highlightNodes: Highlight input nodes

In SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

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. Run help("+.SBGNview") for more information.

Usage

highlightNodes(
  node.set = "all",
  node.set.id.type = "compound.name",
  glyphs.id.type = "pathwayCommons",
  mol.type = "cpd",
  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. Default: "all". Input molecule IDs whose nodes are to be highlighted. It can be any ID types supported by SBGNview.
node.set.id.type	A character string. Default: "compound.name". ID type of input nodes.
glyphs.id.type	A character string. Default: "pathwayCommons". ID type of nodes in SBGN-ML file.
mol.type	A character string. One of 'gene' or 'cpd' (default).
stroke.color	A character string. Default: "black". The border color of highlighted nodes.
stroke.width	Integer. Default: 10. The border stroke width of highlighted nodes.
stroke.opacity	Numeric. Default: 1. The border stroke opacity of highlighted nodes.
show.glyph.id	Logical. Default: F. If set to 'TRUE', glyph IDs are plotted instead of their labels.
select.glyph.class	Character vector. Select glyphs by class. It should be one of the values of XML attribute 'class' of a 'glyph' element. For example 'macromolecule', "simple chemical"
label.x.shift	Integer. Default: 0. Move labels horizontally.
label.y.shift	Integer. Default: 0. Move labels vertically.
label.color	A character string. Default: "black". Change label color.
label.font.size	Integer. Adjust label font size.
label.spliting.string	A character vector. When we split text into multiple lines, these characters will be used to split label (where a new line can be created). For example: label.spliting.string = c(' ','-',';','/','_').
labels	A vector of character strings. The labels to display on the nodes of input molecules. The names of this vector should be the vector of 'node.set'. The values are the new labels to display.

Value

A SBGNview obj

Examples

## Not run: 
obj.new <- SBGNview.obj + highlightNodes(node.set = c('tyrosine', '(+-)-epinephrine'),
                                         stroke.width = 4, 
                                         stroke.color = 'green') 

## End(Not run)

SBGNview documentation built on March 3, 2021, 2 a.m.