RCytoscape.R
In RCytoscape: Display and manipulate graphs in Cytoscape

### R code from vignette source 'RCytoscape.Rnw'

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### code chunk number 1: g0 (eval = FALSE)
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##   library(RCytoscape)
##   g <- new ('graphNEL', edgemode='directed')
##   g <- graph::addNode ('A', g)
##   g <- graph::addNode ('B', g)
##   g <- graph::addNode ('C', g)
##   cw <- new.CytoscapeWindow ('vignette', graph=g)
##   displayGraph (cw)
## 


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### code chunk number 2: g1 (eval = FALSE)
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##   layoutNetwork (cw, layout.name='grid')
##   redraw (cw)


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### code chunk number 3: g2 (eval = FALSE)
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##   g <- cw@graph   # created above, in the section  'A minimal example'
##   g <- initNodeAttribute (graph=g,  attribute.name='moleculeType',
##                           attribute.type='char',
##                           default.value='undefined')
##   g <- initNodeAttribute (graph=g,  'lfc', 'numeric', 0.0)
##   nodeData (g, 'A', 'moleculeType') <- 'kinase'
##   nodeData (g, 'B', 'moleculeType') <- 'TF'
##   nodeData (g, 'C', 'moleculeType') <- 'cytokine'
##   nodeData (g, 'A', 'lfc') <- -1.2
##   nodeData (g, 'B', 'lfc') <- 1.8
##   nodeData (g, 'C', 'lfc') <- 3.2
##   cw = setGraph (cw, g)
##   displayGraph (cw)    # cw's graph is sent to Cytoscape
##   redraw (cw)
##   


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### code chunk number 4: defaults (eval = FALSE)
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##   setDefaultNodeShape (cw, 'octagon')
##   setDefaultNodeColor (cw, '#AAFF88')
##   setDefaultNodeSize  (cw, 80)
##   setDefaultNodeFontSize (cw, 40)
##   redraw (cw)


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### code chunk number 5: g3 (eval = FALSE)
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##   getNodeShapes (cw)   # diamond, ellipse, trapezoid, triangle, etc.
##   print (noa.names (getGraph (cw)))  # what data attributes are defined?
##   print (noa (getGraph (cw), 'moleculeType'))
##   attribute.values <- c ('kinase',  'TF',       'cytokine')
##   node.shapes      <- c ('diamond', 'triangle', 'rect')
##   setNodeShapeRule (cw, node.attribute.name='moleculeType',
##                     attribute.values, node.shapes)
##   redraw (cw)


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### code chunk number 6: g4 (eval = FALSE)
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##   setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0),
##                     c ('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000'),
##                     mode='interpolate')


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### code chunk number 7: g41 (eval = FALSE)
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##   setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0),
##                     c ('#00FF00', '#FFFFFF', '#FF0000'),
##                     mode='interpolate')


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### code chunk number 8: g5 (eval = FALSE)
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##   control.points = c (-1.2, 2.0, 4.0)
##   node.sizes     = c (10, 20, 50, 200, 205)
##   setNodeSizeRule (cw, 'lfc', control.points, node.sizes,
##                    mode='interpolate')
## 


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### code chunk number 9: g6 (eval = FALSE)
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##  
##   g <- cw@graph
##   g <- initEdgeAttribute (graph=g,  attribute.name='edgeType',
##                           attribute.type='char',
##                           default.value='unspecified')
## 
##   g <- graph::addEdge ('A', 'B', g)
##   g <- graph::addEdge ('B', 'C', g)
##   g <- graph::addEdge ('C', 'A', g)
## 
##   edgeData (g, 'A', 'B', 'edgeType') <- 'phosphorylates'
##   edgeData (g, 'B', 'C', 'edgeType') <- 'promotes'
##   edgeData (g, 'C', 'A', 'edgeType') <- 'indirectly activates'
##   cw@graph <- g
##   displayGraph (cw)
## 
##   line.styles = c ('DOT', 'SOLID', 'SINEWAVE')
##   edgeType.values = c ('phosphorylates', 'promotes',
##                        'indirectly activates')
##   setEdgeLineStyleRule (cw, 'edgeType', edgeType.values,
##                         line.styles)
##   redraw (cw)
## 
##   arrow.styles = c ('Arrow', 'Delta', 'Circle')
##   setEdgeTargetArrowRule (cw, 'edgeType', edgeType.values,
##                           arrow.styles)


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### code chunk number 10: g7 (eval = FALSE)
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##   hidePanel (cw, 'Data Panel')
##   floatPanel (cw, 'D')
##   dockPanel (cw, 'd')
##   hidePanel (cw, 'Control Panel')
##   floatPanel (cw, 'control')
##   dockPanel (cw, 'c')


