def drawSVG(self, data, cLength = 2500, offset= (80, 160, 60, 60), size=(1280,880),
XLabel="Marker GMb", YLabel="Transcript GMb"):
entities = {
"colorText" : "fill:darkblue;",
"strokeText" : ";stroke:none;stroke-width:0;",
"allText" : "font-family:Helvetica;",
"titleText" : "font-size:22;font-weight:bold;",
"subtitleText" : "font-size:18;font-weight:bold;",
"headlineText" : "font-size:14;font-weight:bold;",
"normalText" : "font-size:12;",
"legendText" : "font-size:11;text-anchor:end;",
"valuesText" : "font-size:12;",
"boldValuesText" : "font-size:12;font-weight:bold;",
"smallText" : "font-size:10;",
"vText" : "writing-mode:tb-rl",
"rightText" : "text-anchor:end;",
"middleText" : "text-anchor:middle;",
"bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;",
"rectstyle" : "fill:lightblue;stroke:none;opacity:0.2;",
"fillUnbebaut" : "fill:#CCFFD4;stroke:none;",
"fillNodata" : "fill:#E7E7E7;stroke:black;stroke-width:2;stroke-antialiasing:true;",
"fillNodataLegend" : "fill:#E7E7E7;stroke:black;stroke-width:0.5;stroke-antialiasing:true;",
"grundzeitstyle" : "fill:none;stroke:#E00004;stroke-width:60;stroke-antialiasing:true;",
"bezgrenzstyle" : "fill:none;stroke:#11A0FF;stroke-width:40;stroke-antialiasing:true;",
"mapAuthor" : "A. Neumann",
}
cWidth, cHeight = size
canvasSVG = svg.drawing(entities) #create a drawing
drawSpace=svg.svg((0, 0, cWidth, cHeight), cWidth, cHeight, xml__space="preserve",
zoomAndPan="disable", onload="initMap(evt);",
xmlns__a3="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/",
a3__scriptImplementation="Adobe") #create a svg drawingspace
canvasds=svg.description('Genome Graph') #define a description
drawSpace.addElement(canvasds) #add the description to the svg
#need to be modified or deleted
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = cWidth - xLeftOffset - xRightOffset
plotHeight = cHeight - yTopOffset - yBottomOffset
drawSpace.addElement(svg.script("", language="javascript", xlink__href="/javascript/svg.js"))
#add defs
defs = svg.defs()
symbol1= svg.symbol(id="magnifyer", overflow="visible",
style="fill:white;stroke:orange;stroke-width:2;")
symbol1.addElement(svg.line(0, 0, -8, 20))
symbol1.addElement(svg.circle(0, 0, 8))
symbol1.addElement(svg.line(-4, 0, 4, 0, style="stroke:orange;stroke-width:2;"))
defs.addElement(symbol1)
symbol2= svg.symbol(id="magnifyerZoomIn",overflow="visible")
symbol2.addElement(svg.use(link="#magnifyer", id="zoomIn"))
symbol2.addElement(svg.line(0, -4, 0, 4, style="stroke:orange;stroke-width:2;"))
defs.addElement(symbol2)
drawSpace.addElement(defs)
symbol3= svg.symbol(id="msgbox", overflow="visible",
style="fill:white;stroke:orange;stroke-width:1;opacity:0.8;")
symbol3.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
symbol3.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
symbol3.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
symbol3.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;"))
symbol3.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;"))
symbol3.addElement(svg.text(-60, -90, "LRS ", style="&colorText; &allText; &subtitleText; &strokeText;"))
symbol3.addElement(svg.text(-60, -55, "P value ", style="&colorText; &allText; &subtitleText; &strokeText;"))
defs.addElement(symbol3)
g = svg.group("title")
g.addElement(svg.text(cWidth-40, 30, "Genome Graph", style="&colorText; &allText; &titleText; &rightText;"))
g.addElement(svg.text(cWidth-40, 50, "Whole Transcriptome Mapping", style="&colorText; &allText; &subtitleText; &rightText;"))
drawSpace.addElement(g)
#draw Main display area border
mainSquare = cHeight-60
cordZOOM = 10
drawSpace.addElement(svg.rect(8, 8, mainSquare+4, mainSquare+4,'none',"orange",0.5, rx="5", ry="5"))
drawSpace.addElement(svg.text(10+mainSquare/2, 40+mainSquare,'Marker GMb',
style="&colorText; &allText; &titleText; &middleText;", id="XLabel"))
drawSpace.addElement(svg.text(mainSquare + 80, 10+mainSquare/2,'Transcript GMb',
style="&colorText; &allText; &titleText; &middleText; &vText;", id="YLabel"))
