R/plot.utilities.R
In chemokine/OmicsSBGN: Overlay omics data onto SBGN pathway diagram
link.to.sbgn.start = '<a xlink:href="https://cdn.rawgit.com/sbgn/process-descriptions/b2904462d11bd8d65e9c7a1318d95d468048cb50/templates/PD_L1V1.3.svg">'
link.to.sbgn.end = '</a>'
svg.header = '<?xml version="1.0" encoding="UTF-8"?>
<svg width="%f" height="%f"
xmlns="http://www.w3.org/2000/svg" xmlns:svg="http://www.w3.org/2000/svg"
xmlns:xlink="http://www.w3.org/1999/xlink"
>
<metadata id="metadata7">image/svg+xml</metadata>
'
svg.end = '
</svg>'
###############################################
template.text = '
<text
x="%f"
y="%f"
id="%s"
style="font-size:%fpx;text-anchor:%s;font-family:Arial,Helvetica;alignment-baseline:%s;stroke.opacity:%s;dominant-baseline:%s"
fill="%s"
>
%s</text>
'
###############################################
template.path = '
<path
d="%s"
id="%s"
style="fill:%s;fill-opacity:%f;stroke-width:%f;stroke:%s;stroke-opacity:%f"
transform = "rotate(%f %f %f)"
/>
'
plot.path = function(d
,id
,fill.color
,stroke.width
,stroke.color
,angle=0
,rotate.x=0
,rotate.y=0
,fill.opacity=0.6
,stroke.opacity=1
,object){
if("shape" %in% slotNames(object) ){ # if we are ploting a glyph(glyph has slot "shape")
if(length(object@shape$fill.color)>0){
fill.color = object@shape$fill.color
}
if(length(object@shape$fill.opacity)>0){
fill.opacity = object@shape$fill.opacity
}
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(length(object@shape$stroke.opacity)>0){
stroke.opacity = object@shape$stroke.opacity
}
if(length(object@shape$stroke.color)>0){
stroke.color = object@shape$stroke.color
}
# }else{
}else if("edge" %in% slotNames(object) ){ # if we are ploting an arc
fill.color = object@edge$tip.fill.color
fill.opacity = object@edge$tip.fill.opacity
stroke.width = object@edge$tip.stroke.width
stroke.opacity = object@edge$tip.stroke.opacity
stroke.color = object@edge$tip.stroke.color
}else {
message("Plot.path function is not implemented for this object!!! \n Please make sure the object has a slot named 'shape' or 'edge'.")
print(object)
stop()
}
svg = sprintf(template.path,d,id,fill.color,fill.opacity,stroke.width,stroke.color,stroke.opacity,angle,rotate.x,rotate.y)
return(svg)
}
###############################################
template.rectangle = '
<rect
width="%f"
height="%f"
rx="%f"
ry="%f"
x="%f"
y="%f"
id="%s"
style="fill:%s;fill-opacity:%f;stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
#
plot.rectangle = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",stroke.color="black",stroke.width=1,fill.opacity=0.6,stroke.opacity=1,glyph=new("glyph")){
if(length(glyph@shape$fill.color)>0){
fill.color = glyph@shape$fill.color
}
if(length(glyph@shape$fill.opacity)>0){
fill.opacity = glyph@shape$fill.opacity
}
if(length(glyph@shape$stroke.width)>0){
stroke.width = glyph@shape$stroke.width
}
if(length(glyph@shape$stroke.opacity)>0){
stroke.opacity = glyph@shape$stroke.opacity
}
if(length(glyph@shape$stroke.color)>0){
stroke.color = glyph@shape$stroke.color
}
svg = sprintf(template.rectangle,w,h,rx,ry,x,y,id,fill.color,fill.opacity,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
###########################################################
# use path to plot a rectangle that has 1,2,3 or 4 rounded corner. Returns the content for "d" command in "path"
#the r of the rounded corners can be different(can be set using r1,r2,r3,r4: from top left corner, clockwise)
generate.d.for.partly.rounded.corner.rect = function(x,y,w,h,r1,r2,r3,r4){
start.and.upperLeft = paste("M",x,r1+y, "Q",x,y, x+r1,y,sep=" ")
top.and.upperRight = paste("L",x+w-r2,y, "Q",x+w,y, x+w,y+r2,sep=" ")
right.and.lowerRight = paste("L",x+w,y+h-r3, "Q",x+w,y+h, x+w-r3,y+h,sep=" ")
bottom.and.lowerLeft = paste("L",x+r4,y+h, "Q",x,y+h, x,y+h-r4, "Z",sep=" ")
d.content = paste(start.and.upperLeft,top.and.upperRight,right.and.lowerRight,bottom.and.lowerLeft,sep=" ")
return(d.content)
}
###############################################
template.polygon = '
<polygon
points = "%s"
id="line"
style="fill:%s; stroke:%s; stroke-opacity:%s; stroke-width:%f"
transform = "rotate(%f %f %f)"
/>
'
plot.polygon = function(object,points,fill.color,rotate.a,rotate.x,rotate.y){
if(fill.color == "black"){
fill.color = object@edge$tip.fill.color # if the edge has a filled tip(e.g. production), we can change it to user defined color. If the edge type has an empty tip, we can't change it.
}
sprintf(template.polygon,points
,fill.color
,object@edge$tip.stroke.color
,object@edge$tip.stroke.opacity
,object@edge$tip.stroke.width
,rotate.a,rotate.x,rotate.y)
}
###############################################
template.ellipse = '
<ellipse
rx="%f"
ry="%f"
cx="%f"
cy="%f"
id="%s"
style="fill:%s;fill-opacity:%f;stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
plot.ellipse = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",fill.opacity=1,stroke.color="black",stroke.width=1,stroke.opacity=1,glyph=new("glyph")){
if(length(glyph@shape$fill.color)>0){
fill.color = glyph@shape$fill.color
}
if(length(glyph@shape$fill.opacity)>0){
fill.opacity = glyph@shape$fill.opacity
}
if(length(glyph@shape$stroke.width)>0){
stroke.width = glyph@shape$stroke.width
}
if(length(glyph@shape$stroke.opacity)>0){
stroke.opacity = glyph@shape$stroke.opacity
}
if(length(glyph@shape$stroke.color)>0){
stroke.color = glyph@shape$stroke.color
}
svg = sprintf(template.ellipse,w/2,h/2,x,y,id,fill.color,fill.opacity,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
plot.ellipse.edge.tip = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",fill.opacity=1,stroke.color="black",stroke.width=1,stroke.opacity=1,object){
if(fill.color == "black"){
fill.color = object@edge$tip.fill.color # if the edge has a filled tip(e.g. production), we can change it to user defined color. If the edge type has empty tip fill color, we can't change it.
}
svg = sprintf(template.ellipse,w/2,h/2,x,y,id
,fill.color
,object@edge$tip.fill.opacity
,object@edge$tip.stroke.color
,object@edge$tip.stroke.width
,object@edge$tip.stroke.opacity
)
return(svg)
}
###############################################
template.line = '
<line
%s
id="%s"
style="stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
plot.line = function(LineCoordinates,id,stroke.color="black",stroke.opacity=1,stroke.width=1,object=NULL){
if(! is.null(object)){
stroke.color = object@edge$line.stroke.color
stroke.width = object@edge$line.width
}
# stroke.width = 2*stroke.width
svg = template.line
svg = sprintf(template.line,LineCoordinates,id,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
plot.LineWings = function(x,y,w,h,orientation,id){
leftLineCoordinates = paste("x1=",x-w," y1=",y," x2=",x-w/2," y2=",y,"",sep='"')
rightLineCoordinates = paste("x1=",x+w/2," y1=",y," x2=",x+w," y2=",y,"",sep='"')
if (orientation == "vertical"){
leftLineCoordinates = paste("x1=",x," y1=",y-h," x2=",x," y2=",y-h/2,"",sep='"')
rightLineCoordinates = paste("x1=",x," y1=",y+h/2," x2=",x," y2=",y+h,"",sep='"')
}
svg.line.l = plot.line(leftLineCoordinates,id)
svg.line.r = plot.line(rightLineCoordinates,id)
svg = paste(svg.line.l,svg.line.r,sep="\n")
return(svg)
}
##########################################################
#' An object to store glyph information
#' @slot compartment
#'
#' A character string. The compartment this glyph belongs to.
#'
#' @slot x,y,h,w
#'
#' Numeric. The x,y location and hight, width of the glyph
#'
#' @slot id
#'
#' A character string. The ID of the glyph (determined by the "id" attribute in element "glyph")
#'
#' @slot label
#'
#' A character string. label of the glyph. Extracted from the element "label"
#'
#' @slot glyph.class
#'
#' A character string. Class of the glyph
#'
#' @slot user.data
#'
#' A numeric vector. The omics data mapped to this glyph.
#'
#' @slot stroke.width,stroke.opacity,fill.opacity
#'
#' Numeric. Controls glyph border width or opacity of node fill and border.
#'
#' @slot fill.color,stroke.color
#'
#' A character string. The fill color and stroke color of glyph.
#'
#' @slot 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.
#'
#' @slot 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.
#'
#' @slot global.parameters.list
#'
#' A list. This is a copy of parameters in '...' of function \code{\link{SBGNview}}.
#'
#' @slot shape
#'
#' A list. Parameters controlling how the node is rendered. Available elements can be accessed as follow:
#'
#'
#' glyph@@shape$stroke.color\cr
#' -Character (e.g. "red"). The color of glyph border. \cr
#'
#' glyph@@shape$stroke.opacity\cr
#' -Numeric (e.g. 0.8). The opacity of glyph border. Must be between 0 and 1.\cr
#'
#' glyph@@shape$stroke.width\cr
#' -Numeric. The width of glyph border\cr
#'
#' glyph@@shape$fill.opacity\cr
#' -Numeric. The opacity of glyph fill. Must be between 0 and 1.\cr
#'
#' glyph@@shape$fill.color\cr
#' -Numeric. The glyph fill color. Note that this will overwrite colors generated from omics data!\cr
#'
#' @slot text
#'
#' A list. Parameters controlling how node label is rendered. Available elements can be accessed as follow:
#'
#' glyph@@text$y.shift\cr
#' -Numeric. Move glyph label vertically by this value.\cr
#'
#' glyph@@text$x.shift\cr
#' -Numeric. Move glyph label horizontally by this value.\cr
#'
#' glyph@@text$color\cr
#' -A character string. The color of glyph label.\cr
#'
#' glyph@@text$font.size\cr
#' -A character string. The font size of glyph label.\cr
#'
#' @details User can modify glyph objects to change the way how it is rendered.
#'
#' Some of the slots/parameters in a glyph object control similar graph features (e.g. text font, line width/color etc). The priority is determined in the following sequence:
#'
#'
#' 1. glyph@@text, glyph@@shape.
#'
#' 2. Fill color derived from omics data
#'
#' 3. Parameters in slot "glyph@@global.parameters.list"
#'
#' 4. Slots in glyph object: stroke.opacity, fill.color etc.
#'
#' For example, if both of the following parameters are set:
#'
#' 1). glyph@@text$font.size = 5
#'
#' 2). lobal.parameters.list$font.size = 10
#'
#' Then the font size is set by "glyph@@text$font.size = 5".
