Fixing viz attributes from igraph to gexf and vice versa

.Rbuildignore

@@ -21,3 +21,4 @@ demo/gexfplot\.R
 ^dependencies$
 ^makefile$
 ^LICENSE\.md$
+^tests/rundemos\.R$

ChangeLog

@@ -1,8 +1,8 @@
 2017-11-27  George G. Vega Yon <g.vegayon@gmail.com>
 	* R/bugs.r: Function to map colors of a single node.
 
-	* R/igraph.r, R/read.gexf.r: Mapping positions, size and colors. Still a
-	  bit buggy. 
+	* R/igraph.r, R/read.gexf.r: Mapping positions, size and colors, ~~Still a
+	  bit buggy.~~ and positions.
 
 
 2017-11-13  George G. Vega Yon <g.vegayon@gmail.com>

NEWS.md

@@ -1,4 +1,4 @@
-# Changes in rgexf version 0.16.0 (2017-11-06)
+# Changes in rgexf version 0.16.0 (2017-11-27)
 
 ## New features and changes
 
@@ -20,6 +20,10 @@
 * `gexf` has a new argument, `rescale.node.size`. When set to `TRUE`, the
   `size` vector in `nodesVizAtt` is rescaled such that when calling the plot
   method the largest node spans roughly 5% of the plot.
+
+* `read.gexf` now parses viz attributes (color, position and size).
+
+* `igraph.to.gexf` and vice versa now pass viz attributes and layout.
 
 ## New functions
 

R/igraph.r

@@ -27,7 +27,8 @@
 #'   igraph1 <- gexf.to.igraph(gexf1)
 #'   gexf2 <- igraph.to.gexf(igraph1)
 #'   
-#'   # Now, let's do it with a layout!
+#'   # Now, let's do it with a layout! (although we can just use
+#'   # the one that comes with lesmiserables :))
 #'   pos <- igraph::layout_nicely(igraph1)
 #'   plot(
 #'     igraph.to.gexf(igraph1, nodesVizAtt = list(position=cbind(pos, 0))),
@@ -42,56 +43,32 @@ igraph.to.gexf <- function(igraph.obj, ...) {
 
   # Retrive elements from igraph object
   gdata    <- igraph::get.data.frame(g, what="both")
-  tmpedges <- gdata$edges
-  tmpnodes <- gdata$vertices
-  
+  edges <- gdata$edges
+  nodes <- cbind(id = 1L:igraph::vcount(g), gdata$vertices)
+
   # If nodes have no name
-  if (!("name" %in% colnames(tmpnodes))) 
-    tmpnodes <- data.frame(tmpnodes, name=1:nrow(tmpnodes))
-
-  # Nodes and edges list
-  # these steps are dangerous as nodes that are not connected are dropped, creating a mismatched number of rows
-#   nodes <- edge.list(tmpedges[,c(1,2)])
-#   edges <- nodes$edges
-#   nodes <- nodes$nodes
-
-  nodes <- tmpnodes
-  # change name to label
-  names(nodes) <- 'label'
-  # add a column to nodes to hold the IDs
-  nodes$id <- as.integer(as.factor(nodes$label))
-  # put them in the right order
-  nodes <- nodes[, c('id', 'label')]
-
-  ## replace from and to in edges with their IDs
-  # first create a named vector of ids
-  nodesID <- nodes$id
-  names(nodesID) <- gdata$vertices$name
-
-  edges <- tmpedges
-  # now in the edges create the id columns
-  edges$source <- nodesID[edges$from]
-  edges$target <- nodesID[edges$to]
-  # keep just source and target
-  edges <- edges[, c('source', 'target')]
+  namecol <- which(colnames(nodes) == "name")
+  if (!length(namecol)) 
+    nodes <- data.frame(nodes, label=nodes$id)
+  else
+    nodes$label <- nodes$name
 
-  # Building nodes
-  if (length(tmpnodes)) {
-    nodes <-merge(tmpnodes,nodes, by.x="name", by.y="label")
-#    nodes <- nodes[,!(colnames(nodes) %in% c("label"))]
-  }
+
+  edges$source <- nodes$id[match(edges$from, nodes$label)]
+  edges$target <- nodes$id[match(edges$to, nodes$label)]
+  edges <- edges[, c('source', 'target')]
 
