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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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arrow visprops errors #7

Closed m-grimes closed 9 years ago

m-grimes commented 9 years ago

WORKING: setDefaultEdgeLineWidth (windowname, 3) setDefaultEdgeColor (windowname, '#888888') # gray setDefaultEdgeSelectionColor(windowname, "#FF6600")

SETUP: edgecolors = c('#FF0000', '#33FFCC', '#008000', '#EE00EE', '#0000FF', '#CC00FF', '#008000', '#006666', '#000000', '#888888', '#00C78C', '#0000FF', "#FCD116", '#0000FF', '#000000')

red; turquois; green; magenta; blue; violet; green; bluegreen; black; gray; turquoiseblue

edgeTypes <- c("pp", 'homology', 'knowledge', 'experimental', 'combined_score',  "Physical interactions","Pathway", "Predicted", "Genetic interactions", "merged" , "Shared protein domains", "negative correlation", "positive correlation", "intersect", "peptide")  
myarrows <- c ('Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow', 'No Arrow')

NOT WORKING:

setEdgeTargetArrowRule(windowname, 'edgeType', edgeTypes, myarrows, default='No Arrow')
Error. Could not set rule... setEdgeTargetArrowColorRule(windowname, "edgeType", edgeTypes, edgecolors, default.color='#FF0000')
NULL setEdgeSourceArrowColorRule(windowname, "edgeType", edgeTypes, myarrows, default.color='#FF0000')
NULL setEdgeColorRule(windowname, 'edgeType', edgeTypes, edgecolors, mode='lookup', default.color='#888888') # NULL

getArrowShapes(cy) Error in fromJSON(content, handler, default.size, depth, allowComments, : invalid JSON input

POSSIBLY RELATED?

getDefaultBackgroundColor(windowname) Error in fromJSON(rawToChar(request.res$content))[[2]] : subscript out of bounds [Same sessionInfo() as nodeShape issue]

windowname An object of class "CytoscapeWindowClass" (from package "RCy3") Slot "title": [1] "RGS12 RIC8A PPIs"

Slot "window.id": [1] "294"

Slot "graph": A graphNEL graph with directed edges Number of Nodes = 28 Number of Edges = 56

Slot "collectTimings": [1] FALSE

Slot "suid.name.dict": [[1]] [[1]]$name [1] "ARAF"

[[1]]$SUID [1] 306

[[2]] [[2]]$name [1] "BCR"

[[2]]$SUID [1] 307

[[3]] [[3]]$name [1] "CACNA1B"

[[3]]$SUID [1] 308

[[4]] [[4]]$name [1] "CD82"

[[4]]$SUID [1] 309

[[5]] [[5]]$name [1] "DLGAP3"

[[5]]$SUID [1] 310

[[6]] [[6]]$name [1] "EEF1A1"

[[6]]$SUID [1] 311

[[7]] [[7]]$name [1] "GNAI1"

[[7]]$SUID [1] 312

[[8]] [[8]]$name [1] "GNAI2"

[[8]]$SUID [1] 313

[[9]] [[9]]$name [1] "GNAI3"

[[9]]$SUID [1] 314

[[10]] [[10]]$name [1] "GNAS"

[[10]]$SUID [1] 315

[[11]] [[11]]$name [1] "HRAS"

[[11]]$SUID [1] 316

[[12]] [[12]]$name [1] "MAP2K2"

[[12]]$SUID [1] 317

[[13]] [[13]]$name [1] "PAPSS2"

[[13]]$SUID [1] 318

[[14]] [[14]]$name [1] "PHGDH"

[[14]]$SUID [1] 319

[[15]] [[15]]$name [1] "PLCB1"

[[15]]$SUID [1] 320

[[16]] [[16]]$name [1] "PLCB3"

[[16]]$SUID [1] 321

[[17]] [[17]]$name [1] "PRKCI"

[[17]]$SUID [1] 322

[[18]] [[18]]$name [1] "PYGB"

[[18]]$SUID [1] 323

[[19]] [[19]]$name [1] "RGS12"

[[19]]$SUID [1] 324

[[20]] [[20]]$name [1] "RIC8A"

[[20]]$SUID [1] 325

[[21]] [[21]]$name [1] "RPL38"

[[21]]$SUID [1] 326

[[22]] [[22]]$name [1] "SARNP"

[[22]]$SUID [1] 327

[[23]] [[23]]$name [1] "UBQLN1"

[[23]]$SUID [1] 328

[[24]] [[24]]$name [1] "GNA11"

[[24]]$SUID [1] 329

[[25]] [[25]]$name [1] "GNA14"

[[25]]$SUID [1] 330

[[26]] [[26]]$name [1] "GNA15"

[[26]]$SUID [1] 331

[[27]] [[27]]$name [1] "GNAO1"

[[27]]$SUID [1] 332

[[28]] [[28]]$name [1] "GNAQ"

[[28]]$SUID [1] 333

Slot "view.id": numeric(0)

Slot "uri": [1] "http://localhost:1234"