setNodeSizeRule: setNodeSizeRule

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

Description

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

Usage

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

Arguments

obj	a CytoscapeWindowClass object.
node.attribute.name	the node attribute whose values will determine the size of each node.
control.points	A list of (currently, exactly 3) values, which specify the 'control points' to control the sizes 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 sizes: adding a 'below' and an 'above' size. In lookup mode, specify exactly as many control.points as sizes. If data attribute values are found on the nodes which do not appear in your list, they will displayed in the default size.
default.size	the size of nodes not otherwise specified.
vizmap.style.name	visual style name, defaults to the style 'default'.

Value

None.

Author(s)

Tanja Muetze, Georgi Kolishovski, Paul Shannon

See Also

setNodeColorRule

Examples

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

  cw <- CytoscapeWindow ('setNodeSizeRule.test', graph=makeSimpleGraph())
  displayGraph (cw)
  layoutNetwork (cw, 'grid')
  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   B   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; anything above 80 will be 200.
  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')

## End(Not run)

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