   # Nodes Attributes
   x <- igraph::list.vertex.attributes(g)
-  x <- x[!(x %in% c("label","color","size"))]
+  x <- x[!(x %in% c("label","color","size", "name"))]
   if (length(x))
     dots$nodesAtt <- subset(nodes, select=x)
 
   # Edges Attributes
   x <- igraph::list.edge.attributes(g)
   x <- x[!(x %in% c("weight","color","edgesLabel","width"))]
   if (length(x)) 
-    dots$edgesAtt <- subset(tmpedges, select=x)
+    dots$edgesAtt <- subset(edges, select=x)
 
   # Edges Weights
   if (!length(dots$edgesWeight) && length(igraph::E(g)$weight))
@@ -101,14 +78,14 @@ igraph.to.gexf <- function(igraph.obj, ...) {
 
   # Nodes Viz att
   if (!length(dots$nodesVizAtt$color)) {
-    if (length(tmpnodes$color)) {
-      dots$nodesVizAtt$color <- tmpnodes$color
+    if (length(nodes$color)) {
+      dots$nodesVizAtt$color <- nodes$color
     } else 
       dots$nodesVizAtt$color <- NULL
   }
 
-  if (!length(dots$nodesVizAtt$size) && length(tmpnodes$size))
-    dots$nodesVizAtt$size <- tmpnodes$size
+  if (!length(dots$nodesVizAtt$size) && length(nodes$size))
+    dots$nodesVizAtt$size <- nodes$size
 
   positions <- igraph::graph_attr(g, "layout")
 
@@ -119,8 +96,8 @@ igraph.to.gexf <- function(igraph.obj, ...) {
 
   # Edges Viz att
   if (!length(dots$edgesVizAtt$color)) {
-    if (length(tmpedges$color)) {
-      dots$edgesVizAtt$color <- tmpedges$color
+    if (length(edges$color)) {
+      dots$edgesVizAtt$color <- edges$color
     } else
       dots$edgexVizAtt$color <- NULL
   }
@@ -137,8 +114,8 @@ igraph.to.gexf <- function(igraph.obj, ...) {
   # Building graph
   do.call(gexf, c(
     list(
-      nodes = nodes[,c("id","name")],
-      edges = edges
+      nodes = nodes[, c("id","name")],
+      edges = edges[, c("source", "target")]
       ), dots)
   )
 
@@ -171,7 +148,10 @@ gexf.to.igraph <- function(gexf.obj) {
     igraph::V(g2)$size <- x$value
 
   if (length(x <- g$nodesVizAtt$position))
-    g2 <- igraph::set_graph_attr(g2, "layout", unname(x))
+    g2 <- igraph::set_graph_attr(
+      g2, "layout", 
+      unname(as.matrix(x))
+      )
 
   # Nodes atts
   if (length(x <- g$nodes[, !(colnames(g$nodes) %in% c("id", "label"))])) 

R/read.gexf.r

@@ -161,11 +161,13 @@ read.gexf <- function(x) {
 
   class(graph) <- "gexf"
 
+  order <- order(as.integer(graph$nodes$id))
+
   build.and.validate.gexf(
-    nodes            = graph$nodes,
+    nodes            = graph$nodes[order, , drop=FALSE],
     edges            = graph$edges,
     atts.definitions = graph$atts.definitions,
-    nodesVizAtt      = nodesVizAtt,
+    nodesVizAtt      = lapply(nodesVizAtt, "[", i=order, j=, drop=FALSE),
     edgesVizAtt      = edgesVizAtt,
     graph            = graph$graph
     )

demo/gexfigraph.R

@@ -1,3 +1,3 @@
 gexf1 <- read.gexf(system.file("gexf-graphs/lesmiserables.gexf", package="rgexf"))
 igraph1 <- gexf.to.igraph(gexf1)
-gexf2 <- igraph.to.gexf(igraph1)
+gexf2 <- igraph.to.gexf(igraph1)

inst/NEWS

@@ -1,32 +1,34 @@
 
 
-CHANGES IN RGEXF VERSION 0.16.0 (2017-11-06)
+CHANGES IN RGEXF VERSION 0.16.0 (2017-11-27)
 
 
 New features and changes
 
--   Modernization of the project (roxygen, new CRAN standards, etc.)
-
--   Updated emails.
-
--   Remove broken links.
-
 -   Function write.gexf has a new argument for specifying the GEXF
     version for now it only changes the header.
 
