Author: mkirby
Date: 2012-07-11 15:15:01 -0700 (Wed, 11 Jul 2012)
New Revision: 29846
Modified:
csplugins/trunk/soc/mkirby/R/cytobridge.R
Log:
mkirby: R Updated.
Modified: csplugins/trunk/soc/mkirby/R/cytobridge.R
===================================================================
--- csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-07-11 22:13:33 UTC (rev
29845)
+++ csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-07-11 22:15:01 UTC (rev
29846)
@@ -1,51 +1,84 @@
-#make your igraph
-g1 <- graph.ring(100000)
+#------------------------------
+#CytoBridge -------------------
+#Author: Michael Kirby --------
+#Depends On: iGraph, XMLRPC ---
+#------------------------------
-#The Cytobridge class
-setClass(Class="cytobridge",
- representation=representation(a="ANY", s="ANY"),
- prototype=prototype(a=graph(c(0,1))),
- validity=function(object) {
- if(class(object@a)!="igraph") {
- return(paste("Expected iGraph but got ", class(object@a)))
- } else {
- return(TRUE)
- }
- })
+#Pushes the given iGraph to Cytoscape and returns the iGraph with extra
CytoBridge
+#Consistency attributes.
+#name: The name to link this graph to with CytoBridge.
+#g: The iGraph to push.
+#tables: TRUE if push tables also, FALSE otherwise.
+pushNetwork <- function (name,g, tables=TRUE) {
+ if (!('cytobid' %in% list.graph.attributes(g))) {
+ cytob.suid <- 0
+ V(g)$cytobid <- seq(cytob.suid,cytob.suid+length(V(g))-1)
+ cytob.suid <- cytob.suid + length(V(g))-1
+ E(g)$cytobid <- seq(cytob.suid,cytob.suid+length(E(g))-1)
+ cytob.suid <- cytob.suid + length(E(g))-1
+ g <- set.graph.attribute(g, "cytobid", as.integer(cytob.suid))
+ } else {
+ cytob.suid <- get.graph.attribute(g, "cytobid")
+ for(n in 1:length(V(g))) {
+ if (is.na(get.vertex.attribute(g,'cytobid',n))) {
+ cytob.suid <- cytob.suid + 1
+ g <-
set.vertex.attribute(g,'cytobid',n,as.integer(cytob.suid))
+ }
+ }
-#Returns the graph of this CytoBridge
-setGeneric(name="getGraph", def=function(x) standardGeneric("getGraph"))
- setMethod(f="getGraph", signature="cytobridge", definition=function(x)
{
- return(x@a)
- })
+ for(e in 1:length(E(g))) {
+ if (is.na(get.edge.attribute(g,'cytobid',e))) {
+ cytob.suid <- cytob.suid + 1
+ g <-
set.edge.attribute(g,'cytobid',e,as.integer(cytob.suid))
+ }
+ }
+ g <- set.graph.attribute(g, "cytobid", as.integer(cytob.suid))
+ }
+ xml.rpc('localhost:9000', 'Cytoscape.pushNetwork', name,
get.vertex.attribute(g, 'cytobid'), get.edge.attribute(g, 'cytobid'),
get.vertex.attribute(g,"cytobid",get.edges(g,E(g))[,1]),
get.vertex.attribute(g,"cytobid",get.edges(g,E(g))[,2]))
+ if (tables) { pushTables(name, g) }
+ g
+}
-#Send the graph data to the communication Layer
-setGeneric(name="update", def=function(x) standardGeneric("update"))
- setMethod(f="update", signature="cytobridge",
- definition=function(x) {
- socket <- make.socket("localhost", "4444")
- on.exit(close.socket(socket))
- write.socket(socket,
paste(as.character(x@s),toString(x@a),"endRSend"))
- close.socket(socket)
- })
+#Pushes the given iGraphs attributes to Cytoscape.
+#name: The name this graph is linked to with CytoBridge.
+#g: The iGraph with the attributes to push.
+#net: TRUE to push network table.
+#node: TRUE to push node table.
+#edge: TRUE to push edge table.
+pushTables <- function (name,g, net=FALSE, node=FALSE, edge=FALSE) {
+ if (!net && !node && !edge) {
+ net = TRUE
+ node = TRUE
+ edge = TRUE
+ }
+ if (net) {
+ gdata <- c()
+ for(i in 1:length(list.graph.attributes(g))) {
+ gdata <- append(gdata,
get.graph.attribute(g,list.graph.attributes(g)[i]))
+ }
+ xml.rpc('localhost:9000', 'Cytoscape.pushNetTable', name,
as.vector(list.graph.attributes(g)), as.character(gdata))
+ }
+ if (node) {
+ vdata <- c()
+ for(v in 1:length(list.vertex.attributes(g))) {
+ vdata <- append(vdata,
get.vertex.attribute(g,list.vertex.attributes(g)[v]))
+ }
+ xml.rpc('localhost:9000', 'Cytoscape.pushNodeTable', name,
as.vector(list.vertex.attributes(g)), get.vertex.attribute(g, 'cytobid'),
as.character(vdata))
+ }
+ if (edge) {
+ edata <- c()
+ for(e in 1:length(list.edge.attributes(g))) {
+ edata <- append(edata,
get.edge.attribute(g,list.edge.attributes(g)[e]))
+ }
+ xml.rpc('localhost:9000', 'Cytoscape.pushEdgeTable', name,
as.vector(list.edge.attributes(g)), get.edge.attribute(g, 'cytobid'),
as.character(edata))
+ }
+}
-setGeneric(name="connect", def=function(x) standardGeneric("connect"))
- setMethod(f="connect", signature="cytobridge",
- definition=function(x) {
- x@s <- 1234 #some unique id
- return(x)
- })
-
-setGeneric(name="close", def=function(x) standardGeneric("close"))
- setMethod(f="close", signature="cytobridge",
- definition=function(x) {
- socket <- make.socket("localhost", "4444")
- on.exit(close.socket(socket))
- write.socket(socket, "die")
- close.socket(socket)
- x@s <- 0 #resets id
- })
-
-test <- new("cytobridge",a=g1)
-test <- connect(test)
-update(test)
\ No newline at end of file
+#Pushes the specified dataframe as a table to Cytoscape.
+pushTable <- function (name, df) {
+ data <- c()
+ for(i in 1:length(names(df))) {
+ data <- append(data, as.vector(t(df[i])))
+ }
+ xml.rpc('localhost:9000', 'Cytoscape.pushTable', name,
as.vector(names(df)), as.character(data))
+}
\ No newline at end of file
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