Preparing for CRAN

Author: gvegayon

R/grob_vertex.R

@@ -114,8 +114,10 @@ grob_vertex <- function(netenv, v) {
   )
 # If the users is drawing text
   if (length(netenv$vertex.label) && !is.na(netenv$vertex.label[v])) {
+
     # Only if it is big enough
-    if (netenv$label_threshold <= netenv$vertex.size[v])
+    if (netenv$label_threshold <= netenv$vertex.size[v]) {
+
       ans <- grid::addGrob(
         ans,
         grid::textGrob(
@@ -130,9 +132,12 @@ grob_vertex <- function(netenv, v) {
           ),
           vjust         = 0,
           default.units = "native",
-          name = "label"
+          name          = "label",
+          check.overlap = TRUE
         )
       )
+
+    }
   }
   ans
 }

R/netplot.R

@@ -30,8 +30,11 @@ edge_color_mixer <- function(i, j, vcols, p = .5, alpha = .15) {
 #' @param vertex.nsides Numeric vector of length `vcount(x)`. Number of sizes of
 #' the vertex. E.g. three is a triangle, and 100 approximates a circle.
 #' @param vertex.color Vector of length `vcount(x)`. Vertex HEX or built in colors.
-#' @param vertex.size.range Vector of length `vcount(x)` from 0 to 1.
-#' @param vertex.frame.color Vector of length `vcount(x)`. Border of vertex in HEX or built in colors.
+#' @param vertex.size.range 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]`.
+#' @param vertex.frame.color Vector of length `vcount(x)`. Border of vertex in
+#' HEX or built in colors.
 #' @param vertex.frame.prop Vector of length `vcount(x)`. What proportion of the
 #' vertex does the frame occupy (values between 0 and 1).
 #' @param vertex.rot Vector of length `vcount(x)` in Radians. Passed to [npolygon],
@@ -45,19 +48,24 @@ edge_color_mixer <- function(i, j, vcols, p = .5, alpha = .15) {
 #' top ranking according to `vertex.size`.
 #' @param vertex.label.range Numeric vector of size 2 or 3. Relative scale of
 #' `vertex.label.fontsize` in points (see [grid::gpar]).
-#' @param edge.color A vector of length `ecount(x)`. In HEX or built in colors. Can be `NULL` in which case
+#' @param edge.color A vector of length `ecount(x)`. In HEX or built in colors.
+#' Can be `NULL` in which case
 #' the color is picked as a mixture between ego and alters' `vertex.color` values.
-#' @param edge.width Vector of length `ecount(x)` from 0 to 1. All edges will be the same size.
-#' @param edge.width.range Vector of length `ecount(x)` from 0 to 1. Adjusting width according to weight.
+#' @param edge.width Vector of length `ecount(x)` from 0 to 1. All edges will be
+#' the same size.
+#' @param edge.width.range Vector of length `ecount(x)` from 0 to 1. Adjusting
+#' width according to weight.
 #' @param edge.arrow.size Vector of length `ecount(x)` from 0 to 1.
 #' @param edge.curvature Numeric vector of length `ecount(x)`. Curvature of edges
 #' in terms of radians.
-#' @param edge.line.lty Vector of length `ecount(x)`. Line types in R (e.g.- 1 = Solid, 2 = Dashed, etc)
+#' @param edge.line.lty Vector of length `ecount(x)`. Line types in R
+#' (e.g.- 1 = Solid, 2 = Dashed, etc).
 #' @param edge.line.breaks Vector of length `ecount(x)`. Number of vertices to
 #' draw (approximate) the arc (edge).
-#' @param sample.edges Numeric scalar between 0 and 1. Proportion of edges to sample.
-#' @param skip.vertex,skip.edges,skip.arrows Logical scalar. When `TRUE` the object
-#' is not plotted.
+#' @param sample.edges Numeric scalar between 0 and 1. Proportion of edges to
+#' sample.
+#' @param skip.vertex,skip.edges,skip.arrows Logical scalar. When `TRUE` the
+#' object is not plotted.
 #' @param add Logical scalar.
