Fixing bug on processing visual attributes and start working on issue #…

…35

.gitignore

@@ -15,3 +15,4 @@
 *.pdf
 .Rproj.user
 inst/doc
+docs/

.travis.yml

@@ -4,19 +4,35 @@ language: R
 sudo: false
 cache: packages
 
-r:
-  - release
-  - devel # Not working
+matrix:
+  include:
+    # - os: linux
+    #  r: oldrel
+    - os: linux
+      r: release
+      env:
+        - R_CODECOV=true
+        - BUILD_WWW_HERE=true
+    - os: linux
+      r: devel
+    - os: osx
+      osx_image: xcode10.2
 
-os:
-  - linux
-  - osx
-
-osx_image: xcode11
 
 env:
  global:
    - CRAN: http://cran.rstudio.com
 
 after_success:
   - if [ $TRAVIS_OS_NAME == "linux" ]; then Rscript -e 'covr::codecov()'; fi
+
+  # For automatic deploy of the website
+before_deploy: Rscript -e 'remotes::install_cran("pkgdown")'
+deploy:
+  provider: script
+  script: Rscript -e 'pkgdown::deploy_site_github()'
+  skip_cleanup: true
+  on:
+    branch: master
+    condition: $BUILD_WWW_HERE = true
+

R/bugs.r

@@ -182,7 +182,10 @@ viz_att_checks$color <- function(x, type) {
 viz_att_checks$position <- function(x, type) {
 
   # Must be able to be coerced to a matrix
-  x <- as.matrix(x)
+  if (is.vector(x))
+    x <- matrix(x, nrow = 1)
+  else
+    x <- as.matrix(x)
 
   # Is it numeric?
   if (!is.numeric(x))
@@ -197,6 +200,12 @@ viz_att_checks$position <- function(x, type) {
   # Adding z?
   if (ncol(x) == 2)
     x <- cbind(x, 0)
+  if (!(ncol(x) %in% c(2,3)))
+    stop(
+      "Positions should be specified with either 2 (X,Y) or 3 (X, Y, Z) coordinates.",
+      call. = FALSE
+      )
+
 
   dimnames(x) <- list(NULL, paste0("viz.position.",c("x", "y", "z")))
 

R/gexf-js.r

@@ -157,6 +157,22 @@ gexf_js_config <- function(
 #' as specified by `dir`.
 #' 
 #' @details 
+#' 
+#' An important thing for the user to consider is the fact that the function
+#' only works if there are `viz` attributes, this is, color, size, and position.
+#' If the [gexf] object's XML document does not have viz attributes, users can
+#' use the following hack:
+#' 
+#' ```
+#' # Turn the object ot igraph and go back
+#' x <- igraph.to.gexf(gexf.to.igraph(x))
+#' 
+#' # And you are ready to plot!
+#' plot(x)
+#' ```
+#' 
+#' More details on this in the [igraph.to.gexf] function.
+#' 
 #' The files are copied directly from
 #' \Sexpr{system.file("gexf-js", package="rgexf")}. And the 
 #' parameters are set up by modifying the following template file:

R/read.gexf.r

@@ -95,9 +95,18 @@ read.gexf <- function(x) {
   # Extracting attributes
   node.vizattr <- XML::xpathApply(
     gfile, "/r:gexf/r:graph/r:nodes/r:node", namespaces = c(r=ns, v="viz"),
-    fun=XML::xmlChildren)
+    fun=XML::xmlChildren
+    )
+
+  node.attr <- XML::xpathApply(
+    gfile, "/r:gexf/r:graph/r:nodes/r:node/r:attvalues", namespaces = c(r=ns),
+    fun=XML::xmlChildren
+  )
 
+  node.attr <- lapply(node.attr, lapply, XML::xmlAttrs)
+
   node.vizattr <- lapply(node.vizattr, lapply, XML::xmlAttrs)
+  # node.vizattr <- lapply(node.viz)
 
   # Colors
   nodesVizAtt$color <- lapply(node.vizattr, function(a) {
@@ -110,25 +119,29 @@ read.gexf <- function(x) {
   })
 
   nodesVizAtt$color <- do.call(rbind, nodesVizAtt$color)
+
   nodesVizAtt$color <- as.data.frame(nodesVizAtt$color)
   dimnames(nodesVizAtt$color) <- list(
     1L:nrow(nodesVizAtt$color), c("r", "g", "b", "a")
   )
+
 
   # Size
   nodesVizAtt$size <- lapply(node.vizattr, function(a) {
     if (length(a$size)) 
       return(viz_att_checks$size(as.numeric(a$size)))
 
-    check_and_map_color(default_nodeVizAtt$size())
+    viz_att_checks$size(default_nodeVizAtt$size())
   })
 
   nodesVizAtt$size <- do.call(rbind, nodesVizAtt$size)
+
   nodesVizAtt$size <- as.data.frame(nodesVizAtt$size)
   dimnames(nodesVizAtt$size) <- list(
     1L:nrow(nodesVizAtt$size), "value"
   )
 
+
   # Positions
   nodesVizAtt$position <- lapply(node.vizattr, function(a) {
     if (length(a$position)) 

R/rgexf.r

@@ -463,10 +463,7 @@ gexf <- function(
                         b=nodesVizAtt)
   } else NULL
 
-
-
-
-  nNodesVizAtt <- length(nodesVizAtt)
+    nNodesVizAtt <- length(nodesVizAtt)
 
   # Checking the number of digits
   if (!is.integer(digits)) stop("Invalid number of digits ",digits,