setEdgeColorRule: setEdgeColorRule

In tmuetze/Bioconductor_RCy3_the_new_RCytoscape: Display and manipulate graphs in Cytoscape >= 3.3.0

Description

Specify how data attributes – for the specified named attribute – is mapped to edge color.

Usage

setEdgeColorRule(obj, edge.attribute.name, control.points, colors, mode,
                 default.color='#FFFFFF', vizmap.style.name = 'default')

Arguments

obj	a CytoscapeWindowClass object.
edge.attribute.name	the edge attribute whose values will, when thiS rule is applied, determine the color of each edge.
control.points	a list of values, either numeric (for interpolate mode) or character strings (for 'lookup' mode).
colors	a list of colors, expressed as hexadecimal RGB, like this: '#FF0000' or '#FA8800'
mode	either 'interpolate' or 'lookup'.
default.color	a String object, expressed in hexadecimal RGB in this format: "#RRGGBB"
vizmap.style.name	visual style name, defaults to the style 'default'.

Value

None.

Author(s)

Tanja Muetze, Georgi Kolishovski, Paul Shannon

See Also

setNodeShapeRule (detailed example) setEdgeLineStyleRule

Examples

  ## Not run: 
  # first, delete existing windows to save memory:
  deleteAllWindows(CytoscapeConnection())

  cw <- CytoscapeWindow ('setEdgeColorRule.test', graph=makeSimpleGraph())
  displayGraph (cw)
  layoutNetwork (cw, 'force-directed')
  
  edgeType.values = c ('phosphorylates', 'synthetic lethal', 'undefined')
  colors = c ('#FF0000', '#FFFF00', '#00FF00')
  setEdgeColorRule (cw, 'edgeType', edgeType.values, colors, mode='lookup')

  score.values = c (-15, 0, 40);
  colors = c ('#00FF00', '#FFFFFF', '#FF0000')
  setEdgeColorRule (cw, 'score',  score.values, colors, mode='interpolate')
    # now swap the colors around
  colors = c ('#FF0000', '#FFFFFF', '#00FF00')
  setEdgeColorRule (cw, 'score',  score.values, colors, mode='interpolate')

  # redraw (cw) --> not required anymore

## End(Not run)

tmuetze/Bioconductor_RCy3_the_new_RCytoscape documentation built on May 31, 2019, 4:39 p.m.