setNodeOpacityRule: setNodeOpacityRule

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 – are mapped to node opacity. There are two modes: 'interpolate' and 'lookup'. In the former, you specify data values ('control points') and opacitys; when a node's corresponding data attribute value is exactly that of a control point, the specified opacity is used. If the node's data attribute falls between control points, then the opacity is interpolated. 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 opacity. For example: render all receptors with full brightness, all transcription factors faded by 50 and all kinases nearly invisible.

Usage

setNodeOpacityRule(obj, node.attribute.name, control.points, opacities, mode,
                   aspect='all', vizmap.style.name = 'default')

Arguments

obj	a CytoscapeWindowClass object.
node.attribute.name	the node attribute whose values will determine the opacity of each node when this rule is applied.
control.points	a list of values. In interpolate mode, a typical choice is the minimum, the maximum and some sensible midpoint.
opacities	a list of opacities, either two more than the number of control points (if mode='interpolate'), in which case the first opacity is used for all attributes values below the minimum, and the last opacity is used for those above the maximum. Or, if mode='lookup', the same number of opacities as control.points are expected. Opacities are expressed as integers in the range 0:255, from invisible to fully bright rendering.
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 opacitys: adding a 'below' and an 'above' opacity. In lookup mode, specify exactly as many control.points as opacities. If data attribute values are found on the nodes which do not appear in your list, they will be displayed in the default opacity.
aspect	a character string, with one or more of these values: 'border', 'label', 'fill', 'all'

. The first three aspects describe elements of the displayed node: its border, its text label, and its body (or 'fill'). 'all' implies that all elements (border, label and fill) will be operated upon, equally, by this rule. If you want, for instance, the node label (its displayed name) to be visible even if the border and fill are dim, then use 'border, fill' as the aspect.

Value

None.

Author(s)

Tanja Muetze, Georgi Kolishovski, Paul Shannon

See Also

setNodeColorRule, setNodeOpacityDirect

Examples

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

  cw <- CytoscapeWindow ('setNodeOpacityRule.test', graph=makeSimpleGraph())
  displayGraph (cw)
  layoutNetwork (cw, 'force-directed')
  control.points <- c(-3.0, 0.0, 3.0)   # typical range of log-fold-change ratio values
  opacities <- c(128, 80, 255)  
  setNodeOpacityRule (cw, node.attribute.name='lfc', control.points, opacities, mode='interpolate', aspect='all')
    # now restore full opacities
  gene.types <- c("kinase", "transcription factor", "glycoprotein")
  setNodeOpacityRule (cw, 'type', gene.types, c (255, 255, 255),  mode='lookup', aspect='all');
    # leaving node labels fully opaque -- fully visible -- change border and fill opacity
  opacities <- c(10, 80, 255)
  setNodeOpacityRule (cw, node.attribute.name='type', gene.types, opacities, mode='lookup', aspect='border,fill')

## End(Not run)

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