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tmuetze / Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST
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something strange with RCY 99.5? #10

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. selectNodes now fails after plotting this graph

  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