search

tmuetze / Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST
16 stars 10 forks source link

something strange with RCY 99.5? #11

Closed m-grimes closed 9 years ago

m-grimes commented 9 years ago

Again - Attempted to install 99.5 but only 99.2 shows up. There was an error plotting the graph and selectNodes now fails after plotting this graph.

k2.w2 <- CytoscapeWindow("Case 2 CCCN", k2.g2) Cytoscape window named 'Case 2 CCCN' does not exist yet nodes have no label attribute -- adding default labels New window named "Case 2 CCCN" was created in Cytoscape. displayGraph(k2.w2) estimated displayGraph time: 0.3 seconds adding 42 nodes... sending 42 node(s) sendNodes completed adding 6 edges... transforming (6) graph edges to nodePairTable sending 6 edges adding node attributes... [1] "Gene.Name" Error in getAllNodes(cw) : error in evaluating the argument 'obj' in selecting a method for function 'getAllNodes': Error: object 'cw' not found layoutNetwork(k2.w2, "kamada-kawai")

  selectNodes(k2.w2, k2.cf[k2.cf$nodeType=="transcription factor", "Peptide.Name"], preserve=FALSE)

k2.cf[k2.cf$nodeType=="transcription factor", "Peptide.Name"] [1] "PML p 409" "POU2F1 p 279" "BCLAF1 p 758"
[4] "NFKB1 p 908" "CHD8 p 2240" "FOXJ3 p 179"
[7] "RNF4 p 110" "ZNF174 p 165" "CEBPB p 225"
[10] "TCEA1 p 114" "TCF19 p 77" "PML p 403;408"
[13] "PML p 403;409" "PML p 530;535;542" "ERF p 148;150;154"
[16] "BCLAF1 p 255;257;266" "ZMYND8 p 560;567" "BCLAF1 p 658;659"
[19] "AHCTF1 p 1189;1195" "SPEN p 736;749" "YBX1 rme 279"
selectNodes(k2.w2, k2.cf[k2.cf$nodeType=="transcription factor", "Peptide.Name"], preserve=FALSE) getSelectedNodes(k2.w2) [1] NA

sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets [9] methods base

other attached packages: [1] RCy3_0.99.2