Author: mkirby
Date: 2012-08-12 00:28:14 -0700 (Sun, 12 Aug 2012)
New Revision: 30169
Modified:
csplugins/trunk/soc/mkirby/R/cytobridge.R
Log:
mkirby: Latest R code with use of rCurl and JSON.
Modified: csplugins/trunk/soc/mkirby/R/cytobridge.R
===================================================================
--- csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-08-12 07:26:58 UTC (rev
30168)
+++ csplugins/trunk/soc/mkirby/R/cytobridge.R 2012-08-12 07:28:14 UTC (rev
30169)
@@ -1,7 +1,7 @@
#------------------------------
#CytoBridge -------------------
#Author: Michael Kirby --------
-#Depends On: iGraph, rjson ----
+#Depends On: iGraph, rjson, Rcurl ----
#------------------------------
#Pushes the given iGraph to Cytoscape and returns the iGraph with extra
CytoBridge
@@ -25,18 +25,14 @@
} else {
cytob.suid <<- get.graph.attribute(g, "cytobid")
- V(g)$cytobid <- lapply(V(g)$cytobid,testm)
+ V(g)$cytobid <- lapply(V(g)$cytobid,idUpdate)
- E(g)$cytobid <- lapply(E(g)$cytobid,testm)
+ E(g)$cytobid <- lapply(E(g)$cytobid,idUpdate)
g <- set.graph.attribute(g, "cytobid", as.integer(cytob.suid))
}
-
- 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)
+
postForm("http://127.0.0.1:2609/cytobridge/JSONNetwork/",data=toJSON(list(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]))),
style="post")
if (tables) { pushTables(name, g) }
@@ -68,58 +64,84 @@
}
}
+#Pushes the specified graphs Network Table/Attributes.
pushNetworkTable <- function (name, g) {
gdata <- c()
+ gtypes <- c()
for(i in 1:length(list.graph.attributes(g))) {
- gdata <- append(gdata,
get.graph.attribute(g,list.graph.attributes(g)[i]))
+ temp <- get.graph.attribute(g,list.graph.attributes(g)[i])
+ gdata <- append(gdata, temp)
+ gtypes <- append(gtypes, type(temp))
}
- 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)
+ postForm("http://127.0.0.1:2609/cytobridge/JSONNetworkTable/";,
data=toJSON(list(network_name=name,
table_headings=dummy(list.graph.attributes(g)), table_types=dummy(gtypes),
table_data=as.character(dummy(gdata)))),style="post")
}
+#Pushes the specified graphs Node Table/Attributes.
pushNodeTable <- function (name, g) {
vdata <- c()
+ vtypes <- c()
for(v in 1:length(list.vertex.attributes(g))) {
- vdata <- append(vdata,
get.vertex.attribute(g,list.vertex.attributes(g)[v]))
+ temp <- get.vertex.attribute(g,list.vertex.attributes(g)[v])
+ vdata <- append(vdata, temp)
+ vtypes <- append(vtypes,type(unlist(temp)))
}
- 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)
+ postForm("http://127.0.0.1:2609/cytobridge/JSONNodeTable/";,
data=toJSON(list(network_name=name,
table_headings=dummy(list.vertex.attributes(g)), table_types=dummy(vtypes),
node_cytobridge_ids=dummy(get.vertex.attribute(g, 'cytobid')),
table_data=as.character(dummy(vdata)))),style="post")
}
+#Pushes the specified graphs Edge Table/Attributes.
pushEdgeTable <- function(name, g) {
edata <- c()
+ etypes <- c()
for(e in 1:length(list.edge.attributes(g))) {
- edata <- append(edata,
get.edge.attribute(g,list.edge.attributes(g)[e]))
+ temp <- get.edge.attribute(g,list.edge.attributes(g)[e])
+ edata <- append(edata, temp)
+ etypes <- append(etypes,type(unlist(temp)))
}
- 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)
+ postForm("http://127.0.0.1:2609/cytobridge/JSONEdgeTable/";,
data=toJSON(list(network_name=name,
table_headings=dummy(list.edge.attributes(g)), table_types=dummy(etypes),
edge_cytobridge_ids=dummy(get.edge.attribute(g, 'cytobid')),
table_data=as.character(dummy(edata)))),style="post")
}
#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])))
+ types <- c()
+ for(i in names(df)) {
+ temp <- df[[i]]
+ data <- append(data, temp)
+ types <- append(types,type(temp))
}
- xml.rpc('localhost:9000', 'Cytoscape.pushTable', name,
as.vector(names(df)), as.character(data))
+ postForm("http://127.0.0.1:2609/cytobridge/JSONTable/";,
data=toJSON(list(table_name=name, table_headings=dummy(names(df)),
table_types=dummy(types), row_ids=dummy(row.names(df)),
table_data=as.character(dummy(data)))), style="post")
+ df
}
+#Helper function to append one extra element to a list (since singleton
wouldn't be list)
+dummy <- function(l) {
+ append(l,0)
+}
-
-testm <- function(x) {
+#Helper Function to update a list with CytoBIDs (if unspecified)
+idUpdate <- function(x) {
if (is.na(x)) {
cytob.suid <<- cytob.suid + 1
as.integer(cytob.suid)
} else {
x
}
+}
+
+#Helper Function to return the Java appropriate type of the R Data
+type <- function(l) {
+ if (is.logical(l)) {
+ "Boolean"
+ } else if (is.numeric(l)) {
+ if (all.equal(as.integer(l),l)==TRUE) {
+ "Integer"
+ } else {
+ "Double"
+ }
+ } else {
+ "String"
+ }
}
\ No newline at end of file
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