glyph-class: An object to store glyph information

In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram

Description

An object to store glyph information

Details

User can modify glyph objects to change the way how it is rendered.

Some of the slots/parameters in a glyph object control similar graph features (e.g. text font, line width/color etc). The priority is determined in the following sequence:

1. glyph@text, glyph@shape.

2. Fill color derived from omics data

3. Parameters in slot "[e-mail]"

4. Slots in glyph object: stroke.opacity, fill.color etc.

For example, if both of the following parameters are set:

1). glyph@text$font.size = 5

2). lobal.parameters.list$font.size = 10

Then the font size is set by "glyph@text$font.size = 5".

Slots

compartment

A character string. The compartment this glyph belongs to.

x,y,h,w

Numeric. The x,y location and hight, width of the glyph

id

A character string. The ID of the glyph (determined by the "id" attribute in element "glyph")

label

A character string. label of the glyph. Extracted from the element "label"

glyph.class

A character string. Class of the glyph

user.data

A numeric vector. The omics data mapped to this glyph.

stroke.width,stroke.opacity,fill.opacity

Numeric. Controls glyph border width or opacity of node fill and border.

fill.color,stroke.color

A character string. The fill color and stroke color of glyph.

label_location

A character string. One of "center" or "top". If set to "center", the glyph label text will be displayed at the center of the glyph. If set to "top", the label will be displayed at the top of the glyph.

orientation

A character string. One of "left","right","up","down". This is specific to glyphs of classes "terminal" and "tag". It will change the orientation of the node.

global.parameters.list

A list. This is a copy of parameters in '...' of function SBGNview.

shape

A list. Parameters controlling how the node is rendered. Available elements can be accessed as follow:

glyph@shape$stroke.color
-Character (e.g. "red"). The color of glyph border.

glyph@shape$stroke.opacity
-Numeric (e.g. 0.8). The opacity of glyph border. Must be between 0 and 1.

glyph@shape$stroke.width
-Numeric. The width of glyph border

glyph@shape$fill.opacity
-Numeric. The opacity of glyph fill. Must be between 0 and 1.

glyph@shape$fill.color
-Numeric. The glyph fill color. Note that this will overwrite colors generated from omics data!

text

A list. Parameters controlling how node label is rendered. Available elements can be accessed as follow:

glyph@text$y.shift
-Numeric. Move glyph label vertically by this value.

glyph@text$x.shift
-Numeric. Move glyph label horizontally by this value.

glyph@text$color
-A character string. The color of glyph label.

glyph@text$font.size
-A character string. The font size of glyph label.

chemokine/OmicsSBGN documentation built on June 27, 2019, 7:52 p.m.