 -   plot.gexf method now uses gexf-js instead of sigma.js.
 
 -   Now igraph.to.gexf passes arguments to gexf. Before it was only
-    passing position. This way users have more flexibility specifying
-    attributes.
+    passing position. This way users have more flexibility
+    specifying attributes.
 
 -   gexf's nodesVizAtt now has defaults for color, size and position.
     This is a requirement of gexf-js.
 
+-   gexf's nodesVizAtt color and size now support passing a default for
+    all the nodes. Also, color can be specified as a character scalar
+    (name of the) color, or as an integer (number in colors()).
+
 -   gexf has a new argument, rescale.node.size. When set to TRUE, the
     size vector in nodesVizAtt is rescaled such that when calling the
     plot method the largest node spans roughly 5% of the plot.
 
+-   read.gexf now parses viz attributes (color, position and size).
+
+-   igraph.to.gexf and vice versa now pass viz attributes and layout.
+
 
 New functions
 
@@ -36,6 +38,15 @@ New functions
     vers 0.17.0
 
 
+Misc changes
+
+-   Modernization of the project (roxygen, new CRAN standards, etc.)
+
+-   Updated emails.
+
+-   Remove broken links.
+
+
 
 CHANGES IN RGEXF VERSION 0.15.3 (2015-03-24)
 
@@ -70,9 +81,9 @@ Bug fixes
 
 Development
 
--   Option -keepFactors- default is now in -FALSE- (used to be in
-    -TRUE-). When set to -TRUE- and there are factors, a warning message
-    will appear (reported in issue 18, thanks Tim Smith!).
+-   Option -keepFactors- default is now in -FALSE- (used to be
+    in -TRUE-). When set to -TRUE- and there are factors, a warning
+    message will appear (reported in issue 18, thanks Tim Smith!).
 
 
 
@@ -81,8 +92,8 @@ CHANGES IN RGEXF VERSION 0.13.11 (2013-11-27)
 
 Bug fixes
 
--   Included class checks in -gexf- class functions (thanks to Samuel
-    Finegold).
+-   Included class checks in -gexf- class functions (thanks to
+    Samuel Finegold).
 
 -   write.gexf does not fails when dynamics different from double are
     passed (thank you Samuel Finegold!).
@@ -120,8 +131,8 @@ CHANGES IN RGEXF VERSION 0.13.05 (2013-05-09)
 
 Bug fixes
 
--   sprintf error when using other formats rather than double (issue
-    10).
+-   sprintf error when using other formats rather than double
+    (issue 10).
 
 -   in .addNodesEdges, add support to case “!attributes &&
     vizattributes” (issue 9).
@@ -163,8 +174,8 @@ Bug fixes
 Development
 
 -   .addNodesEdges rewritten now works faster in most of CPUs (some of
-    them with very high speedups) (Thanks to Duncan Temple Lang, RXML
-    author)
+    them with very high speedups) (Thanks to Duncan Temple Lang,
+    RXML author)
 
 -   Several code routines have been extracted from “bigger functions”
     and written as functions themselves.
@@ -180,8 +191,8 @@ New features and changes
     rm.gexf.node and rm.gexf.edge allow to build and manipulate gexf
     objects from scratch.
 
--   New function read.gexf allows to import gexf files as gexf class
-    objects.
+-   New function read.gexf allows to import gexf files as gexf
+    class objects.
 
 -   gexf function now it is called write.gexf.
 
@@ -192,8 +203,8 @@ New features and changes
 
 -   Real-life datasets have been includded.
 
--   New function edge.list builds a dataframe of nodes from an edge
-    list.
+-   New function edge.list builds a dataframe of nodes from an
+    edge list.
 
 -   New methods for gexf objects: print.gexf and summary.gexf.
 

tests/testthat/test-examples.r

@@ -1,3 +1,3 @@
-# context("Examples")
+context("Examples")
 
-# test_examples()
+test_examples()