RCytoscape (version 1.22.0)

setNodeColorRule: setNodeColorRule

Description

Specify how data attributes -- for the specified named attribute -- are mapped to node color. There are two modes: 'interpolate' and 'lookup'. In the former, you specify data values ('control points') and colors; when a node's corresponding data attribute value is exactly that of a control point, the specified color is used. If the node's data attribute falls between control points, then the color is interpolated. Note! In the 'interpolate' mode, you almost always want to provide two additional colors: one for node data values falling below the minimum control point, one for node data values falling above the maximum control point. If you provide an equal number of colors and control.points, the default.color is used to paint nodes above and below the specified range. A useful data exploration strategy would be to use default.color <- '#000000' causing all extreme nodes to be painted black.

The 'lookup' mode provides no interpoloation, and is useful when you have a node attribute with a finite set of discrete values, each of which you you want to display in a specific color. For example: render all receptors in yellow, all transcription factors in blue, and all kinases in dark red.

Usage

setNodeColorRule(obj, node.attribute.name, control.points, colors, mode, default.color='#FFFFFF')

Arguments

obj

a CytoscapeWindowClass object.

node.attribute.name

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

control.points

a list of values. In the interpolate mode, a typical choice is the minimum, the maximum, some sensible midpoint.

colors

a list of colors, either two more than the number of control points (if mode='interpolate'), in which case the first color is used for all attributes values below the minimum, and the last color is used for those above the maximum. Or, if mode='lookup', the same number of colors as control.points are expected. Colors are expressed as quoted hexadecimal RGB strings, e.g., '#FF0000' or '#FA8800'

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.color

'#000000' (black) by default, to catch your eye. Used primarily in mode=='lookup' and in mode='interpolate' if you fail to specify 'above' and 'below' values.

Value

None.

See Also

setNodeShapeRule

Examples

  cw <- new.CytoscapeWindow ('setNodeColorRule.test', graph=makeSimpleGraph())
  control.points <- c (-3.0, 0.0, 3.0)   # typical range of log-fold-change ratio values
    # paint negative values shades of green, positive values shades of
    # red, out-of-range low values are dark green; out-of-range high
    # values are dark red
  node.colors <- c ("#00AA00", "#00FF00", "#FFFFFF", "#FF0000", "#AA0000")
  setNodeColorRule (cw, node.attribute.name='lfc', control.points, node.colors, mode='interpolate')
  displayGraph (cw)
  redraw (cw)
  data.values <- c ("kinase", "transcription factor", "glycoprotein")
  node.colors <- c ("#0000AA", "#FFFF00", "#0000AA") 
  setNodeColorRule (cw, node.attribute.name='type', data.values,   node.colors, mode='lookup', default.color='#AA0000')