#'
setClass(
"glyph"
,representation (compartment = "character", x="numeric",y="numeric",h="numeric",w="numeric",id = "character",label="character",label.margin = "numeric" ,label_location="character",svg.port = "character" ,orientation="character",user.data = "vector",clone = "list", fill.color = "character", stroke.width = "numeric",stroke.color="character",stroke.opacity="numeric",fill.opacity="numeric",global.parameters.list="list",glyph.class="character",text="list",shape="list")
)
setClass(
"port"
,contains="glyph"
# ,representation (x="numeric",y="numeric",id = "character")
)
##########################################################
#' An object to store arc information.
#' @slot target,source,id,arc.class
#' A character string. Information extracted from element "arc"
#' @slot start.x,start.y,end.x,end.y
#' Numeric. Information extracted from elements "start", "end" or "next"
#' @slot stroke.opacity
#' Numeric. Controls the line of an arc (not tip of arc).
#' @slot 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.
#'
#' @slot 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.\cr
#' arc@@edge$line.stroke.color\cr
#' arc@@edge$line.stroke.opacity\cr
#' arc@@edge$line.width\cr
#'
#'
#' The following five paremeters control the tip.\cr
#' arc@@edge$tip.stroke.opacity\cr
#' arc@@edge$tip.stroke.color\cr
#' arc@@edge$tip.stroke.width\cr
#' arc@@edge$tip.fill.color\cr
#' arc@@edge$tip.fill.opacity\cr
#'
#' @details Arc information comes from two sources:1. SBGN-ML file's "arc" element ("source", "target", coordinates etc.). 2. Parameters specified when running \code{\link{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.
#'
#'
setClass(
"arc"
,representation (target="character",source="character",id="character",arc.class="character",start.y="numeric",start.x="numeric",end.y="numeric",end.x="numeric",stroke.opacity = "numeric",global.parameters.list="list",edge = "list")
)
setClass(
"spline"
,representation (id="character",spline.coords = "vector",edge="list",global.parameters.list="list")
)
##########################################################
#' An object to store information for spline formated arcs.
#' @slot target,source,id,arc.class
#' A character string. Information extracted from element "arc.spline"
#' @slot start.x,start.y,end.x,end.y
#' Numeric. Information extracted from elements "start", "end" or "next"
#' @slot stroke.opacity
#' Numeric. Controls the line of an arc (not tip of arc).
#' @slot 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.
#' @slot 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.
#'
#' @slot 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.\cr
#' arc@@edge$line.stroke.color\cr
#' arc@@edge$line.stroke.opacity\cr
#' arc@@edge$line.width\cr
#'
#'
#' The following five paremeters control the tip.\cr
#' arc@@edge$tip.stroke.opacity\cr
#' arc@@edge$tip.stroke.color\cr
#' arc@@edge$tip.stroke.width\cr
#' arc@@edge$tip.fill.color\cr
#' arc@@edge$tip.fill.opacity\cr
#'
#' @details Arc information comes from two sources:1. SBGN-ML file's "arc" element ("source", "target", coordinates etc.). 2. Parameters specified when running \code{\link{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.
#'
#'
setClass(
"spline.arc"
,representation (id="character", source = "character",target="character",arc.class="character",edge="list",components="list",global.parameters.list="list")
)
setGeneric(
"plot.glyph"
, function(object){
standardGeneric("plot.glyph")
}
)
setGeneric(
"plot.arc"
, function(object){
standardGeneric("plot.arc")
}
)
###############################################
setClass("macromolecule.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("macromolecule.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.color=1
if(length(object@stroke.color)>0){
stroke.color = object@stroke.color
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
fill.opacity=1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,sep="\n")
svg=""
if(is.na(user.data[1])){
}
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@fill.opacity = 1
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.1
glyph.data.i@stroke.opacity = 0.5
glyph.data.i@stroke.color = "black"
glyph.data.i@shape$stroke.opacity = 0.5 # if we are plotting data shape, don't plot the border
glyph.data.i@shape$stroke.width = 0.1 # if we are plotting data shape, don't plot the border
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity = 0
stroke.opacity = 1
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity = stroke.opacity,fill.opacity = fill.opacity)
svg = paste(svg,svg.rect,svg.text,sep="\n")
return(svg)
}
)
###############################################
setClass("entity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("entity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
stroke.width=1
stroke.opacity=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
rx = min(h,w)/10
ry = min(h,w)/10
# svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,stroke.opacity = stroke.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,stroke.opacity = stroke.opacity)
svg = paste(svg,svg.rect,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("compartment.sbgn",contains="glyph",representation(max.x="numeric"))
setMethod(
"plot.glyph"
,signature("compartment.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location = "top"
# ry = rx
max.x = object@max.x
rx = ry = 20
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = object@shape$stroke.width,fill.opacity = global.parameters.list$compartment.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location,max.x=max.x)
svg = paste(svg.rect,svg.text,sep="\n")
# svg = ""
return(svg)
}
)
############################################
setClass("complex.sbgn",contains="glyph",representation(if.complex.empty="logical"))
setMethod(
"plot.glyph"
,signature("complex.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y -h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
if ( length(nchar(object@label_location))==0 ){
label.location = "top"
}else if( object@label_location != "center" ){
label.location = "top"
}else{
label.location = object@label_location
}
if.complex.empty= FALSE
if(length(object@if.complex.empty) !=0){
if.complex.empty = object@if.complex.empty
}
if(if.complex.empty){
label.location = "center"
}
rx = ry = 8
corner.r = rx
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
d1 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
# label="complex" # try not to show complex name
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path1,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("complex_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("complex_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y -h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
corner.r = global.parameters.list$edge.tip.size*3
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
d1 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",fill.opacity = 1)
x = x+global.parameters.list$edge.tip.size*3/2; y = y+global.parameters.list$edge.tip.size*3/2
d2 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path2,svg.path1,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("state_variable.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("state_variable.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = gsub(" ","",object@label)
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = global.parameters.list$auxiliary.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("unspecified_entity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("unspecified_entity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
# if(length(object@fill.opacity)>0){
# fill.opacity = object@fill.opacity
# }
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
# svg = paste(svg.ellipse,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity = 0)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
svg.path.1 = plot.path(object=object,d=d.1,id=id,fill.color=fill.color,stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object,d=d.2,id=id,fill.color="white",stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
}
fill.opacity = 0
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("unit_of_information.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("unit_of_information.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
object@label = gsub(" ","",object@label)
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width,fill.opacity = global.parameters.list$auxiliary.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("stoichiometry.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("stoichiometry.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("cardinality.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("cardinality.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("biological_activity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("biological_activity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("submap.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("submap.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "top"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg = svg.rect
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,svg.wings,sep="\n")
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = ""
}else{
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg = svg.rect
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("uncertain_process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("uncertain_process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = "?"
}else{
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("and.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("and.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "AND"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("or.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("or.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "OR"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("not.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("not.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "NOT"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("tau.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("tau.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "t"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("macromolecule_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("macromolecule_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity=1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
object@label = object@label
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.rect.up = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width,fill.opacity = 1)
svg.rect.down = plot.rectangle(glyph=object,x=x-w/2+global.parameters.list$multimer.margin,y=y-h/2+global.parameters.list$multimer.margin,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect.down,svg.rect.up,sep="\n")
svg = paste(svg.rect.down,sep="\n")
# svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = new("macromolecule.sbgn")
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@compartment = object@compartment
glyph.data.i@y=y
glyph.data.i@h=h
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@id=paste(id,"user.data",i,sep="_")
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
glyph.data.i@fill.opacity = 1
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
svg.rect.up = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg = paste(svg,svg.rect.up,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("outcome.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("outcome.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
print (orientation)
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color="black",stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = svg.ellipse
return(svg)
}
)
###########################################################
setClass("simple_chemical_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("simple_chemical_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
w=h
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label = object@label
label.location = "center"
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
# if(length(object@fill.opacity)>0){
# fill.opacity = object@fill.opacity
# }
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg.ellipse2 = plot.ellipse(glyph=object,x+5,y+5,h,w,id)
svg = paste(svg.ellipse2,sep="\n")
if(!identical(user.data[1],"no.user.data")){
# if(user.data[1] != "no.user.data"){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,fill.opacity = 1)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@fill.opacity=1
# glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
svg.path.1 = plot.path(object=object,d=d.1,id=id,fill.color=fill.color,stroke.width= 1,stroke.color = "black",fill.opacity = 1,stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object,d=d.2,id=id,fill.color="white",stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
}
fill.opacity=0
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("omitted_process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("omitted_process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = '\\\\'
}else{
object@label = object@label
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
###########################################################
setClass("simple_chemical.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("simple_chemical.sbgn")
, function(object){
w = object@w
h = object@h ;
w=h
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
stroke.color=1
if(length(object@stroke.color)>0){
stroke.color = object@stroke.color
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.ellipse,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity=0.5)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
svg.sep.data.line = ""
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
# glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
Coordinates = paste("x1=",start.x," y1=",start.y.1," x2=",start.x," y2=",start.y.2,"",sep='"')
svg.sep.data.line = paste(svg.sep.data.line
,plot.line(LineCoordinates = Coordinates,id = id,stroke.width = 0.1,stroke.opacity = 0.5),sep="\n")
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
object.data = object # if we are ploting shape for data, don't plot border
object.data@shape$stroke.opacity = 0
svg.path.1 = plot.path(object=object.data,d=d.1,id=id,fill.color=fill.color,stroke.width= 0.1,stroke.color = "black",stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object.data,d=d.2,id=id,fill.color="white",stroke.width= 0.1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
