Replace deprecated igraph commands

Author: assaron

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gatom
 Title: Finding an Active Metabolic Module in Atom Transition Network
-Version: 1.9.0
+Version: 1.9.1
 Authors@R: 
     c(
     person("Anastasiia", "Gainullina", role = c("aut")),

R/gatom.R

@@ -220,7 +220,7 @@ makeMetabolicGraph <- function(network,
         setnames(vertex.table, "name", "name.orig")
     }
 
-    g <- graph.data.frame(edge.table, directed=FALSE, vertices = vertex.table)
+    g <- graph_from_data_frame(edge.table, directed=FALSE, vertices = vertex.table)
 
     if (!is.null(met.to.filter)) {
         nodes.to.del <- V(g)[metabolite %in% met.to.filter]
@@ -233,7 +233,7 @@ makeMetabolicGraph <- function(network,
 
     if (largest.component) {
         gc <- components(g)
-        g <- induced.subgraph(g, gc$membership == which.max(gc$csize))
+        g <- induced_subgraph(g, gc$membership == which.max(gc$csize))
     }
 
     g
@@ -383,7 +383,7 @@ connectAtomsInsideMetabolite <- function(m) {
     z <- matrix(c(toCollapse$v.x, toCollapse$v.y),
                 nrow=2,
                 byrow=TRUE)
-    res <- igraph::add.edges(m, t(as.matrix(toCollapse[, c("v.x", "v.y")])))
+    res <- igraph::add_edges(m, t(as.matrix(toCollapse[, c("v.x", "v.y")])))
     res
 }
 
@@ -414,7 +414,7 @@ collapseAtomsIntoMetabolites <- function(m) {
     edge.table.c <- edge.table.c[!duplicated(edge.table.c[, list(from, to)])]
 
 
-    res <- graph.data.frame(edge.table.c, directed=FALSE, vertices=vertex.table.c)
+    res <- graph_from_data_frame(edge.table.c, directed=FALSE, vertices=vertex.table.c)
     res
 }
 
@@ -435,7 +435,7 @@ collapseAtomsIntoMetabolites <- function(m) {
 #'
 #' @export
 addHighlyExpressedEdges <- function(m, g, top=3000) {
-    if (!"signalRank" %in% list.edge.attributes(g)) {
+    if (!"signalRank" %in% edge_attr_names(g)) {
         warning("No signalRank edge attribute, returing graph as is")
         return(m)
     }
@@ -455,5 +455,5 @@ addHighlyExpressedEdges <- function(m, g, top=3000) {
         rbind.fill(edge.table, toAdd.edge.table) %>%
         subset(!duplicated(paste0(from, "_", to)))
 
-    res <- graph.data.frame(res.edge.table, directed=FALSE, vertices=vertex.table)
+    res <- graph_from_data_frame(res.edge.table, directed=FALSE, vertices=vertex.table)
 }

R/io.R

@@ -28,7 +28,8 @@ saveModuleToPdf <- function(module, file, name=NULL, n_iter=100, force=1e-5) {
                 size=node_attrs$width, max_size=25, node.color=node_attrs$color,
                 node.label=V(module)$label, label.size=node_attrs$fontsize, label.color="grey13",
                 edge.size=edge_attrs$penwidth, edge.color=edge_attrs$color,
-                edge.label.fill=NA, edge.label=E(module)$label, edge.label.size=edge_attrs$fontsize,
+                edge.label.fill=NA,
+                edge.label=E(module)$label, edge.label.size=edge_attrs$fontsize,
                 legend.size=0, legend.position="up") +
          ggplot2::ggtitle(name) +
          ggplot2::theme(plot.title=
@@ -311,9 +312,9 @@ getEdgeXmlStrings <- function(module, indent="") {
     attr.values <- as_data_frame(module, what="edges")
     attr.xmlStrings <- getAttrXmlStrings(attr.values, paste0(indent, "  "))
 
-    edgelist.names <- get.edgelist(module, names=TRUE)
+    edgelist.names <- as_edgelist(module, names=TRUE)
     edgelist.names <- paste(edgelist.names[,1], edgelist.names[,2], sep=" (pp) ")
-    edgelist.ids <- get.edgelist(module, names=FALSE)
+    edgelist.ids <- as_edgelist(module, names=FALSE)
 
     xmlHeaders <- paste0(indent,
                          "<edge",
@@ -510,9 +511,9 @@ getEdgeDotStrings <- function(module, indent="", extra.attrs=NULL) {
                                  getAttrDotStrings(data.frame(URL=url, target="_blank")))
     }
 
-    edgelist.names <- get.edgelist(module, names=TRUE)
+    edgelist.names <- as_edgelist(module, names=TRUE)
     edgelist.names <- paste(edgelist.names[,1], edgelist.names[,2], sep=" (pp) ")
-    edgelist.ids <- get.edgelist(module, names=FALSE)
+    edgelist.ids <- as_edgelist(module, names=FALSE)
 
     edge.attrs <- apply(attr.dotStrings, 1, function(x) paste(na.omit(x), collapse=", "))
     edgeStrings <- sprintf("%sn%s -- n%s [ %s ];\n",
@@ -581,7 +582,7 @@ createShinyCyJSWidget <- function(module,
 
     nodes <- getJsNodeStyleAttributes(vertex.table)
 
-    positions <- layout.graphopt(module)
+    positions <-  layout_with_graphopt(module)
     nodes$position.x <- positions[, 1]
     nodes$position.y <- positions[, 2]
 

tests/testthat/test_gatom.R

@@ -47,7 +47,7 @@ test_that("overall pipeline works", {
     components <- components[sapply(components, length) > 1]
     for (component in components) {
         for (v in component) {
-            expect_equivalent(setdiff(component, V(m.connected)[nei(v)]$name), v)
+            expect_equivalent(setdiff(component, V(m.connected)[.nei(v)]$name), v)
         }
     }