inst/doc/RCy3.R

### R code from vignette source 'RCy3.Rnw'

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### code chunk number 1: g0 (eval = FALSE)
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##     library(RCy3)
##     g <- new ('graphNEL', edgemode='directed')
##     g <- graph::addNode ('A', g)
##     g <- graph::addNode ('B', g)
##     g <- graph::addNode ('C', g)
##     cw <- CytoscapeWindow ('vignette', graph=g, overwrite=TRUE)
##     displayGraph (cw)
## 


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


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### code chunk number 3: g2 (eval = FALSE)
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##     g <- [email protected]   # 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
## 


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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)


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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', 'RECTANGLE')
##     setNodeShapeRule (cw, node.attribute.name='moleculeType',
##                       attribute.values, node.shapes)


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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 <- [email protected]
##     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'
##     [email protected] <- g
##     displayGraph (cw)
##     
##     line.styles = c ('DOT', 'SOLID', 'SINEWAVE')
##     edgeType.values = c ('phosphorylates', 'promotes',
##                          'indirectly activates')
##     setEdgeLineStyleRule (cw, 'edgeType', edgeType.values,
##                           line.styles)
##     
##     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: 8a (eval = FALSE)
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##     selectNodes (cw, 'B')


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### code chunk number 12: g8 (eval = FALSE)
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##     getSelectedNodes (cw)


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### code chunk number 13: g9 (eval = FALSE)
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##     selectFirstNeighborsOfSelectedNodes (cw)


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### code chunk number 14: g10 (eval = FALSE)
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##     nodes <- getSelectedNodes (cw)


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### code chunk number 15: position (eval = FALSE)
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##     cwe <- CytoscapeWindow ('vignette.setNodePosition',
##                             graph=RCy3::makeSimpleGraph (), overwrite=TRUE)
##     displayGraph (cwe)
##     layoutNetwork (cwe, 'grid')
##     
##     center.x <- 200
##     center.y <- 200
##     radius <- 200
##     # sweep through full revoltion 3 times, 5 degrees at a time
##     angles <- seq (0, 360, 90)
##     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)
##     }
##     # RCy3 will not create windows with duplicate names, so clear the decks for a subsequent possible run


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### code chunk number 16: moviePrep (eval = FALSE)
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##     g <- RCy3::makeSimpleGraph ()
##     g <- initNodeAttribute (g, 'pval', 'numeric', 1.0)
##     
##     cwm <- CytoscapeWindow ('movie', graph=g, overwrite=TRUE)
##     displayGraph (cwm)
##     layoutNetwork (cwm, 'grid')


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### code chunk number 17: 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 18: 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)
##         system ('sleep 0.3')
##         
##         setNodeAttributesDirect (cwm, 'lfc',  'numeric', c ('A', 'B', 'C'),
##                                  lfc.timepoint.2)
##         setNodeAttributesDirect (cwm, 'pval', 'numeric', c ('A', 'B', 'C'),
##                                  pval.timepoint.2)
##         system ('sleep 0.3')
##         
##         setNodeAttributesDirect (cwm, 'lfc',  'numeric', c ('A', 'B', 'C'),
##                                  lfc.timepoint.3)
##         setNodeAttributesDirect (cwm, 'pval', 'numeric', c ('A', 'B', 'C'),
##                                  pval.timepoint.3)
##         system ('sleep 0.3')
##     }
## 


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### code chunk number 19: 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)    
##         }
##     }

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RCy3 documentation built on Nov. 17, 2017, 1:22 p.m.