svg = paste(svg,svg.sep.data.line,sep="\n")
}
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = 0)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
###########################################################
setClass("dissociation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("dissociation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse.o = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.ellipse.i = plot.ellipse(glyph=object,x,y,h/2,w/2,id)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = paste(svg.ellipse.o,svg.ellipse.i,svg.wings,sep="\n")
return(svg)
}
)
######################################################
setClass("nucleic_acid_feature_multimer.sbgn",contains="glyph",representation(r4="numeric",r3="numeric"))
setMethod(
"plot.glyph"
,signature("nucleic_acid_feature_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
if(length(object@r4)>0){
r4 = object@r4
}
if(length(object@r3)>0){
r3 = object@r3
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
d2 = generate.d.for.partly.rounded.corner.rect(x=x-w/2+global.parameters.list$multimer.margin,y=y-h/2+global.parameters.list$multimer.margin,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",stroke.opacity = 1)
# svg = paste(svg.path2,svg.path,sep="\n")
svg = paste(svg.path2,sep="\n")
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = new("nucleic_acid_feature.sbgn")
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@y = y
glyph.data.i@h = h
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@compartment = object@compartment
glyph.data.i@id=paste(id,"user.data",i,sep="_")
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
glyph.data.i@fill.opacity = 1
if(i == 1){
glyph.data.i@r3 = 0
}else if(i==length(user.data)){
glyph.data.i@r4 = 0
}else{
glyph.data.i@r4=0
glyph.data.i@r3=0
}
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black",fill.opacity = fill.opacity,stroke.opacity = 1)
svg = paste(svg,svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("nucleic_acid_feature.sbgn",contains="glyph",representation(r4="numeric",r3="numeric"))
setMethod(
"plot.glyph"
,signature("nucleic_acid_feature.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
if(length(object@r4)>0){
r4 = object@r4
}
if(length(object@r3)>0){
r3 = object@r3
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@fill.opacity = 1
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
if(i == 1){
glyph.data.i@r3 = 0
}else if(i==length(user.data)){
glyph.data.i@r4 = 0
}else{
glyph.data.i@r4=0
glyph.data.i@r3=0
}
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color=fill.color,stroke.width=stroke.width,stroke.color = "black",stroke.opacity=stroke.opacity,fill.opacity = fill.opacity )
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg,svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("perturbation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("perturbation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x,y,x+h/3,y+h/2 ,x,y+h ,x+w,y+h ,x+w-h/3,y+h/2, x+w,y,"Z",sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("perturbing_agent.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("perturbing_agent.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x,y,x+h/3,y+h/2 ,x,y+h ,x+w,y+h ,x+w-h/3,y+h/2, x+w,y,"Z",sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
# svg.ellipse = plot.ellipse(glyph=object,180,210,5,5,id,fill.color = "red")
svg = paste(svg.path,svg.text,sep="\n")
# svg = paste(svg.path,svg.text,svg.ellipse,sep="\n")
return(svg)
}
)
######################################################
setClass("annotation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("annotation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w
y = object@y-h
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
# stroke.opacity = object@stroke.opacity
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
label.location="center"
d1 = (paste("M",x,y, x,y+h, x+w/4,y+h, x+min(h,w)/10,y+3*h/2, x+w/2,y+h, x+w,y+h, x+w,y+h/5, x+w-h/5,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=1,stroke.color = "black",stroke.opacity = stroke.opacity)
d2 = (paste("M",x+w-h/5,y+h/5, x+w,y+h/5, x+w-h/5,y ,"Z",sep=" "))
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="black",stroke.width=1,stroke.color = "black",stroke.opacity = stroke.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location,stroke.opacity = stroke.opacity)
svg = paste(svg.path1,svg.path2,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("existence.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("existence.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color = "white",stroke.width = stroke.width)
d = (paste("M",x,y-h/2,"a",h/2,h/2 ,0, 0,1 ,0,h,sep=" "))
svg.path = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black")
svg = paste(svg.ellipse,svg.path,sep="\n")
return(svg)
}
)
######################################################
setClass("clone_simple_chemical.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone_simple_chemical.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = "clone"
# label = object@label
label.location="center"
start.x=x-w/2+w/20
start.y = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
d = (paste("M",start.x,start.y,"A",w/2,h/2 ,1, 0,0 ,x+w/2-w/20,start.y,sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width= stroke.width,stroke.color = "black")
svg = svg.path
return(svg)
}
)
######################################################
setClass("clone.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = "clone"
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
d1 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y+h/2-h/5,w=w,h=h/5,r1=r1,r2=r2,r3=r3,r4=r4)
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path.bigbox = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y+h/2-h/10,h=h,w=w,id=id,label.location=label.location,color="white")
svg = paste(svg.path.bigbox,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("clone_marker.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone_marker.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=min(h,w)/10;r4=min(h,w)/10
d1 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path.bigbox = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
d2 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2+3/5*h,w=w,h=2/5*h,r1=r1,r2=r2,r3=r3,r4=r4)
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path.innerbox = plot.path(object=object,d=d2,id=id,fill.color="gray",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y-1/5*h,h=h,w=w,id=id,label.location=label.location)
white.top.line.to.cover = paste("M",x-w/2,y-h/2,x+w/2,y-h/2,sep=" ")
svg.path.topWhiteLine = plot.path(object=object,d=white.top.line.to.cover,id=id,fill.color="gray",stroke.width=5,stroke.color = "white")
svg = paste(svg.path.bigbox,svg.path.innerbox,svg.path.topWhiteLine,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("terminal.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("terminal.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
orientation = object@orientation
label.location="center"
d = (paste("M",x+h/3,y,x,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w,y+h/2, x+w-h/3,y,"Z",sep=" "))
if (orientation == "right"){
d = (paste("M",x,y ,x,y+h ,x+w-w/3,y+h ,x+w,y+h/2, x+w-w/3,y,"Z",sep=" "))
}else if (orientation == "left"){
d = (paste("M",x+w/3,y,x,y+h/2 ,x+w/3,y+h ,x+w,y+h ,x+w,y,"Z",sep=" "))
}else if (orientation == "up"){
d = (paste("M",x+w/2,y,x,y+h/3 ,x,y+h ,x+w,y+h ,x+w,y+h/3,"Z",sep=" "))
}else if (orientation == "down"){
d = (paste("M",x,y ,x,y+h-h/3, x+w/2,y+h ,x+w,y+h-h/3 ,x+w,y,"Z",sep=" "))
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("tag.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("tag.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
orientation = object@orientation
label.location="center"
d = (paste("M",x+h/3,y,x,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w,y+h/2, x+w-h/3,y,"Z",sep=" "))
if (orientation == "right"){
d = (paste("M",x,y ,x,y+h ,x+w-w/3,y+h ,x+w,y+h/2, x+w-w/3,y,"Z",sep=" "))
}else if (orientation == "left"){
d = (paste("M",x+w/3,y,x,y+h/2 ,x+w/3,y+h ,x+w,y+h ,x+w,y,"Z",sep=" "))
}else if (orientation == "up"){
d = (paste("M",x+w/2,y,x,y+h/3 ,x,y+h ,x+w,y+h ,x+w,y+h/3,"Z",sep=" "))
}else if (orientation == "down"){
d = (paste("M",x,y ,x,y+h-h/3, x+w/2,y+h ,x+w,y+h-h/3 ,x+w,y,"Z",sep=" "))
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("phenotype.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("phenotype.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x+h/3,y,x+5,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w-5,y+h/2, x+w-h/3,y,"Z",sep=" "))
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("association.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("association.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color="black",stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = paste(svg.ellipse,svg.wings,sep="\n")
return(svg)
}
)
######################################################
setClass("interaction.sbgn.arc",contains="glyph")
setMethod(
"plot.glyph"
,signature("interaction.sbgn.arc")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg = svg.ellipse
return(svg)
}
)
######################################################
setClass("interaction.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("interaction.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg.line = plot.line(Coordinates,id)
svg = svg.ellipse
return(svg)
}
)
##########################################################
setClass("delay.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("delay.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "t"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("source_and_sink.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("source_and_sink.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg.line = plot.line(Coordinates,id)
svg = paste(svg.ellipse,svg.line,sep="\n")
return(svg)
}
)
######################################################
setClass("location.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("location.sbgn")
, function(object){
w = object@w
h = object@h ;
h = w
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id)
angle = pi/6
Coordinates1 = paste("x1=",x-w/2*cos(angle)," y1=",y+h/2*sin(angle)," x2=",x+w/2*sin(angle)," y2=",y-h/2*cos(angle),"",sep='"')
svg.line1 = plot.line(Coordinates1,id)
Coordinates2 = paste("x1=",x-w/2*(cos(angle)-sin(angle))/2," y1=",y+h/2*(sin(angle)-cos(angle))/2," x2=",x+w/2*sin(pi/4)," y2=",y+h/2*cos(pi/4),"",sep='"')
svg.line2 = plot.line(Coordinates2,id)
svg = paste(svg.ellipse,svg.line1,svg.line2,sep="\n")
return(svg)
}
)
######################################################
setClass("state_variable.ER.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("state_variable.ER.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = h/2 ;r2=r1;r3=r1;r4=r1
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black",fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("variable_value.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("variable_value.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = h/2 ;r2=r1;r3=r1;r4=r1
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setMethod(
"plot.arc"
,signature("spline.arc")
, function(object){
components = object@components
svg = ""
for (i in seq_len(length.out = length(components))){
component = components[[i]]
component@edge = object@edge
component@global.parameters.list = object@global.parameters.list
if(!is(component, "spline")){
component@edge$line.stroke.opacity = 0
}
svg = paste(svg,plot.arc(component),sep="\n")
}
return(svg)
}
)
######################################################
spline.svg.template = '<path d="M%s %s C %s %s, %s %s,%s %s" stroke="%s" stroke-opacity="%s" stroke-width="%s" fill-opacity="0" fill="transparent"/>'
setMethod(
"plot.arc"
,signature("spline")
, function(object){
svg = do.call(sprintf,c(list(spline.svg.template)
,c(object@spline.coords
,object@edge$line.stroke.color
,object@edge$line.stroke.opacity
,object@edge$line.width
)
)
)
return(svg)
}
)
######################################################
setClass("absolute_stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("absolute_stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
points2 = paste(end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*6,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*6,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
svg.triangle2 = plot.polygon(object=object,points2,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
svg.triangle2= plot.polygon(object=object,points2,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,svg.triangle2,sep="\n")
return(svg)
}
)
######################################################
setClass("absolute_inhibition.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("absolute_inhibition.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
global.parameters.list = object@global.parameters.list
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
d = (paste("M",end.x-1,end.y-global.parameters.list$edge.tip.size*3/2,end.x-1,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
if (start.x<end.x){
d1 = (paste("M",end.x-global.parameters.list$edge.tip.size*3/4,end.y-global.parameters.list$edge.tip.size*3/2,end.x-global.parameters.list$edge.tip.size*3/4,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine1 = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
d1 = (paste("M",end.x+global.parameters.list$edge.tip.size*3/4,end.y-global.parameters.list$edge.tip.size*3/2,end.x+global.parameters.list$edge.tip.size*3/4,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine1 = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.endLine,svg.endLine1,sep="\n")
return(svg)
}
)
######################################################
setClass("necessary_stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("necessary_stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
end.line.length = global.parameters.list$edge.tip.size*3/2
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-end.line.length," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+end.line.length,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
d = (paste("M",end.x-global.parameters.list$edge.tip.size*4,end.y-end.line.length-global.parameters.list$edge.tip.size*3/4,end.x-global.parameters.list$edge.tip.size*4,end.y+end.line.length+global.parameters.list$edge.tip.size*3/4,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
