highlight.nodes: Highlight input nodes

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

Description

Change node properties such as border color and width to highlight a list of input nodes. This function should be used as the second argument to function +.SBGNview.

Usage

highlight.nodes(node.set = "all", node.set.id.type = "CompoundName",
  glyphs.id.type = "pathwayCommons", cpd.or.gene = "compound",
  stroke.color = "black", stroke.width = 10, stroke.opacity = 1,
  show.glyph.id = FALSE, select.glyph.class = c(), label.x.shift = 0,
  label.y.shift = 0, label.color = "black", label.font.size = NULL,
  label.spliting.string = NULL, labels = NULL)

Arguments

node.set	A vector of character strings. Input node set that need to be highlighted. It can be any ID types supported by SBGNview.
node.set.id.type	A character string. ID type of input nodes.
glyphs.id.type	A character string. ID type of nodes in SBGN-ML file, which is used as node IDs in the SBGNview object returned by the SBGNview() function.
cpd.or.gene	A character string. One of "gene" or "compound". Currently highlight.node() only supports highlighting macromolecule and simple chemical nodes. This parameter is used to find the ID mapping between input node set IDs and glyph IDs.
stroke.color	A character string. The vorder color of highlighted nodes.
stroke.width	A character string. The border width of highlighted nodes.
stroke.opacity	Numeric
show.glyph.id	Logic
select.glyph.class	Character
label.x.shift	Numeric
label.y.shift	Numeric
label.color	Character
label.font.size	Numeric
label.spliting.string	Character
labels	Character

Value

A SBGNview obj

Examples

 data(SBGNview.obj)
## Not run: 
data("SBGNview.obj" )
obj.new = SBGNview.obj + 
       highlight.nodes(node.set = c("tyrosine", "(+-)-epinephrine"),
                      stroke.width = 4, stroke.color = "green") 
 
## End(Not run)

chemokine/OmicsSBGN documentation built on June 27, 2019, 7:52 p.m.