 #' @param zero.margins Logical scalar.
 #' @importFrom igraph layout_with_fr degree vcount ecount
@@ -98,15 +106,15 @@ nplot <- function(
   bg.col                  = "transparent",
   vertex.nsides           = 10,
   vertex.color            = grDevices::hcl.colors(1),
-  vertex.size.range       = c(.01, .03),
+  vertex.size.range       = c(.01, .03, 4),
   vertex.frame.color      = NULL,
   vertex.rot              = 0,
   vertex.frame.prop       = .2,
   vertex.label            = NULL,
   vertex.label.fontsize   = NULL,
-  vertex.label.color      = "black",
-  vertex.label.fontfamily = "HersheySans",
-  vertex.label.fontface   = "bold",
+  vertex.label.color      = adjustcolor("black", alpha.f = .80),
+  vertex.label.fontfamily = "sans",
+  vertex.label.fontface   = "plain",
   vertex.label.show       = .3,
   vertex.label.range      = c(5, 15),
   edge.width              = 1,
@@ -138,15 +146,15 @@ nplot.igraph <- function(
   bg.col                  = "transparent",
   vertex.nsides           = 10,
   vertex.color            = grDevices::hcl.colors(1),
-  vertex.size.range       = c(.01, .03),
+  vertex.size.range       = c(.01, .03, 4),
   vertex.frame.color      = NULL,
   vertex.rot              = 0,
   vertex.frame.prop       = .2,
   vertex.label            = igraph::vertex_attr(x, "name"),
   vertex.label.fontsize   = NULL,
-  vertex.label.color      = "black",
-  vertex.label.fontfamily = "HersheySans",
-  vertex.label.fontface   = "bold",
+  vertex.label.color      = adjustcolor("black", alpha.f = .80),
+  vertex.label.fontfamily = "sans",
+  vertex.label.fontface   = "plain",
   vertex.label.show       = .3,
   vertex.label.range      = c(5, 15),
   edge.width              = igraph::edge_attr(x, "weight"),
@@ -215,15 +223,15 @@ nplot.network <- function(
   bg.col                  = "transparent",
   vertex.nsides           = 10,
   vertex.color            = grDevices::hcl.colors(1),
-  vertex.size.range       = c(.01, .03),
+  vertex.size.range       = c(.01, .03, 4),
   vertex.frame.color      = NULL,
   vertex.rot              = 0,
   vertex.frame.prop       = .2,
   vertex.label            =  network::get.vertex.attribute(x, "vertex.names"),
   vertex.label.fontsize   = NULL,
-  vertex.label.color      = "black",
-  vertex.label.fontfamily = "HersheySans",
-  vertex.label.fontface   = "bold",
+  vertex.label.color      = adjustcolor("black", alpha.f = .80),
+  vertex.label.fontfamily = "sans",
+  vertex.label.fontface   = "plain",
   vertex.label.show       = .3,
   vertex.label.range      = c(5, 15),
   edge.width              = 1,
@@ -288,15 +296,15 @@ nplot.matrix <- function(
   bg.col                  = "transparent",
   vertex.nsides           = 10,
   vertex.color            = grDevices::hcl.colors(1),
-  vertex.size.range       = c(.01, .03),
+  vertex.size.range       = c(.01, .03, 4),
   vertex.frame.color      = NULL,
   vertex.rot              = 0,
   vertex.frame.prop       = .2,
   vertex.label            = NULL,
   vertex.label.fontsize   = NULL,
-  vertex.label.color      = "black",
-  vertex.label.fontfamily = "HersheySans",
-  vertex.label.fontface   = "bold",
+  vertex.label.color      = adjustcolor("black", alpha.f = .80),
+  vertex.label.fontfamily = "sans",
+  vertex.label.fontface   = "plain",
   vertex.label.show       = .3,
   vertex.label.range      = c(5, 15),
   edge.width              = 1,
@@ -399,7 +407,7 @@ netplot_theme <- (function() {
 dev_size <- function(...) {
 
   if (length(grDevices::dev.list())) {
-    
+
     grDevices::dev.size(...)
 