d = (paste("M",end.x+global.parameters.list$edge.tip.size*4,end.y-end.line.length-global.parameters.list$edge.tip.size*3/4,end.x+global.parameters.list$edge.tip.size*4,end.y+end.line.length+global.parameters.list$edge.tip.size*3/4,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("equivalence_arc.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("equivalence_arc.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
######################################################
setClass("consumption.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("consumption.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
######################################################
setClass("next.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("next.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
###############################################
setClass("production.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("production.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
#############################
# if(grepl("arc_292_output_257",id)){
# cat("printing object")
# }
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
end.size = global.parameters.list$edge.tip.size*2
points = paste(end.x,",",end.y," ",end.x-end.size,",",end.y-end.size/2," ",end.x-end.size,",",end.y+end.size/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("interaction.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("interaction.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points.end = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*2,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
points.start = paste(start.x,",",start.y," ",start.x+global.parameters.list$edge.tip.size*3,",",start.y-global.parameters.list$edge.tip.size," ",start.x+global.parameters.list$edge.tip.size*2,",",start.y," ",start.x+global.parameters.list$edge.tip.size*3,",",start.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle.end = plot.polygon(object=object,points.end,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
svg.triangle.start = plot.polygon(object=object,points.start,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,start.x,start.y)
}else{
svg.triangle.end = plot.polygon(object=object,points.end,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
svg.triangle.start = plot.polygon(object=object,points.start,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,start.x,start.y)
}
svg = paste(svg.line,svg.triangle.end,svg.triangle.start,sep="\n")
return(svg)
}
)
######################################################
setClass("assignment.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("assignment.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*2,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("catalysis.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("catalysis.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
global.parameters.list = object@global.parameters.list
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
angle = atan((start.y-end.y)/(start.x-end.x))
circle.r = global.parameters.list$edge.tip.size
if (start.x<end.x){
circle.center.x = end.x - circle.r * cos(angle)
circle.center.y = end.y - circle.r * sin(angle)
}else {
circle.center.x = end.x + circle.r * cos(angle)
circle.center.y = end.y + circle.r * sin(angle)
}
svg.ellipse = plot.ellipse.edge.tip(circle.center.x,circle.center.y,circle.r*2,circle.r*2,id,fill.opacity = 0.8,object=object)
svg = paste(svg.line,svg.ellipse,sep="\n")
return(svg)
}
)
######################################################
setClass("positive_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("positive_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("negative_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("negative_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
if (start.x<end.x){
d = (paste("M",end.x-global.parameters.list$inhibition.edge.end.shift,end.y-global.parameters.list$edge.tip.size*3/2,end.x-global.parameters.list$inhibition.edge.end.shift,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
d = (paste("M",end.x+global.parameters.list$inhibition.edge.end.shift,end.y-global.parameters.list$edge.tip.size*3/2,end.x+global.parameters.list$inhibition.edge.end.shift,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("inhibition.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("inhibition.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
inhibition.edge.end.shift = global.parameters.list$inhibition.edge.end.shift
line.length = ((start.x-end.x)**2 + (start.y-end.y)**2) ** 0.5
if (start.x<end.x){
# if(grepl("arc_165_inhibitor_28",object@id)){
# print("start x smaller than end x")
# print(start.x)
# print(end.x)
# print("printed two x es")
# }
d1 = (paste("M"
# ,start.x
,end.x - line.length
,end.y
,end.x-inhibition.edge.end.shift
,end.y
,sep=" "))
svg.line = plot.path(object=object
,d=d1
,id=id
,fill.color="white"
,stroke.color = "white"
,stroke.width=1
,angle = atan((start.y-end.y)/(start.x-end.x))/pi*180
,rotate.x = end.x
,rotate.y = end.y
)
d = (paste("M"
,end.x-inhibition.edge.end.shift
# ,end.x - line.length
,end.y-global.parameters.list$edge.tip.size*3/2
,end.x-inhibition.edge.end.shift
,end.y+global.parameters.list$edge.tip.size*3/2
,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black"
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
}else{
d1 = (paste("M"
,end.x + line.length
,end.y
,end.x+inhibition.edge.end.shift
,end.y
,sep=" "))
svg.line = plot.path(object=object
,d=d1
,id=id
,fill.color="white"
,stroke.color = "white"
,stroke.width=1
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
d = (paste("M"
,end.x+inhibition.edge.end.shift
,end.y-global.parameters.list$edge.tip.size*3/2
,end.x+inhibition.edge.end.shift
,end.y+global.parameters.list$edge.tip.size*3/2
,sep=" "))
# object@edge$tip.stroke.color = "purple"
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black"
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
}
svg = paste(svg.line,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("unknown_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("unknown_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y-global.parameters.list$edge.tip.size*3/2," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y+global.parameters.list$edge.tip.size*3/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("modulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("modulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y-global.parameters.list$edge.tip.size*3/2," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y+global.parameters.list$edge.tip.size*3/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("logic_arc.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("logic_arc.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
plot.text = function(x,y,h,w,id,label.location,color="black",glyph.class="",stroke.opacity=1,max.x=0,if.generate.text.box= FALSE,global.parameters.list,glyph){
label = glyph@label
if(length(glyph@text$color)>0){
color = glyph@text$color
}
if(length(glyph@text$x.shift)>0){
x = x + glyph@text$x.shift
}
if(length(glyph@text$y.shift)>0){
y = y + glyph@text$y.shift
}
label = gsub("&","-",label)
label = gsub("<[^><]+>","",label) # when using paxtools::toSBGN to convert biopax files to SBGN files, some text in the SBGN files contain special characters :label text="<i>p</i>-chloromercuribenzoate" . the "<" and ">" will create problem in the svg file. So we need remove them.
if (length(nchar(label))==0){ # when the label is empty, don't plot it
print("no label")
return ("")
}
result.list = break.text.into.segments(w,glyph.class,global.parameters.list = global.parameters.list,max.x=max.x,glyph=glyph)
label = result.list$words.segments
font.size = result.list$font.size
global.parameters.list$complex.compartment.label.margin.use = global.parameters.list$complex.compartment.label.margin
if(glyph.class == "compartment"){
if(max.x>0){ # if the graph is large, make label larger
global.parameters.list$complex.compartment.label.margin.use = global.parameters.list$complex.compartment.label.margin.use * max(1,max.x/2000)
}
}
label.segments = strsplit(label,'\n') # the label text in some of the input sbgn files are labeled with "
" in order to be seperated to different lines
label.segments = label.segments[[1]]
align.shift = font.size/3
text.anchor = "middle"
alignment.baseline = "middle"
x.label.box = x
if (length(label.segments)>1){ # if the text is labeled to be seperated into different lines
svg = ""
n.lines = length(label.segments)
h.label.box = n.lines * font.size
for (i in seq_len(length.out = n.lines)){
label.segment = label.segments[i]
w.label.box = nchar(label.segment)*font.size
if(label.location == "center"){
alignment.baseline = "baseline"
first.segment.shift = (n.lines-1)/2*font.size
start.y = y- first.segment.shift
y.segment = start.y + (i-1)*font.size
y.segment = y.segment+align.shift
if(i == 1){
y.label.box = y.segment+align.shift
}
}else if(label.location == "top"){
y.segment = y-h/2+2 + (i-1)*font.size
if(glyph.class %in% c("complex","compartment")){
y.segment = y-h/2-n.lines*font.size + (i-1)*font.size
}
text.anchor = "middle"
alignment.baseline = "baseline"
y.segment = y.segment+align.shift*2
if(i == 1){
y.label.box = y.segment+align.shift
}
}
svg.segment = sprintf(template.text,x,y.segment,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label.segment)
svg = paste(svg,svg.segment,sep="\n")
}
} else{
w.label.box = nchar(label)*font.size *0.5
h.label.box = font.size
if(glyph.class %in% c("compartment","complex")){
align.shift = 0
}
svg = template.text
if(label.location == "center"){
alignment.baseline = "baseline"
svg = sprintf(template.text,x,y+align.shift,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
y.label.box = y+align.shift
}else if(label.location == "top"){
text.anchor = "middle"
# alignment.baseline = "hanging"
if(glyph.class %in% c("complex","compartment")){
alignment.baseline = "baseline"
svg = sprintf(template.text,x,y+align.shift-h/2-global.parameters.list$complex.compartment.label.margin.use,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
}else{
svg = sprintf(template.text,x,y+align.shift-h/2+4,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
}
y.label.box = y -h/2 -global.parameters.list$complex.compartment.label.margin.use - h.label.box/3
}
}
return(svg)
}
chemokine/OmicsSBGN documentation built on June 27, 2019, 7:52 p.m.
R Package Documentation
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link.to.sbgn.start = '<a xlink:href="https://cdn.rawgit.com/sbgn/process-descriptions/b2904462d11bd8d65e9c7a1318d95d468048cb50/templates/PD_L1V1.3.svg">'
link.to.sbgn.end = '</a>'
svg.header = '<?xml version="1.0" encoding="UTF-8"?>
<svg width="%f" height="%f"
xmlns="http://www.w3.org/2000/svg" xmlns:svg="http://www.w3.org/2000/svg"
xmlns:xlink="http://www.w3.org/1999/xlink"
>
<metadata id="metadata7">image/svg+xml</metadata>
'
svg.end = '
</svg>'
###############################################
template.text = '
<text
x="%f"
y="%f"
id="%s"
style="font-size:%fpx;text-anchor:%s;font-family:Arial,Helvetica;alignment-baseline:%s;stroke.opacity:%s;dominant-baseline:%s"
fill="%s"
>
%s</text>
'
###############################################
template.path = '
<path
d="%s"
id="%s"
style="fill:%s;fill-opacity:%f;stroke-width:%f;stroke:%s;stroke-opacity:%f"
transform = "rotate(%f %f %f)"
/>
'
plot.path = function(d
,id
,fill.color
,stroke.width
,stroke.color
,angle=0
,rotate.x=0
,rotate.y=0
,fill.opacity=0.6
,stroke.opacity=1
,object){
if("shape" %in% slotNames(object) ){ # if we are ploting a glyph(glyph has slot "shape")
if(length(object@shape$fill.color)>0){
fill.color = object@shape$fill.color
}
if(length(object@shape$fill.opacity)>0){
fill.opacity = object@shape$fill.opacity
}
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(length(object@shape$stroke.opacity)>0){
stroke.opacity = object@shape$stroke.opacity
}
if(length(object@shape$stroke.color)>0){
stroke.color = object@shape$stroke.color
}
# }else{
}else if("edge" %in% slotNames(object) ){ # if we are ploting an arc
fill.color = object@edge$tip.fill.color
fill.opacity = object@edge$tip.fill.opacity
stroke.width = object@edge$tip.stroke.width
stroke.opacity = object@edge$tip.stroke.opacity
stroke.color = object@edge$tip.stroke.color
}else {
message("Plot.path function is not implemented for this object!!! \n Please make sure the object has a slot named 'shape' or 'edge'.")
print(object)
stop()
}
svg = sprintf(template.path,d,id,fill.color,fill.opacity,stroke.width,stroke.color,stroke.opacity,angle,rotate.x,rotate.y)
return(svg)
}
###############################################
template.rectangle = '
<rect
width="%f"
height="%f"
rx="%f"
ry="%f"
x="%f"
y="%f"
id="%s"
style="fill:%s;fill-opacity:%f;stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
#
plot.rectangle = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",stroke.color="black",stroke.width=1,fill.opacity=0.6,stroke.opacity=1,glyph=new("glyph")){
if(length(glyph@shape$fill.color)>0){
fill.color = glyph@shape$fill.color
}
if(length(glyph@shape$fill.opacity)>0){
fill.opacity = glyph@shape$fill.opacity
}
if(length(glyph@shape$stroke.width)>0){
stroke.width = glyph@shape$stroke.width
}
if(length(glyph@shape$stroke.opacity)>0){
stroke.opacity = glyph@shape$stroke.opacity
}
if(length(glyph@shape$stroke.color)>0){
stroke.color = glyph@shape$stroke.color
}
svg = sprintf(template.rectangle,w,h,rx,ry,x,y,id,fill.color,fill.opacity,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
###########################################################
# use path to plot a rectangle that has 1,2,3 or 4 rounded corner. Returns the content for "d" command in "path"
#the r of the rounded corners can be different(can be set using r1,r2,r3,r4: from top left corner, clockwise)
generate.d.for.partly.rounded.corner.rect = function(x,y,w,h,r1,r2,r3,r4){
start.and.upperLeft = paste("M",x,r1+y, "Q",x,y, x+r1,y,sep=" ")
top.and.upperRight = paste("L",x+w-r2,y, "Q",x+w,y, x+w,y+r2,sep=" ")
right.and.lowerRight = paste("L",x+w,y+h-r3, "Q",x+w,y+h, x+w-r3,y+h,sep=" ")
bottom.and.lowerLeft = paste("L",x+r4,y+h, "Q",x,y+h, x,y+h-r4, "Z",sep=" ")
d.content = paste(start.and.upperLeft,top.and.upperRight,right.and.lowerRight,bottom.and.lowerLeft,sep=" ")
return(d.content)
}
###############################################
template.polygon = '
<polygon
points = "%s"
id="line"
style="fill:%s; stroke:%s; stroke-opacity:%s; stroke-width:%f"
transform = "rotate(%f %f %f)"
/>
'
plot.polygon = function(object,points,fill.color,rotate.a,rotate.x,rotate.y){
if(fill.color == "black"){
fill.color = object@edge$tip.fill.color # if the edge has a filled tip(e.g. production), we can change it to user defined color. If the edge type has an empty tip, we can't change it.
