### R code from vignette source 'RCy3.Rnw'
###################################################
### code chunk number 1: g0 (eval = FALSE)
###################################################
## 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)
##
###################################################
### code chunk number 2: g1 (eval = FALSE)
###################################################
## layoutNetwork (cw, layout.name='grid')
##
###################################################
### code chunk number 3: g2 (eval = FALSE)
###################################################
## 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
##
###################################################
### code chunk number 4: defaults (eval = FALSE)
###################################################
## setDefaultNodeShape (cw, 'OCTAGON')
## setDefaultNodeColor (cw, '#AAFF88')
## setDefaultNodeSize (cw, 80)
## setDefaultNodeFontSize (cw, 40)
###################################################
### code chunk number 5: g3 (eval = FALSE)
###################################################
## 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)
###################################################
### code chunk number 6: g4 (eval = FALSE)
###################################################
## setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0),
## c ('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000'),
## mode='interpolate')
###################################################
### code chunk number 7: g41 (eval = FALSE)
###################################################
## setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0),
## c ('#00FF00', '#FFFFFF', '#FF0000'),
## mode='interpolate')
###################################################
### code chunk number 8: g5 (eval = FALSE)
###################################################
## 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')
##
###################################################
### code chunk number 9: g6 (eval = FALSE)
###################################################
## 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)
##
## arrow.styles = c ('Arrow', 'Delta', 'Circle')
## setEdgeTargetArrowRule (cw, 'edgeType', edgeType.values,
## arrow.styles)
###################################################
### code chunk number 10: g7 (eval = FALSE)
###################################################
## hidePanel (cw, 'Data Panel')
## floatPanel (cw, 'D')
## dockPanel (cw, 'd')
## hidePanel (cw, 'Control Panel')
## floatPanel (cw, 'control')
## dockPanel (cw, 'c')
###################################################
### code chunk number 11: 8a (eval = FALSE)
###################################################
## selectNodes (cw, 'B')
###################################################
### code chunk number 12: g8 (eval = FALSE)
###################################################
## getSelectedNodes (cw)
###################################################
### code chunk number 13: g9 (eval = FALSE)
###################################################
## selectFirstNeighborsOfSelectedNodes (cw)
###################################################
### code chunk number 14: g10 (eval = FALSE)
###################################################
## nodes <- getSelectedNodes (cw)
###################################################
### code chunk number 15: position (eval = FALSE)
###################################################
## 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
###################################################
### code chunk number 16: moviePrep (eval = FALSE)
###################################################
## g <- RCy3::makeSimpleGraph ()
## g <- initNodeAttribute (g, 'pval', 'numeric', 1.0)
##
## cwm <- CytoscapeWindow ('movie', graph=g, overwrite=TRUE)
## displayGraph (cwm)
## layoutNetwork (cwm, 'grid')
###################################################
### code chunk number 17: movieRules (eval = FALSE)
###################################################
## 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')
###################################################
### code chunk number 18: animate (eval = FALSE)
###################################################
##
## 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')
## }
##
###################################################
### code chunk number 19: deleteWindows (eval = FALSE)
###################################################
## 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)
## }
## }