### R code from vignette source 'vignettes/RCytoscape/inst/doc/RCytoscape.Rnw' ################################################### ### code chunk number 1: g0 ################################################### 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) ################################################### ### code chunk number 2: g1 ################################################### layoutNetwork (cw, layout.name='grid') redraw (cw) ################################################### ### code chunk number 3: g2 ################################################### 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) ################################################### ### code chunk number 4: defaults ################################################### setDefaultNodeShape (cw, 'octagon') setDefaultNodeColor (cw, '#AAFF88') setDefaultNodeSize (cw, 80) setDefaultNodeFontSize (cw, 40) redraw (cw) ################################################### ### code chunk number 5: g3 ################################################### 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) ################################################### ### code chunk number 6: g4 ################################################### setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0), c ('#00AA00', '#00FF00', '#FFFFFF', '#FF0000', '#AA0000'), mode='interpolate') ################################################### ### code chunk number 7: g41 ################################################### setNodeColorRule (cw, 'lfc', c (-3.0, 0.0, 3.0), c ('#00FF00', '#FFFFFF', '#FF0000'), mode='interpolate') ################################################### ### code chunk number 8: g5 ################################################### 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 ################################################### 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) ################################################### ### code chunk number 10: g7 ################################################### hidePanel (cw, 'Data Panel') floatPanel (cw, 'D') dockPanel (cw, 'd') hidePanel (cw, 'Control Panel') floatPanel (cw, 'control') dockPanel (cw, 'c') ################################################### ### code chunk number 11: g8 ################################################### getSelectedNodes (cw) ################################################### ### code chunk number 12: g9 ################################################### selectFirstNeighborsOfSelectedNodes (cw) ################################################### ### code chunk number 13: g10 ################################################### nodes <- getSelectedNodes (cw) ################################################### ### code chunk number 14: position ################################################### 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 ################################################### ### code chunk number 15: moviePrep ################################################### g <- RCytoscape::makeSimpleGraph () g <- initNodeAttribute (g, 'pval', 'numeric', 1.0) cwm <- new.CytoscapeWindow ('movie', graph =g) displayGraph (cwm) layoutNetwork (cwm, 'jgraph-spring') redraw (cwm) ################################################### ### code chunk number 16: movieRules ################################################### 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 17: animate ################################################### 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') } ################################################### ### code chunk number 18: deleteWindows ################################################### 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)