}
sprintf(template.polygon,points
,fill.color
,object@edge$tip.stroke.color
,object@edge$tip.stroke.opacity
,object@edge$tip.stroke.width
,rotate.a,rotate.x,rotate.y)
}
###############################################
template.ellipse = '
<ellipse
rx="%f"
ry="%f"
cx="%f"
cy="%f"
id="%s"
style="fill:%s;fill-opacity:%f;stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
plot.ellipse = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",fill.opacity=1,stroke.color="black",stroke.width=1,stroke.opacity=1,glyph=new("glyph")){
if(length(glyph@shape$fill.color)>0){
fill.color = glyph@shape$fill.color
}
if(length(glyph@shape$fill.opacity)>0){
fill.opacity = glyph@shape$fill.opacity
}
if(length(glyph@shape$stroke.width)>0){
stroke.width = glyph@shape$stroke.width
}
if(length(glyph@shape$stroke.opacity)>0){
stroke.opacity = glyph@shape$stroke.opacity
}
if(length(glyph@shape$stroke.color)>0){
stroke.color = glyph@shape$stroke.color
}
svg = sprintf(template.ellipse,w/2,h/2,x,y,id,fill.color,fill.opacity,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
plot.ellipse.edge.tip = function(x,y,h,w,id,rx=0,ry=0,fill.color="white",fill.opacity=1,stroke.color="black",stroke.width=1,stroke.opacity=1,object){
if(fill.color == "black"){
fill.color = object@edge$tip.fill.color # if the edge has a filled tip(e.g. production), we can change it to user defined color. If the edge type has empty tip fill color, we can't change it.
}
svg = sprintf(template.ellipse,w/2,h/2,x,y,id
,fill.color
,object@edge$tip.fill.opacity
,object@edge$tip.stroke.color
,object@edge$tip.stroke.width
,object@edge$tip.stroke.opacity
)
return(svg)
}
###############################################
template.line = '
<line
%s
id="%s"
style="stroke:%s;stroke-width:%f;stroke-opacity:%f" />
'
plot.line = function(LineCoordinates,id,stroke.color="black",stroke.opacity=1,stroke.width=1,object=NULL){
if(! is.null(object)){
stroke.color = object@edge$line.stroke.color
stroke.width = object@edge$line.width
}
# stroke.width = 2*stroke.width
svg = template.line
svg = sprintf(template.line,LineCoordinates,id,stroke.color,stroke.width,stroke.opacity)
return(svg)
}
plot.LineWings = function(x,y,w,h,orientation,id){
leftLineCoordinates = paste("x1=",x-w," y1=",y," x2=",x-w/2," y2=",y,"",sep='"')
rightLineCoordinates = paste("x1=",x+w/2," y1=",y," x2=",x+w," y2=",y,"",sep='"')
if (orientation == "vertical"){
leftLineCoordinates = paste("x1=",x," y1=",y-h," x2=",x," y2=",y-h/2,"",sep='"')
rightLineCoordinates = paste("x1=",x," y1=",y+h/2," x2=",x," y2=",y+h,"",sep='"')
}
svg.line.l = plot.line(leftLineCoordinates,id)
svg.line.r = plot.line(rightLineCoordinates,id)
svg = paste(svg.line.l,svg.line.r,sep="\n")
return(svg)
}
##########################################################
#' An object to store glyph information
#' @slot compartment
#'
#' A character string. The compartment this glyph belongs to.
#'
#' @slot x,y,h,w
#'
#' Numeric. The x,y location and hight, width of the glyph
#'
#' @slot id
#'
#' A character string. The ID of the glyph (determined by the "id" attribute in element "glyph")
#'
#' @slot label
#'
#' A character string. label of the glyph. Extracted from the element "label"
#'
#' @slot glyph.class
#'
#' A character string. Class of the glyph
#'
#' @slot user.data
#'
#' A numeric vector. The omics data mapped to this glyph.
#'
#' @slot stroke.width,stroke.opacity,fill.opacity
#'
#' Numeric. Controls glyph border width or opacity of node fill and border.
#'
#' @slot fill.color,stroke.color
#'
#' A character string. The fill color and stroke color of glyph.
#'
#' @slot 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.
#'
#' @slot 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.
#'
#' @slot global.parameters.list
#'
#' A list. This is a copy of parameters in '...' of function \code{\link{SBGNview}}.
#'
#' @slot shape
#'
#' A list. Parameters controlling how the node is rendered. Available elements can be accessed as follow:
#'
#'
#' glyph@@shape$stroke.color\cr
#' -Character (e.g. "red"). The color of glyph border. \cr
#'
#' glyph@@shape$stroke.opacity\cr
#' -Numeric (e.g. 0.8). The opacity of glyph border. Must be between 0 and 1.\cr
#'
#' glyph@@shape$stroke.width\cr
#' -Numeric. The width of glyph border\cr
#'
#' glyph@@shape$fill.opacity\cr
#' -Numeric. The opacity of glyph fill. Must be between 0 and 1.\cr
#'
#' glyph@@shape$fill.color\cr
#' -Numeric. The glyph fill color. Note that this will overwrite colors generated from omics data!\cr
#'
#' @slot text
#'
#' A list. Parameters controlling how node label is rendered. Available elements can be accessed as follow:
#'
#' glyph@@text$y.shift\cr
#' -Numeric. Move glyph label vertically by this value.\cr
#'
#' glyph@@text$x.shift\cr
#' -Numeric. Move glyph label horizontally by this value.\cr
#'
#' glyph@@text$color\cr
#' -A character string. The color of glyph label.\cr
#'
#' glyph@@text$font.size\cr
#' -A character string. The font size of glyph label.\cr
#'
#' @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 "glyph@@global.parameters.list"
#'
#' 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$font.size = 5".
#'
setClass(
"glyph"
,representation (compartment = "character", x="numeric",y="numeric",h="numeric",w="numeric",id = "character",label="character",label.margin = "numeric" ,label_location="character",svg.port = "character" ,orientation="character",user.data = "vector",clone = "list", fill.color = "character", stroke.width = "numeric",stroke.color="character",stroke.opacity="numeric",fill.opacity="numeric",global.parameters.list="list",glyph.class="character",text="list",shape="list")
)
setClass(
"port"
,contains="glyph"
# ,representation (x="numeric",y="numeric",id = "character")
)
##########################################################
#' An object to store arc information.
#' @slot target,source,id,arc.class
#' A character string. Information extracted from element "arc"
#' @slot start.x,start.y,end.x,end.y
#' Numeric. Information extracted from elements "start", "end" or "next"
#' @slot stroke.opacity
#' Numeric. Controls the line of an arc (not tip of arc).
#' @slot global.parameters.list
#' A list. This is a copy of parameters in '...' of SBGNview. It can affect glyph behavior if the element has a corresponding feature of the arc. For example "edge.tip.size" affects the arc but "compartment.opacity" doesn't. See details for more information. This will be improved in future versions to remove unrelated parameters.
#'
#' @slot edge
#'
#' A list. An arc in SBGN map normally consists of a line and a tip shape at the end of the line. This list holds variables that controls arc properties. Available elements can be accessed as follow:
#'
#' The following three paremeters control the line.\cr
#' arc@@edge$line.stroke.color\cr
#' arc@@edge$line.stroke.opacity\cr
#' arc@@edge$line.width\cr
#'
#'
#' The following five paremeters control the tip.\cr
#' arc@@edge$tip.stroke.opacity\cr
#' arc@@edge$tip.stroke.color\cr
#' arc@@edge$tip.stroke.width\cr
#' arc@@edge$tip.fill.color\cr
#' arc@@edge$tip.fill.opacity\cr
#'
#' @details Arc information comes from two sources:1. SBGN-ML file's "arc" element ("source", "target", coordinates etc.). 2. Parameters specified when running \code{\link{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.
#'
#'
setClass(
"arc"
,representation (target="character",source="character",id="character",arc.class="character",start.y="numeric",start.x="numeric",end.y="numeric",end.x="numeric",stroke.opacity = "numeric",global.parameters.list="list",edge = "list")
)
setClass(
"spline"
,representation (id="character",spline.coords = "vector",edge="list",global.parameters.list="list")
)
##########################################################
#' An object to store information for spline formated arcs.
#' @slot target,source,id,arc.class
#' A character string. Information extracted from element "arc.spline"
#' @slot start.x,start.y,end.x,end.y
#' Numeric. Information extracted from elements "start", "end" or "next"
#' @slot stroke.opacity
#' Numeric. Controls the line of an arc (not tip of arc).
#' @slot 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.
#' @slot 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.
#'
#' @slot 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.\cr
#' arc@@edge$line.stroke.color\cr
#' arc@@edge$line.stroke.opacity\cr
#' arc@@edge$line.width\cr
#'
#'
#' The following five paremeters control the tip.\cr
#' arc@@edge$tip.stroke.opacity\cr
#' arc@@edge$tip.stroke.color\cr
#' arc@@edge$tip.stroke.width\cr
#' arc@@edge$tip.fill.color\cr
#' arc@@edge$tip.fill.opacity\cr
#'
#' @details Arc information comes from two sources:1. SBGN-ML file's "arc" element ("source", "target", coordinates etc.). 2. Parameters specified when running \code{\link{SBGNview}}. User can modify arc objects to change the way how it is rendered. Some of the slots/parameters in arc object controls similar graph features such as text font, line width/color etc.
#'
#' The priority is determined in the following sequence:
#'
#' 1. arc@@edge
#'
#' 2. Parameters in slot "arc@@global.parameters.list"
#'
#' 3. Slots in arc object: stroke.opacity, fill.color etc.
