RCytoscape (version 1.22.0)

setNodeSizeRule: setNodeSizeRule

Description

Specify how data attributes how the specified node attribute values determine the node size.

Usage

setNodeSizeRule (obj, node.attribute.name, control.points, node.sizes,mode, default.size=40)

Arguments

obj

a CytoscapeWindowClass object.

node.attribute.name

the node attribute whose values will, when this rule is applied, determine the size of each node.

control.points

A list of (currently, exactly 3) values, which specify the 'control points' to control the coloring of nodes

node.sizes

The nodes sizes which correspond to the control points.

mode

'interpolate' or 'lookup'. This roughly corresponds to the visual mapping of continuously varying data (i.e., lfc or pValue), versus visual mapping of discrete data (i.e., molecule type, or phosphorylation status). With the interpolation mode, you must specify n+2 colors: adding a 'below' and an 'above' color. In lookup mode, specify exactly as many control.points as colors. If are data attribute values are found on the nodes which do not appear in your list, they will displayed in the default color.

default.size

the size of nodes not otherwise specified. Does not work in Cytoscape 2.7.

Value

None.

See Also

setNodeColorRule

Examples

  cw <- new.CytoscapeWindow ('setNodeSizeRule.test', graph=makeSimpleGraph())
  displayGraph (cw)
  layoutNetwork(cw, 'jgraph-spring')
  redraw (cw)
  control.points <- c (10, 30, 80)
  node.sizes  <- c (20, 50, 80)
  node.attribute.name <- 'count'   # previously defined, has values which  range between 2 and 100
     # remind yourself of the values of count on each of the three nodes
  print (noa (getGraph (cw), 'count'))
     #  A.A   B.B   C.C 
     #  "2"  "30" "100" 
  setNodeSizeRule (cw, node.attribute.name, control.points, node.sizes, mode='interpolate')  # a warning is issued; below and above sizes must be inferred

     # now make a new rule.  explicitly specify below and above sizes
   node.sizes    <- c (1, 20, 50, 80, 200)   # anything below 20 will have size of 1; anothing above 80 will be 200.  this should be easy to see and check
   setNodeSizeRule (cw, node.attribute.name, control.points, node.sizes, mode='interpolate')  # a warning is issued; below and above sizes must be inferred

    # now use a mode='lookup' rule.  specify a size for two of the molecule types
    # look to see that the third type, glycoprotein, gets the tiny default.size of 5

  molecule.types <- c ('kinase', 'transcription factor')
  node.sizes     <- c (60,        80)
  setNodeSizeRule (cw, 'type', molecule.types,  node.sizes, default.size= 5, mode='lookup')
  redraw (cw)