spline.arc-class: An object to store information of spline arcs
In SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Description
An object to store information of spline 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 they are rendered. See the "arcs.user" argument in renderSbgn.
Slots
target,source,id,arc.classA character string. Information extracted from element 'arc.spline'.
start.x,start.y,end.x,end.yNumeric. Information extracted from elements 'start', 'end' or 'next'.
stroke.opacityNumeric. Controls the line of an arc (not tip of arc).
componentsA 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.
parameters.listA 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 spline.arc objects in the output SBGNview object will be an empty list. You can add named elements to this slot to customize each individual spline.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).
edgeA 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 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.
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Description
An object to store information of spline 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 they are rendered. See the "arcs.user" argument in renderSbgn.
Slots
target,source,id,arc.classA character string. Information extracted from element 'arc.spline'.
start.x,start.y,end.x,end.yNumeric. Information extracted from elements 'start', 'end' or 'next'.
stroke.opacityNumeric. Controls the line of an arc (not tip of arc).
componentsA 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.
parameters.listA list. The parameters.list slot is a copy of the global.parameters.list. The global.parameters.list contains the '...' parameters passed into
SBGNviewwhich will be used byrenderSbgn. By default this slot for all spline.arc objects in the output SBGNview object will be an empty list. You can add named elements to this slot to customize each individual spline.arc. For information about which parameters can be set in the parameters.list slot, see the arguments inrenderSbgn. A customized list of arc objects can be passed as input into SBGNview function using the ‘arcs.user’ argument (seerenderSbgnfor more information).edgeA 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 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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