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### code chunk number 11: g8 (eval = FALSE)
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##   getSelectedNodes (cw)
##     


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### code chunk number 12: g9 (eval = FALSE)
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##   selectFirstNeighborsOfSelectedNodes (cw)


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### code chunk number 13: g10 (eval = FALSE)
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##   nodes <- getSelectedNodes (cw)


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### code chunk number 14: position (eval = FALSE)
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##   cwe <- new.CytoscapeWindow ('vignette.setNodePosition',
##                               graph=RCytoscape::makeSimpleGraph ())
##   displayGraph (cwe)
##   layoutNetwork (cwe, 'jgraph-spring')
##   redraw (cwe)
## 
##   center.x <- 200
##   center.y <- 200
##   radius <- 200
##     # sweep through full revoltion 3 times, 5 degrees at a time
##   angles <- rep (seq (0, 360, 5), 3)
##   for (angle in angles) {
##     angle.in.radians <- angle * pi / 180
##     x <- center.x + (radius * cos (angle.in.radians))
##     y <- center.y + (radius * sin (angle.in.radians))
##     setNodePosition (cwe, 'A', x, y)
##     }
##     # RCy will not create windows with duplicate names, so clear the decks for a subsequent possible run
## 


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### code chunk number 15: moviePrep (eval = FALSE)
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##   g <- RCytoscape::makeSimpleGraph ()
##   g <- initNodeAttribute (g, 'pval', 'numeric', 1.0)
## 
##   cwm <- new.CytoscapeWindow ('movie', graph =g)
##   displayGraph (cwm)
##   layoutNetwork (cwm, 'jgraph-spring')
##   redraw (cwm)
## 


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### code chunk number 16: movieRules (eval = FALSE)
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##   lfc.control.points <- c (-3.0, 0.0, 3.0)
##   lfc.colors <- c ('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000')
##   setNodeColorRule (cwm, 'lfc', lfc.control.points, lfc.colors,
##                     mode='interpolate')
## 
##   pval.control.points <- c (0.1, 0.05, 0.01, 0.0001)
##   pval.sizes          <- c (30, 50, 70, 100)
##   setNodeSizeRule (cwm, 'pval', pval.control.points, pval.sizes,
##                    mode='interpolate')
## 


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### code chunk number 17: animate (eval = FALSE)
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## 
##   pval.timepoint.1 <- c (0.01, 0.3, 0.05)
##   pval.timepoint.2 <- c (0.05, 0.01, 0.01)
##   pval.timepoint.3 <- c (0.0001, 0.005, 0.1)
## 
##   lfc.timepoint.1 <- c (-1.0, 1.0, 0.0)
##   lfc.timepoint.2 <- c (2.0, 3.0, -2.0)
##   lfc.timepoint.3 <- c (2.5, 2.0, 0.0)
## 
##   for (i in 1:5) {  # run this loop 5 times
##     setNodeAttributesDirect (cwm, 'lfc',  'numeric', c ('A', 'B', 'C'),
##                              lfc.timepoint.1)
##     setNodeAttributesDirect (cwm, 'pval', 'numeric', c ('A', 'B', 'C'),
##                              pval.timepoint.1)
##     redraw (cwm)
##     msg (cwm, 'timepoint 1')
##     system ('sleep 1')
## 
##     setNodeAttributesDirect (cwm, 'lfc',  'numeric', c ('A', 'B', 'C'),
##                              lfc.timepoint.2)
##     setNodeAttributesDirect (cwm, 'pval', 'numeric', c ('A', 'B', 'C'),
##                              pval.timepoint.2)
##     redraw (cwm)
##     msg (cwm, 'timepoint 2')
##     system ('sleep 1')
## 
##     setNodeAttributesDirect (cwm, 'lfc',  'numeric', c ('A', 'B', 'C'), lfc.timepoint.3)
##     setNodeAttributesDirect (cwm, 'pval', 'numeric', c ('A', 'B', 'C'), pval.timepoint.3)
##     redraw (cwm)
##     msg (cwm, 'timepoint 3')
##     system ('sleep 1')
##     }
## 


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### code chunk number 18: deleteWindows (eval = FALSE)
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##   cy <- CytoscapeConnection ()
##   window.names <- c ('vignette', 'vignette.setNodePosition', 'movie')
##   for (window.name in window.names)
##     if (window.name %in% as.character (getWindowList (cy)))
##       deleteWindow (cy, window.name)
##