arc-class: An object to store arc information

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

Description

An object to store arc information

Details

Information in an 'arc' object comes from two sources: 1. SBGN-ML file's 'arc' element ('source', 'target', coordinates etc.). 2. Parameters specified when running function SBGNview. User can modify arc objects to change the way how they are rendered. See the "arcs.user" argument in renderSbgn.

Slots

target,source,id,arc.class

A character string. Information extracted from element 'arc'.

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 the arc).

parameters.list

A list. The parameters.list slot is a copy of the global.parameters.list. The global.parameters.list contains the '...' parameters passed into SBGNview which will be used by renderSbgn. By default this slot for all arc objects in the output SBGNview object will be an empty list. You can add named elements to this slot to customize each individual arc. For information about which parameters can be set in the parameters.list slot, see the arguments in renderSbgn. A customized list of arc objects can be passed as input into SBGNview function using the ‘arcs.user’ argument (see renderSbgn for more information).

edge

A list. An arc in SBGN map normally consists of a line and a tip at the end of the line. This list holds variables that controls arc properties. Available elements can be accessed as follow: The following three parameters control the line:
arc@edge$line.stroke.color
arc@edge$line.stroke.opacity
arc@edge$line.width

The following five parameters 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

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