   } else
@@ -435,15 +443,15 @@ nplot.default <- function(
   bg.col                  = "transparent",
   vertex.nsides           = 10,
   vertex.color            = grDevices::hcl.colors(1),
-  vertex.size.range       = c(.01, .03),
+  vertex.size.range       = c(.01, .03, 4),
   vertex.frame.color      = NULL,
   vertex.rot              = 0,
   vertex.frame.prop       = .2,
   vertex.label            = NULL,
   vertex.label.fontsize   = NULL,
-  vertex.label.color      = "black",
-  vertex.label.fontfamily = "HersheySans",
-  vertex.label.fontface   = "bold",
+  vertex.label.color      = adjustcolor("black", alpha.f = .80),
+  vertex.label.fontfamily = "sans",
+  vertex.label.fontface   = "plain",
   vertex.label.show       = .3,
   vertex.label.range      = c(5, 15),
   edge.width              = 1,
@@ -649,7 +657,7 @@ nplot.default <- function(
   if (!skip.vertex) {
     grob.vertex <- vector("list", netenv$N)
     for (v in 1:netenv$N)
-      grob.vertex[[v]] <- grob_vertex(netenv, v) 
+      grob.vertex[[v]] <- grob_vertex(netenv, v)
   } else
     grob.vertex <- NULL
 

R/netplot_base.R

@@ -35,7 +35,7 @@ nplot_base <- function(
   bg.col              = "transparent",
   vertex.nsides       = 10,
   vertex.color        = grDevices::hcl.colors(1),
-  vertex.size.range   = c(.01, .03),
+  vertex.size.range   = c(.01, .03, 4),
   vertex.frame.color  = grDevices::adjustcolor(vertex.color, red.f = .75, green.f = .75, blue.f = .75),
   vertex.rot          = 0,
   vertex.frame.prop   = .1,

README.md

@@ -0,0 +1,184 @@
+
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+[![CRAN
+status](https://www.r-pkg.org/badges/version/netplot.png)](https://cran.r-project.org/package=netplot)
+[![CRAN](https://cranlogs.r-pkg.org/badges/netplot.png)](https://cran.r-project.org/package=netplot)
+[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/rgexf.png)](https://cran.r-project.org/package=rgexf)
+[![R](https://github.com/USCCANA/netplot/actions/workflows/ci.yml/badge.svg)](https://github.com/USCCANA/netplot/actions/workflows/ci.yml)
+[![Build
+status](https://ci.appveyor.com/api/projects/status/3k2m3oq6o99qcs0r?svg=true.png)](https://ci.appveyor.com/project/gvegayon/netplot)
+[![USC’s Department of Preventive
+Medicine](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-uscprevmed-badge.svg)](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
+```
+
+<img src="man/figures/README-example-1.png" style="width:85.0%" />
+
+``` r
+
+V(UKfaculty)$ss <- runif(vcount(UKfaculty))
+nplot(UKfaculty, layout = l) # ala netplot
+```
+
+<img src="man/figures/README-example-2.png" style="width:85.0%" />
+
+``` r
+sna::gplot(intergraph::asNetwork(UKfaculty), coord=l)
+```
+
+<img src="man/figures/README-example-3.png" style="width:85.0%" />
+
+### UKfaculty
+
+``` r
+# Random names
+set.seed(1)
+nam <- sample(babynames::babynames$name, vcount(UKfaculty))
+
+ans <- nplot(
+  UKfaculty,
+  layout                = l,
+  vertex.color          = ~ Group,
+  vertex.nsides         = ~ Group,
+  vertex.label          = nam,
+  vertex.size.range     = c(.01, .03, 4),
+  bg.col                = "transparent",
+  vertex.label.show     = .25,
+  vertex.label.range    = c(10, 25),
+  edge.width.range      = c(1, 4, 5),
+  vertex.label.fontfamily = "sans"
+  )
+
+# Plot it!
+ans
+```
+
+<img src="man/figures/README-fig-uk-faculty-1.png" id="fig-uk-faculty"
+style="width:85.0%" />
+
+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)
+      }))
+```
+
+<img src="man/figures/README-fig-uk-faculty-gradient-1.png"
+id="fig-uk-faculty-gradient" style="width:85.0%" />
+
+### 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
+  )
+```
+
+<img src="man/figures/README-fig-us-airports-1.png" id="fig-us-airports"
+style="width:85.0%" />