#'
#'
setClass(
"spline.arc"
,representation (id="character", source = "character",target="character",arc.class="character",edge="list",components="list",global.parameters.list="list")
)
setGeneric(
"plot.glyph"
, function(object){
standardGeneric("plot.glyph")
}
)
setGeneric(
"plot.arc"
, function(object){
standardGeneric("plot.arc")
}
)
###############################################
setClass("macromolecule.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("macromolecule.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.color=1
if(length(object@stroke.color)>0){
stroke.color = object@stroke.color
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
fill.opacity=1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,sep="\n")
svg=""
if(is.na(user.data[1])){
}
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@fill.opacity = 1
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.1
glyph.data.i@stroke.opacity = 0.5
glyph.data.i@stroke.color = "black"
glyph.data.i@shape$stroke.opacity = 0.5 # if we are plotting data shape, don't plot the border
glyph.data.i@shape$stroke.width = 0.1 # if we are plotting data shape, don't plot the border
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity = 0
stroke.opacity = 1
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity = stroke.opacity,fill.opacity = fill.opacity)
svg = paste(svg,svg.rect,svg.text,sep="\n")
return(svg)
}
)
###############################################
setClass("entity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("entity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
stroke.width=1
stroke.opacity=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
rx = min(h,w)/10
ry = min(h,w)/10
# svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,stroke.opacity = stroke.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,rx=rx,ry=ry,stroke.width = stroke.width,stroke.opacity = stroke.opacity)
svg = paste(svg,svg.rect,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("compartment.sbgn",contains="glyph",representation(max.x="numeric"))
setMethod(
"plot.glyph"
,signature("compartment.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location = "top"
# ry = rx
max.x = object@max.x
rx = ry = 20
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = object@shape$stroke.width,fill.opacity = global.parameters.list$compartment.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location,max.x=max.x)
svg = paste(svg.rect,svg.text,sep="\n")
# svg = ""
return(svg)
}
)
############################################
setClass("complex.sbgn",contains="glyph",representation(if.complex.empty="logical"))
setMethod(
"plot.glyph"
,signature("complex.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y -h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
if ( length(nchar(object@label_location))==0 ){
label.location = "top"
}else if( object@label_location != "center" ){
label.location = "top"
}else{
label.location = object@label_location
}
if.complex.empty= FALSE
if(length(object@if.complex.empty) !=0){
if.complex.empty = object@if.complex.empty
}
if(if.complex.empty){
label.location = "center"
}
rx = ry = 8
corner.r = rx
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
d1 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
# label="complex" # try not to show complex name
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path1,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("complex_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("complex_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y -h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
corner.r = global.parameters.list$edge.tip.size*3
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
d1 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",fill.opacity = 1)
x = x+global.parameters.list$edge.tip.size*3/2; y = y+global.parameters.list$edge.tip.size*3/2
d2 = (paste("M",x,y+corner.r, x,y+h-corner.r, x+corner.r,y+h, x+w-corner.r,y+h, x+w,y+h-corner.r, x+w,y+corner.r, x+w-corner.r,y, x+corner.r,y ,"Z",sep=" "))
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path2,svg.path1,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("state_variable.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("state_variable.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = gsub(" ","",object@label)
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = global.parameters.list$auxiliary.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("unspecified_entity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("unspecified_entity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
# if(length(object@fill.opacity)>0){
# fill.opacity = object@fill.opacity
# }
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
# svg = paste(svg.ellipse,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity = 0)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
svg.path.1 = plot.path(object=object,d=d.1,id=id,fill.color=fill.color,stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object,d=d.2,id=id,fill.color="white",stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
}
fill.opacity = 0
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("unit_of_information.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("unit_of_information.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
object@label = gsub(" ","",object@label)
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width,fill.opacity = global.parameters.list$auxiliary.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("stoichiometry.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("stoichiometry.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("cardinality.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("cardinality.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("biological_activity.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("biological_activity.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("submap.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("submap.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "top"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg = svg.rect
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect,svg.wings,sep="\n")
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = ""
}else{
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg = svg.rect
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("uncertain_process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("uncertain_process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = "?"
}else{
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("and.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("and.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "AND"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("or.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("or.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "OR"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("not.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("not.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "NOT"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("tau.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("tau.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "t"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("macromolecule_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("macromolecule_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity=1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
object@label = object@label
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
label.location = "center"
rx = min(h,w)/10
ry = min(h,w)/10
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.rect.up = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width,fill.opacity = 1)
svg.rect.down = plot.rectangle(glyph=object,x=x-w/2+global.parameters.list$multimer.margin,y=y-h/2+global.parameters.list$multimer.margin,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.rect.down,svg.rect.up,sep="\n")
svg = paste(svg.rect.down,sep="\n")
# svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = new("macromolecule.sbgn")
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@compartment = object@compartment
glyph.data.i@y=y
glyph.data.i@h=h
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@id=paste(id,"user.data",i,sep="_")
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
glyph.data.i@fill.opacity = 1
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
svg.rect.up = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,id=id,h=h,w=w,rx=rx,ry=ry,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg = paste(svg,svg.rect.up,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("outcome.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("outcome.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
print (orientation)
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color="black",stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = svg.ellipse
return(svg)
}
)
###########################################################
setClass("simple_chemical_multimer.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("simple_chemical_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
w=h
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
label = object@label
label.location = "center"
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
# if(length(object@fill.opacity)>0){
# fill.opacity = object@fill.opacity
# }
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg.ellipse2 = plot.ellipse(glyph=object,x+5,y+5,h,w,id)
svg = paste(svg.ellipse2,sep="\n")
if(!identical(user.data[1],"no.user.data")){
# if(user.data[1] != "no.user.data"){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,fill.opacity = 1)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@fill.opacity=1
# glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
svg.path.1 = plot.path(object=object,d=d.1,id=id,fill.color=fill.color,stroke.width= 1,stroke.color = "black",fill.opacity = 1,stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object,d=d.2,id=id,fill.color="white",stroke.width= 1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
}
fill.opacity=0
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = fill.opacity)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
############################################
setClass("omitted_process.sbgn",contains="glyph",representation(if.show.label="logical"))
setMethod(
"plot.glyph"
,signature("omitted_process.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if(!object@if.show.label){
object@label = '\\\\'
}else{
object@label = object@label
}
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.rect = plot.rectangle(glyph=object,x=x-w/2,y=y-h/2,h=h,w=w,id=id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.rect,svg.wings,svg.text,sep="\n")
return(svg)
}
)
###########################################################
setClass("simple_chemical.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("simple_chemical.sbgn")
, function(object){
w = object@w
h = object@h ;
w=h
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
# label = object@label
label.location = "center"
stroke.color=1
if(length(object@stroke.color)>0){
stroke.color = object@stroke.color
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
# svg = paste(svg.ellipse,sep="\n")
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
fill.color = color.from.01.value(user.data[1],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.color = fill.color,stroke.opacity=0.5)
svg = paste(svg,svg.ellipse,sep="\n")
if(length(user.data)>1){
svg.sep.data.line = ""
for(i in 2: length(user.data)){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="compond")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
# glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1) * w/length(user.data)
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
start.x=x -w/2 + (i-1) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
Coordinates = paste("x1=",start.x," y1=",start.y.1," x2=",start.x," y2=",start.y.2,"",sep='"')
svg.sep.data.line = paste(svg.sep.data.line
,plot.line(LineCoordinates = Coordinates,id = id,stroke.width = 0.1,stroke.opacity = 0.5),sep="\n")
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.1 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0 ,start.x,start.y.2,sep=" "))
object.data = object # if we are ploting shape for data, don't plot border
object.data@shape$stroke.opacity = 0
svg.path.1 = plot.path(object=object.data,d=d.1,id=id,fill.color=fill.color,stroke.width= 0.1,stroke.color = "black",stroke.opacity = 0)
start.x=x -w/2 + (i) * w/length(user.data)
start.y.1 = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
start.y.2 = y-(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
if(start.x>x){
large.flag = 0
}else{
large.flag = 1
}
d.2 = (paste("M",start.x,start.y.1,"A",w/2,h/2 ,1, large.flag,0,start.x,start.y.2,sep=" "))
svg.path.2 = plot.path(object=object.data,d=d.2,id=id,fill.color="white",stroke.width= 0.1,stroke.color = "black",stroke.opacity = 0)
svg = paste(svg,svg.path.1,svg.path.2,sep="\n")
}
svg = paste(svg,svg.sep.data.line,sep="\n")
}
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width,fill.opacity = 0)
svg = paste(svg,svg.ellipse,svg.text,sep="\n")
return(svg)
}
)
###########################################################
setClass("dissociation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("dissociation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse.o = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.ellipse.i = plot.ellipse(glyph=object,x,y,h/2,w/2,id)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = paste(svg.ellipse.o,svg.ellipse.i,svg.wings,sep="\n")
return(svg)
}
)
######################################################
setClass("nucleic_acid_feature_multimer.sbgn",contains="glyph",representation(r4="numeric",r3="numeric"))
setMethod(
"plot.glyph"
,signature("nucleic_acid_feature_multimer.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
if(length(object@r4)>0){
r4 = object@r4
}
if(length(object@r3)>0){
r3 = object@r3
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
# svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
d2 = generate.d.for.partly.rounded.corner.rect(x=x-w/2+global.parameters.list$multimer.margin,y=y-h/2+global.parameters.list$multimer.margin,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black",stroke.opacity = 1)
# svg = paste(svg.path2,svg.path,sep="\n")
svg = paste(svg.path2,sep="\n")
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = new("nucleic_acid_feature.sbgn")
glyph.data.i@fill.color = fill.color
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@y = y
glyph.data.i@h = h
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@compartment = object@compartment
glyph.data.i@id=paste(id,"user.data",i,sep="_")
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
glyph.data.i@fill.opacity = 1
if(i == 1){
glyph.data.i@r3 = 0
}else if(i==length(user.data)){
glyph.data.i@r4 = 0
}else{
glyph.data.i@r4=0
glyph.data.i@r3=0
}
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black",fill.opacity = fill.opacity,stroke.opacity = 1)
svg = paste(svg,svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("nucleic_acid_feature.sbgn",contains="glyph",representation(r4="numeric",r3="numeric"))
setMethod(
"plot.glyph"
,signature("nucleic_acid_feature.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
fill.color = "white"
if(length(object@fill.color)>0){
fill.color = object@fill.color
}
fill.opacity = 1
if(length(object@fill.opacity)>0){
fill.opacity = object@fill.opacity
}
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
if(length(object@r4)>0){
r4 = object@r4
}
if(length(object@r3)>0){
r3 = object@r3
}
stroke.width=1
if(length(object@shape$stroke.width)>0){
stroke.width = object@shape$stroke.width
}
stroke.opacity=1
if(length(object@stroke.opacity)>0){
stroke.opacity = object@stroke.opacity
}
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg=""
# if(user.data[1] != "no.user.data"){
if(!identical(user.data[1],"no.user.data")){
for(i in seq_len(length.out = length(user.data))){
fill.color = color.from.01.value(user.data[i],global.parameters.list=global.parameters.list,gene.or.cpd="gene")
glyph.data.i = object
glyph.data.i@fill.color = fill.color
glyph.data.i@fill.opacity = 1
glyph.data.i@user.data = c("no.user.data")
glyph.data.i@w = w/length(user.data)
glyph.data.i@x = x -w/2 + (i-1/2) * glyph.data.i@w
glyph.data.i@label = " "
glyph.data.i@shape$stroke.width = 0.5
glyph.data.i@stroke.opacity = 0
if(i == 1){
glyph.data.i@r3 = 0
}else if(i==length(user.data)){
glyph.data.i@r4 = 0
}else{
glyph.data.i@r4=0
glyph.data.i@r3=0
}
svg = paste(svg,plot.glyph(glyph.data.i),sep="\n")
}
fill.opacity=0
}
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color=fill.color,stroke.width=stroke.width,stroke.color = "black",stroke.opacity=stroke.opacity,fill.opacity = fill.opacity )
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg,svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("perturbation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("perturbation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x,y,x+h/3,y+h/2 ,x,y+h ,x+w,y+h ,x+w-h/3,y+h/2, x+w,y,"Z",sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("perturbing_agent.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("perturbing_agent.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x,y,x+h/3,y+h/2 ,x,y+h ,x+w,y+h ,x+w-h/3,y+h/2, x+w,y,"Z",sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
# svg.ellipse = plot.ellipse(glyph=object,180,210,5,5,id,fill.color = "red")
svg = paste(svg.path,svg.text,sep="\n")
# svg = paste(svg.path,svg.text,svg.ellipse,sep="\n")
return(svg)
}
)
######################################################
setClass("annotation.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("annotation.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w
y = object@y-h
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
# stroke.opacity = object@stroke.opacity
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
label.location="center"
d1 = (paste("M",x,y, x,y+h, x+w/4,y+h, x+min(h,w)/10,y+3*h/2, x+w/2,y+h, x+w,y+h, x+w,y+h/5, x+w-h/5,y ,"Z",sep=" "))
svg.path1 = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=1,stroke.color = "black",stroke.opacity = stroke.opacity)
d2 = (paste("M",x+w-h/5,y+h/5, x+w,y+h/5, x+w-h/5,y ,"Z",sep=" "))
svg.path2 = plot.path(object=object,d=d2,id=id,fill.color="black",stroke.width=1,stroke.color = "black",stroke.opacity = stroke.opacity)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location,stroke.opacity = stroke.opacity)
svg = paste(svg.path1,svg.path2,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("existence.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("existence.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color = "white",stroke.width = stroke.width)
d = (paste("M",x,y-h/2,"a",h/2,h/2 ,0, 0,1 ,0,h,sep=" "))
svg.path = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black")
svg = paste(svg.ellipse,svg.path,sep="\n")
return(svg)
}
)
######################################################
setClass("clone_simple_chemical.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone_simple_chemical.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = "clone"
# label = object@label
label.location="center"
start.x=x-w/2+w/20
start.y = y+(h/2/(w/2)*((w/2)**2-(start.x-x)**2)**0.5)
d = (paste("M",start.x,start.y,"A",w/2,h/2 ,1, 0,0 ,x+w/2-w/20,start.y,sep=" "))
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width= stroke.width,stroke.color = "black")
svg = svg.path
return(svg)
}
)
######################################################
setClass("clone.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = "clone"
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=max(h,w)/10;r4=max(h,w)/10
d1 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y+h/2-h/5,w=w,h=h/5,r1=r1,r2=r2,r3=r3,r4=r4)
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path.bigbox = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y+h/2-h/10,h=h,w=w,id=id,label.location=label.location,color="white")
svg = paste(svg.path.bigbox,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("clone_marker.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("clone_marker.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = 0;r2=0;r3=min(h,w)/10;r4=min(h,w)/10
d1 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path.bigbox = plot.path(object=object,d=d1,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
d2 = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2+3/5*h,w=w,h=2/5*h,r1=r1,r2=r2,r3=r3,r4=r4)
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path.innerbox = plot.path(object=object,d=d2,id=id,fill.color="gray",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y-1/5*h,h=h,w=w,id=id,label.location=label.location)
white.top.line.to.cover = paste("M",x-w/2,y-h/2,x+w/2,y-h/2,sep=" ")
svg.path.topWhiteLine = plot.path(object=object,d=white.top.line.to.cover,id=id,fill.color="gray",stroke.width=5,stroke.color = "white")
svg = paste(svg.path.bigbox,svg.path.innerbox,svg.path.topWhiteLine,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("terminal.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("terminal.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
orientation = object@orientation
label.location="center"
d = (paste("M",x+h/3,y,x,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w,y+h/2, x+w-h/3,y,"Z",sep=" "))
if (orientation == "right"){
d = (paste("M",x,y ,x,y+h ,x+w-w/3,y+h ,x+w,y+h/2, x+w-w/3,y,"Z",sep=" "))
}else if (orientation == "left"){
d = (paste("M",x+w/3,y,x,y+h/2 ,x+w/3,y+h ,x+w,y+h ,x+w,y,"Z",sep=" "))
}else if (orientation == "up"){
d = (paste("M",x+w/2,y,x,y+h/3 ,x,y+h ,x+w,y+h ,x+w,y+h/3,"Z",sep=" "))
}else if (orientation == "down"){
d = (paste("M",x,y ,x,y+h-h/3, x+w/2,y+h ,x+w,y+h-h/3 ,x+w,y,"Z",sep=" "))
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("tag.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("tag.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
orientation = object@orientation
label.location="center"
d = (paste("M",x+h/3,y,x,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w,y+h/2, x+w-h/3,y,"Z",sep=" "))
if (orientation == "right"){
d = (paste("M",x,y ,x,y+h ,x+w-w/3,y+h ,x+w,y+h/2, x+w-w/3,y,"Z",sep=" "))
}else if (orientation == "left"){
d = (paste("M",x+w/3,y,x,y+h/2 ,x+w/3,y+h ,x+w,y+h ,x+w,y,"Z",sep=" "))
}else if (orientation == "up"){
d = (paste("M",x+w/2,y,x,y+h/3 ,x,y+h ,x+w,y+h ,x+w,y+h/3,"Z",sep=" "))
}else if (orientation == "down"){
d = (paste("M",x,y ,x,y+h-h/3, x+w/2,y+h ,x+w,y+h-h/3 ,x+w,y,"Z",sep=" "))
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=stroke.width,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("phenotype.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("phenotype.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x-w/2
y = object@y-h/2
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
d = (paste("M",x+h/3,y,x+5,y+h/2 ,x+h/3,y+h ,x+w-h/3,y+h ,x+w-5,y+h/2, x+w-h/3,y,"Z",sep=" "))
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x+w/2,y=y+h/2,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
##########################################################
setClass("association.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("association.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,fill.color="black",stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg = paste(svg.ellipse,svg.wings,sep="\n")
return(svg)
}
)
######################################################
setClass("interaction.sbgn.arc",contains="glyph")
setMethod(
"plot.glyph"
,signature("interaction.sbgn.arc")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg = svg.ellipse
return(svg)
}
)
######################################################
setClass("interaction.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("interaction.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg.line = plot.line(Coordinates,id)
svg = svg.ellipse
return(svg)
}
)
##########################################################
setClass("delay.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("delay.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
object@label = "t"
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
label.location = "center"
rx = 0
ry = 0
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
svg.wings = plot.LineWings(x,y,w,h,orientation,id)
svg.wings = ""
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.ellipse,svg.wings,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("source_and_sink.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("source_and_sink.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
if (length(object@orientation)>0){
orientation = object@orientation
}else{
orientation = "horizontal"
}
stroke.width=1
if(object@compartment == "free.node.within.compartment"){
stroke.width = 3
}
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id,stroke.width = stroke.width)
Coordinates = paste("x1=",x-w/2," y1=",y+h/2," x2=",x+w/2," y2=",y-h/2,"",sep='"')
svg.line = plot.line(Coordinates,id)
svg = paste(svg.ellipse,svg.line,sep="\n")
return(svg)
}
)
######################################################
setClass("location.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("location.sbgn")
, function(object){
w = object@w
h = object@h ;
h = w
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
svg.ellipse = plot.ellipse(glyph=object,x,y,h,w,id)
angle = pi/6
Coordinates1 = paste("x1=",x-w/2*cos(angle)," y1=",y+h/2*sin(angle)," x2=",x+w/2*sin(angle)," y2=",y-h/2*cos(angle),"",sep='"')
svg.line1 = plot.line(Coordinates1,id)
Coordinates2 = paste("x1=",x-w/2*(cos(angle)-sin(angle))/2," y1=",y+h/2*(sin(angle)-cos(angle))/2," x2=",x+w/2*sin(pi/4)," y2=",y+h/2*cos(pi/4),"",sep='"')
svg.line2 = plot.line(Coordinates2,id)
svg = paste(svg.ellipse,svg.line1,svg.line2,sep="\n")
return(svg)
}
)
######################################################
setClass("state_variable.ER.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("state_variable.ER.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = h/2 ;r2=r1;r3=r1;r4=r1
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black",fill.opacity = 1)
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setClass("variable_value.sbgn",contains="glyph")
setMethod(
"plot.glyph"
,signature("variable_value.sbgn")
, function(object){
w = object@w
h = object@h ;
x = object@x
y = object@y
global.parameters.list = object@global.parameters.list
id = object@id ; user.data = object@user.data
# label = object@label
label.location="center"
r1 = h/2 ;r2=r1;r3=r1;r4=r1
d = generate.d.for.partly.rounded.corner.rect(x=x-w/2,y=y-h/2,w=w,h=h,r1=r1,r2=r2,r3=r3,r4=r4)
svg.path = plot.path(object=object,d=d,id=id,fill.color="white",stroke.width=1,stroke.color = "black")
svg.text = plot.text(glyph=object,glyph.class=object@glyph.class,global.parameters.list=global.parameters.list,x=x,y=y,h=h,w=w,id=id,label.location=label.location)
svg = paste(svg.path,svg.text,sep="\n")
return(svg)
}
)
######################################################
setMethod(
"plot.arc"
,signature("spline.arc")
, function(object){
components = object@components
svg = ""
for (i in seq_len(length.out = length(components))){
component = components[[i]]
component@edge = object@edge
component@global.parameters.list = object@global.parameters.list
if(!is(component, "spline")){
component@edge$line.stroke.opacity = 0
}
svg = paste(svg,plot.arc(component),sep="\n")
}
return(svg)
}
)
######################################################
spline.svg.template = '<path d="M%s %s C %s %s, %s %s,%s %s" stroke="%s" stroke-opacity="%s" stroke-width="%s" fill-opacity="0" fill="transparent"/>'
setMethod(
"plot.arc"
,signature("spline")
, function(object){
svg = do.call(sprintf,c(list(spline.svg.template)
,c(object@spline.coords
,object@edge$line.stroke.color
,object@edge$line.stroke.opacity
,object@edge$line.width
)
)
)
return(svg)
}
)
######################################################
setClass("absolute_stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("absolute_stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
points2 = paste(end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*6,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*6,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
