arc-class: An object to store arc information.
In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram
Description
An object to store arc information.
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.classA character string. Information extracted from element "arc"
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).
global.parameters.listA 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.
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 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
chemokine/OmicsSBGN documentation built on June 27, 2019, 7:52 p.m.
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Description
An object to store arc information.
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.classA character string. Information extracted from element "arc"
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).
global.parameters.listA 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.
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 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
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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