plotInCytoscape, Failed to connect to localhost port 9000: Connection refused

[p.z...@griffith.edu.au]

Dear all,

I am trying the R package "clipper" for the first time. Actually followed the scripted in the manual "clipper.pdf" from Bioconductor.  When I used plotInCytoscape, there was an error message: 

"Error in function (type, msg, asError = TRUE)  : 

 Failed to connect to localhost port 9000: Connection refused"

Anybody can help me with that? It would be very much appreciated!

Below is exactly what I did in R:

library(graphite)

kegg <- pathways("hsapiens", "kegg")

graph <- convertIdentifiers(kegg[["Chronic myeloid leukemia"]], "entrez")

graph <- pathwayGraph(graph)

genes <- nodes(graph)

library(ALL)

data(ALL)

dim(pData(ALL))  ### 128 21

pAllB <- pData(ALL)[grep("B", pData(ALL)$BT),]

dim(pAllB)   ### 95 21

NEG <- pAllB$'mol.biol' == "NEG"

BCR <- pAllB$'mol.biol' == "BCR/ABL"

pAll <- pAllB[(NEG | BCR),]  ## 79 21

##Now we have to build the vector of classes.

classesUn <- as.character(pAll$'mol.biol')

classesUn[classesUn=="BCR/ABL"] <- 2

classesUn[classesUn=="NEG"] <- 1

classesUn <- as.numeric(classesUn)

names(classesUn) <- row.names(pAll)

classes <- sort(classesUn)

##Now that we have the vector of classes, we can isolate the subset of sample from the original expression set and

#subsequently we convert affymetrix probe names into entrez gene ids.

library("hgu95av2.db")

all <- ALL[,names(classes)]

probesIDS <- row.names(exprs(all))

featureNames(all@assayData)<-unlist(mget(probesIDS, hgu95av2ENTREZID))

all <- all[(!is.na(row.names(exprs(all))))]

library(graph)

genes <- intersect(genes, row.names(exprs(all)))

graph <- subGraph(genes, graph)

exp <- all[genes,,drop=FALSE]

dim(exprs(exp))

library(clipper)

pathwayAnalysis <- pathQ(exp, classes, graph, nperm=100, alphaV=0.05, b=100)

clipped <- clipper(exp, classes, graph, "var", trZero=0.01, permute=FALSE)

clipped[,1:5]

clipped <- prunePaths(clipped, thr=0.2)

clipped[,1:5]

plotInCytoscape(graph, clipped[1,])

Error here!

Thanks in advance!

Ping

[Barry Demchak]

It sounds like you're trying to use R with Cytoscape v3.x???

If so, your product versions would be mismatched.

The existing R packages work with cytoscape v2 and the RCytoscape plugin.

To use R with Cytoscape v3, see the cyREST app and the Rcy3 package, which is in Beta test.

Does this sound right for you??

Barry Demchak -- from my mobile phone

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[p.z...@griffith.edu.au]

Thanks for the reply Barry!

It is nice to know that the version matching issues. 

I was running the R code (below), which seems to me, it submits the job to cytoscape server. At the moment, I didn't even install Cytoscape on my computer at all. 

Anyway, I am now trying Cytoscape on my local computer. May ask more questions later :)

Thanks again.

Ping

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[Barry Demchak]

Best of luck!

Barry Demchak -- from my mobile phone

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