Author: mkirby
Date: 2012-07-23 23:06:45 -0700 (Mon, 23 Jul 2012)
New Revision: 29972
Modified:
csplugins/trunk/soc/mkirby/R/cytobridge.R
Log:
mkirby: R using sockets+JSON.
Modified: csplugins/trunk/soc/mkirby/R/cytobridge.R
===================================================================
--- csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-07-24 02:37:44 UTC (rev
29971)
+++ csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-07-24 06:06:45 UTC (rev
29972)
@@ -1,7 +1,7 @@
#------------------------------
#CytoBridge -------------------
#Author: Michael Kirby --------
-#Depends On: iGraph, XMLRPC ---
+#Depends On: iGraph, rjson ----
#------------------------------
#Pushes the given iGraph to Cytoscape and returns the iGraph with extra
CytoBridge
@@ -10,6 +10,11 @@
#g: The iGraph to push.
#tables: TRUE if push tables also, FALSE otherwise.
pushNetwork <- function (name,g, tables=TRUE) {
+ isGN <- FALSE
+ if (class(g) == "graphNEL") {
+ g <- igraph.from.graphNEL(g)
+ isGN <- TRUE
+ }
if (!('cytobid' %in% list.graph.attributes(g))) {
cytob.suid <- 0
V(g)$cytobid <- seq(cytob.suid,cytob.suid+length(V(g))-1)
@@ -18,24 +23,25 @@
cytob.suid <- cytob.suid + length(E(g))-1
g <- set.graph.attribute(g, "cytobid", as.integer(cytob.suid))
} else {
- cytob.suid <- get.graph.attribute(g, "cytobid")
- for(n in 1:length(V(g))) {
- if (is.na(get.vertex.attribute(g,'cytobid',n))) {
- cytob.suid <- cytob.suid + 1
- g <-
set.vertex.attribute(g,'cytobid',n,as.integer(cytob.suid))
- }
- }
+ cytob.suid <<- get.graph.attribute(g, "cytobid")
- for(e in 1:length(E(g))) {
- if (is.na(get.edge.attribute(g,'cytobid',e))) {
- cytob.suid <- cytob.suid + 1
- g <-
set.edge.attribute(g,'cytobid',e,as.integer(cytob.suid))
- }
- }
+ V(g)$cytobid <- lapply(V(g)$cytobid,testm)
+
+ E(g)$cytobid <- lapply(E(g)$cytobid,testm)
+
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]))
+
+
+ socket <- make.socket("localhost", "4444")
+ on.exit(close.socket(socket))
+ system.time(write.socket(socket, toJSON(list(type="JSONNetwork",
network_name=name, node_cytobridge_ids=get.vertex.attribute(g, 'cytobid'),
edge_cytobridge_ids=get.edge.attribute(g, 'cytobid'),
edge_source_cytobridge_ids=get.vertex.attribute(g,"cytobid",get.edges(g,E(g))[,1]),
edge_target_cytobridge_ids=get.vertex.attribute(g,"cytobid",get.edges(g,E(g))[,2])))))
+ close.socket(socket)
+
if (tables) { pushTables(name, g) }
+
+ if (isGN) { g <- igraph.to.graphNEL(g) }
+
g
}
@@ -52,28 +58,52 @@
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))
+ pushNetworkTable(name, g)
}
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))
+ pushNodeTable(name, g)
}
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))
+ pushEdgeTable(name, g)
}
}
+pushNetworkTable <- function (name, g) {
+ gdata <- c()
+ for(i in 1:length(list.graph.attributes(g))) {
+ gdata <- append(gdata,
get.graph.attribute(g,list.graph.attributes(g)[i]))
+ }
+
+ socket <- make.socket("localhost", "4444")
+ on.exit(close.socket(socket))
+ system.time(write.socket(socket, toJSON(list(type="JSONNetworkTable",
network_name=name, table_headings=as.vector(list.graph.attributes(g)),
table_data=as.character(gdata)))))
+ close.socket(socket)
+}
+
+pushNodeTable <- function (name, g) {
+ vdata <- c()
+ for(v in 1:length(list.vertex.attributes(g))) {
+ vdata <- append(vdata,
get.vertex.attribute(g,list.vertex.attributes(g)[v]))
+ }
+
+ socket <- make.socket("localhost", "4444")
+ on.exit(close.socket(socket))
+ system.time(write.socket(socket, toJSON(list(type="JSONNodeTable",
network_name=name, table_headings=as.vector(list.vertex.attributes(g)),
node_cytobridge_ids=get.vertex.attribute(g, 'cytobid'),
table_data=as.character(vdata)))))
+ close.socket(socket)
+}
+
+pushEdgeTable <- function(name, g) {
+ edata <- c()
+ for(e in 1:length(list.edge.attributes(g))) {
+ edata <- append(edata,
get.edge.attribute(g,list.edge.attributes(g)[e]))
+ }
+
+ socket <- make.socket("localhost", "4444")
+ on.exit(close.socket(socket))
+ system.time(write.socket(socket, toJSON(list(type="JSONEdgeTable",
network_name=name, table_headings=as.vector(list.edge.attributes(g)),
edge_cytobridge_ids=get.edge.attribute(g, 'cytobid'),
table_data=as.character(edata)))))
+ close.socket(socket)
+}
+
#Pushes the specified dataframe as a table to Cytoscape.
pushTable <- function (name, df) {
data <- c()
@@ -81,4 +111,15 @@
data <- append(data, as.vector(t(df[i])))
}
xml.rpc('localhost:9000', 'Cytoscape.pushTable', name,
as.vector(names(df)), as.character(data))
+}
+
+
+
+testm <- function(x) {
+ if (is.na(x)) {
+ cytob.suid <<- cytob.suid + 1
+ as.integer(cytob.suid)
+ } else {
+ x
+ }
}
\ No newline at end of file
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