-pressure-1.png b/man/figures/README-pressure-1.png
deleted file mode 100644
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