svg.triangle2 = plot.polygon(object=object,points2,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
svg.triangle2= plot.polygon(object=object,points2,fill.color = "white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,svg.triangle2,sep="\n")
return(svg)
}
)
######################################################
setClass("absolute_inhibition.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("absolute_inhibition.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
global.parameters.list = object@global.parameters.list
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
d = (paste("M",end.x-1,end.y-global.parameters.list$edge.tip.size*3/2,end.x-1,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
if (start.x<end.x){
d1 = (paste("M",end.x-global.parameters.list$edge.tip.size*3/4,end.y-global.parameters.list$edge.tip.size*3/2,end.x-global.parameters.list$edge.tip.size*3/4,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine1 = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
d1 = (paste("M",end.x+global.parameters.list$edge.tip.size*3/4,end.y-global.parameters.list$edge.tip.size*3/2,end.x+global.parameters.list$edge.tip.size*3/4,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine1 = plot.path(object=object,d=d1,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.endLine,svg.endLine1,sep="\n")
return(svg)
}
)
######################################################
setClass("necessary_stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("necessary_stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
end.line.length = global.parameters.list$edge.tip.size*3/2
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-end.line.length," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+end.line.length,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
d = (paste("M",end.x-global.parameters.list$edge.tip.size*4,end.y-end.line.length-global.parameters.list$edge.tip.size*3/4,end.x-global.parameters.list$edge.tip.size*4,end.y+end.line.length+global.parameters.list$edge.tip.size*3/4,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
d = (paste("M",end.x+global.parameters.list$edge.tip.size*4,end.y-end.line.length-global.parameters.list$edge.tip.size*3/4,end.x+global.parameters.list$edge.tip.size*4,end.y+end.line.length+global.parameters.list$edge.tip.size*3/4,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("equivalence_arc.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("equivalence_arc.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
######################################################
setClass("consumption.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("consumption.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
######################################################
setClass("next.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("next.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
###############################################
setClass("production.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("production.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
#############################
# if(grepl("arc_292_output_257",id)){
# cat("printing object")
# }
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
end.size = global.parameters.list$edge.tip.size*2
points = paste(end.x,",",end.y," ",end.x-end.size,",",end.y-end.size/2," ",end.x-end.size,",",end.y+end.size/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("interaction.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("interaction.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points.end = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*2,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
points.start = paste(start.x,",",start.y," ",start.x+global.parameters.list$edge.tip.size*3,",",start.y-global.parameters.list$edge.tip.size," ",start.x+global.parameters.list$edge.tip.size*2,",",start.y," ",start.x+global.parameters.list$edge.tip.size*3,",",start.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle.end = plot.polygon(object=object,points.end,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
svg.triangle.start = plot.polygon(object=object,points.start,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,start.x,start.y)
}else{
svg.triangle.end = plot.polygon(object=object,points.end,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
svg.triangle.start = plot.polygon(object=object,points.start,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,start.x,start.y)
}
svg = paste(svg.line,svg.triangle.end,svg.triangle.start,sep="\n")
return(svg)
}
)
######################################################
setClass("assignment.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("assignment.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*2,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"black",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("catalysis.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("catalysis.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
global.parameters.list = object@global.parameters.list
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
angle = atan((start.y-end.y)/(start.x-end.x))
circle.r = global.parameters.list$edge.tip.size
if (start.x<end.x){
circle.center.x = end.x - circle.r * cos(angle)
circle.center.y = end.y - circle.r * sin(angle)
}else {
circle.center.x = end.x + circle.r * cos(angle)
circle.center.y = end.y + circle.r * sin(angle)
}
svg.ellipse = plot.ellipse.edge.tip(circle.center.x,circle.center.y,circle.r*2,circle.r*2,id,fill.opacity = 0.8,object=object)
svg = paste(svg.line,svg.ellipse,sep="\n")
return(svg)
}
)
######################################################
setClass("positive_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("positive_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("stimulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("stimulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y-global.parameters.list$edge.tip.size," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y+global.parameters.list$edge.tip.size,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("negative_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("negative_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
if (start.x<end.x){
d = (paste("M",end.x-global.parameters.list$inhibition.edge.end.shift,end.y-global.parameters.list$edge.tip.size*3/2,end.x-global.parameters.list$inhibition.edge.end.shift,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
d = (paste("M",end.x+global.parameters.list$inhibition.edge.end.shift,end.y-global.parameters.list$edge.tip.size*3/2,end.x+global.parameters.list$inhibition.edge.end.shift,end.y+global.parameters.list$edge.tip.size*3/2,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}
svg = paste(svg.line,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("inhibition.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("inhibition.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
inhibition.edge.end.shift = global.parameters.list$inhibition.edge.end.shift
line.length = ((start.x-end.x)**2 + (start.y-end.y)**2) ** 0.5
if (start.x<end.x){
# if(grepl("arc_165_inhibitor_28",object@id)){
# print("start x smaller than end x")
# print(start.x)
# print(end.x)
# print("printed two x es")
# }
d1 = (paste("M"
# ,start.x
,end.x - line.length
,end.y
,end.x-inhibition.edge.end.shift
,end.y
,sep=" "))
svg.line = plot.path(object=object
,d=d1
,id=id
,fill.color="white"
,stroke.color = "white"
,stroke.width=1
,angle = atan((start.y-end.y)/(start.x-end.x))/pi*180
,rotate.x = end.x
,rotate.y = end.y
)
d = (paste("M"
,end.x-inhibition.edge.end.shift
# ,end.x - line.length
,end.y-global.parameters.list$edge.tip.size*3/2
,end.x-inhibition.edge.end.shift
,end.y+global.parameters.list$edge.tip.size*3/2
,sep=" "))
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black"
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
}else{
d1 = (paste("M"
,end.x + line.length
,end.y
,end.x+inhibition.edge.end.shift
,end.y
,sep=" "))
svg.line = plot.path(object=object
,d=d1
,id=id
,fill.color="white"
,stroke.color = "white"
,stroke.width=1
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
d = (paste("M"
,end.x+inhibition.edge.end.shift
,end.y-global.parameters.list$edge.tip.size*3/2
,end.x+inhibition.edge.end.shift
,end.y+global.parameters.list$edge.tip.size*3/2
,sep=" "))
# object@edge$tip.stroke.color = "purple"
svg.endLine = plot.path(object=object,d=d,id=id,fill.color="black",stroke.width=1,stroke.color = "black"
,atan((start.y-end.y)/(start.x-end.x))/pi*180
,end.x
,end.y)
}
svg = paste(svg.line,svg.endLine,sep="\n")
return(svg)
}
)
######################################################
setClass("unknown_influence.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("unknown_influence.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y-global.parameters.list$edge.tip.size*3/2," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y+global.parameters.list$edge.tip.size*3/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("modulation.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("modulation.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
global.parameters.list = object@global.parameters.list
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
points = paste(end.x,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y-global.parameters.list$edge.tip.size*3/2," ",end.x-global.parameters.list$edge.tip.size*3,",",end.y," ",end.x-global.parameters.list$edge.tip.size*3/2,",",end.y+global.parameters.list$edge.tip.size*3/2,sep="")
if (start.x<end.x){
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180,end.x,end.y)
}else{
svg.triangle = plot.polygon(object=object,points,"white",atan((start.y-end.y)/(start.x-end.x))/pi*180+180,end.x,end.y)
}
svg = paste(svg.line,svg.triangle,sep="\n")
return(svg)
}
)
######################################################
setClass("logic_arc.sbgn.arc",contains="arc")
setMethod(
"plot.arc"
,signature("logic_arc.sbgn.arc")
, function(object){
start.x = object@start.x
start.y = object@start.y
end.x = object@end.x
end.y = object@end.y
id = object@id ;
if(length(object@stroke.opacity) !=0) stroke.opacity = object@stroke.opacity else stroke.opacity = 1
LineCoordinates = paste("x1=",start.x," y1=",start.y," x2=",end.x," y2=",end.y,"",sep='"')
svg.line = plot.line(object=object,LineCoordinates,id,stroke.opacity=stroke.opacity)
svg = svg.line
return(svg)
}
)
plot.text = function(x,y,h,w,id,label.location,color="black",glyph.class="",stroke.opacity=1,max.x=0,if.generate.text.box= FALSE,global.parameters.list,glyph){
label = glyph@label
if(length(glyph@text$color)>0){
color = glyph@text$color
}
if(length(glyph@text$x.shift)>0){
x = x + glyph@text$x.shift
}
if(length(glyph@text$y.shift)>0){
y = y + glyph@text$y.shift
}
label = gsub("&","-",label)
label = gsub("<[^><]+>","",label) # when using paxtools::toSBGN to convert biopax files to SBGN files, some text in the SBGN files contain special characters :label text="<i>p</i>-chloromercuribenzoate" . the "<" and ">" will create problem in the svg file. So we need remove them.
if (length(nchar(label))==0){ # when the label is empty, don't plot it
print("no label")
return ("")
}
result.list = break.text.into.segments(w,glyph.class,global.parameters.list = global.parameters.list,max.x=max.x,glyph=glyph)
label = result.list$words.segments
font.size = result.list$font.size
global.parameters.list$complex.compartment.label.margin.use = global.parameters.list$complex.compartment.label.margin
if(glyph.class == "compartment"){
if(max.x>0){ # if the graph is large, make label larger
global.parameters.list$complex.compartment.label.margin.use = global.parameters.list$complex.compartment.label.margin.use * max(1,max.x/2000)
}
}
label.segments = strsplit(label,'\n') # the label text in some of the input sbgn files are labeled with "
" in order to be seperated to different lines
label.segments = label.segments[[1]]
align.shift = font.size/3
text.anchor = "middle"
alignment.baseline = "middle"
x.label.box = x
if (length(label.segments)>1){ # if the text is labeled to be seperated into different lines
svg = ""
n.lines = length(label.segments)
h.label.box = n.lines * font.size
for (i in seq_len(length.out = n.lines)){
label.segment = label.segments[i]
w.label.box = nchar(label.segment)*font.size
if(label.location == "center"){
alignment.baseline = "baseline"
first.segment.shift = (n.lines-1)/2*font.size
start.y = y- first.segment.shift
y.segment = start.y + (i-1)*font.size
y.segment = y.segment+align.shift
if(i == 1){
y.label.box = y.segment+align.shift
}
}else if(label.location == "top"){
y.segment = y-h/2+2 + (i-1)*font.size
if(glyph.class %in% c("complex","compartment")){
y.segment = y-h/2-n.lines*font.size + (i-1)*font.size
}
text.anchor = "middle"
alignment.baseline = "baseline"
y.segment = y.segment+align.shift*2
if(i == 1){
y.label.box = y.segment+align.shift
}
}
svg.segment = sprintf(template.text,x,y.segment,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label.segment)
svg = paste(svg,svg.segment,sep="\n")
}
} else{
w.label.box = nchar(label)*font.size *0.5
h.label.box = font.size
if(glyph.class %in% c("compartment","complex")){
align.shift = 0
}
svg = template.text
if(label.location == "center"){
alignment.baseline = "baseline"
svg = sprintf(template.text,x,y+align.shift,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
y.label.box = y+align.shift
}else if(label.location == "top"){
text.anchor = "middle"
# alignment.baseline = "hanging"
if(glyph.class %in% c("complex","compartment")){
alignment.baseline = "baseline"
svg = sprintf(template.text,x,y+align.shift-h/2-global.parameters.list$complex.compartment.label.margin.use,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
}else{
svg = sprintf(template.text,x,y+align.shift-h/2+4,id,font.size,text.anchor,alignment.baseline,stroke.opacity,alignment.baseline,color,label)
}
y.label.box = y -h/2 -global.parameters.list$complex.compartment.label.margin.use - h.label.box/3
}
}
return(svg)
}
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