spline.arc-class {SBGNview} | R Documentation

## An object to store information for spline formated arcs.

### Description

An object to store information for spline formated arcs.

### Details

Arc information comes from two sources:1. SBGN-ML file's "arc" element ("source", "target", coordinates etc.). 2. Parameters specified when running `SBGNview`. User can modify arc objects to change the way how it is rendered. Some of the slots/parameters in arc object controls similar graph features such as text font, line width/color etc.

The priority is determined in the following sequence:

1. arc@edge

2. Parameters in slot "arc@global.parameters.list"

3. Slots in arc object: stroke.opacity, fill.color etc.

### Slots

`target,source,id,arc.class`

  A character string. Information extracted from element "arc.spline"

`start.x,start.y,end.x,end.y`

  Numeric. Information extracted from elements "start", "end" or "next"

`stroke.opacity`

  Numeric. Controls the line of an arc (not tip of arc).

`components`

  A list of "arc" and "spline" objects. A spline arc is represented by several components: 1. The two ends of the arc are represented by straight line "arc" objects. 2. splines connecting the ends are represented by "spline" objects.

`global.parameters.list`

  A list. This is a copy of parameters in '...' of SBGNview. It can affect glyph behavior if the element has a corresponding feature of the arc. For example "edge.tip.size" affects the arc but "compartment.opacity" doesn't. See details for more information. This will be improved in future versions to remove unrelated parameters.

`edge`

  A list. An arc in SBGN map normally consists of a line and a tip shape at the end of the line. This list holds variables that controls arc properties. Available elements can be accessed as follow:

  The following three paremeters control the line.
  arc@edge$line.stroke.color
  arc@edge$line.stroke.opacity
  arc@edge$line.width

  The following five paremeters control the tip.
  arc@edge$tip.stroke.opacity
  arc@edge$tip.stroke.color
  arc@edge$tip.stroke.width
  arc@edge$tip.fill.color
  arc@edge$tip.fill.opacity

[Package SBGNview version 1.1.0 Index]