#draw overview display area
drawSpace.addElement(svg.rect(cWidth-40-260, 60, 260, 260,'none',"orange",0.5, rx="5", ry="5"))
drawSpaceThumb= svg.svg(id="overviewPlot",x=cWidth-40-260,y="60",width="260",
height="260",viewBox=(0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM))
g = svg.group(style="&bezgrenzstyle;")
g.addElement(svg.use("#grid"))
drawSpaceThumb.addElement(g)
drawSpaceThumb.addElement(svg.rect(id="overviewRect",style="&rectstyle;",
x="0",y="0",width=mainSquare*cordZOOM,height=mainSquare*cordZOOM,
onmouseover="statusChange('click and drag rectangle to change extent');",
onmousedown="beginPan(evt);", onmousemove="doPan(evt);",
onmouseup="endPan();", onmouseout="endPan();"))
drawSpace.addElement(drawSpaceThumb)
#draw navigator
g = svg.group(id="navigatorElements")
g.addElement(svg.use("#magnifyerZoomIn", id="zoomIn", transform="translate(%d,350)" % (cWidth-40-130-20),
onmouseover="magnify(evt,1.3,'in');", onmouseout="magnify(evt,1,'in');", onclick="zoomIt('in');"))
g.addElement(svg.use("#magnifyer", id="zoomOut", transform="translate(%d,350)" % (cWidth-40-130+20),
onmouseover="magnify(evt,1.3,'out');",onmouseout="magnify(evt,1,'out');", onclick="zoomIt('out');"))
drawSpace.addElement(g)
g = svg.group(id="statusBar")
g.addElement(svg.text(cWidth-40-260, 360, "ZOOM: 100%", style="fill:orange; font-size:14;", id="zoomValueObj"))
g.addElement(svg.text(cWidth-40-260, 380, "Status:", style="&colorText; &allText; &smallText;"))
g.addElement(svg.text(cWidth-40-260, 395, "Loading Plot", style="&colorText; &allText; &smallText;", id="statusText"))
drawSpace.addElement(g)
#draw main display area
drawSpaceMain= svg.svg((0, 0, mainSquare*cordZOOM, mainSquare*cordZOOM), mainSquare, mainSquare,
id="mainPlot",x="10",y="10")
mPlotWidth = mPlotHeight = 0.8*mainSquare*cordZOOM
drawSpaceMain.addElement(svg.rect(mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1, mPlotWidth, mPlotHeight,style="fill:white",
onmousemove="showChr(evt);", onmouseover="showChr(evt);", onmouseout="showNoChr(evt);"))
#draw grid
g = svg.group("grid", style="stroke:lightblue;stroke-width:3",
transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
if 1: #self.grid == "on":
js = []
for key in self.mouseChrLengthDict.keys():
length = self.mouseChrLengthDict[key]
js.append(mPlotWidth*length/cLength)
if length != 0:
yCoord = mPlotHeight*(1.0-length/cLength)
l = svg.line(0,yCoord ,mPlotWidth, yCoord)
g.addElement(l)
xCoord = mPlotWidth*length/cLength
l = svg.line(xCoord, 0 ,xCoord, mPlotHeight)
g.addElement(l)
js.sort()
drawSpace.addElement(svg.script("",language="javascript", cdata="var openURL=\"%s\";\nvar chrLength=%s;\n" % (self.openURL, js)))
g.addElement(svg.rect(0, 0, mPlotWidth, mPlotHeight,'none','black',10))
drawSpaceMain.addElement(g)
#draw Scale
g = svg.group("scale", style="stroke:black;stroke-width:0",
transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1))
i = 100
scaleFontSize = 11*cordZOOM
while i < cLength:
yCoord = mPlotHeight - mPlotHeight*i/cLength
l = svg.line(0,yCoord ,-5*cordZOOM, yCoord)
g.addElement(l)
t = svg.text(-40*cordZOOM, yCoord +5*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag Y
g.addElement(t)
xCoord = mPlotWidth*i/cLength
l = svg.line(xCoord, mPlotHeight, xCoord, mPlotHeight+5*cordZOOM)
g.addElement(l)
if i%200 == 0:
t = svg.text(xCoord, mPlotHeight+10*cordZOOM, "%d"% i, 100, "verdana") # coordinate tag X
g.addElement(t)
i += 100
drawSpaceMain.addElement(g)
#draw Points
finecolors = Plot.colorSpectrumSVG(12)
finecolors.reverse()
g = preColor = ""
for item in data:
_probeset, _chr, _Mb, _marker, _pvalue = item[2:]
try:
_idx = int((-math.log10(_pvalue))*12/6.0) # add module name
_color = finecolors[_idx]
except:
_color = finecolors[-1]
if _color != preColor:
preColor = _color
if g:
drawSpaceMain.addElement(g)
g = svg.group("points", style="stroke:%s;stroke-width:5" % _color,
transform="translate(%d,%d)" % (mainSquare*cordZOOM*0.1, mainSquare*cordZOOM*0.1),
onmouseover="mvMsgBox(evt);", onmouseout="hdMsgBox();", onmousedown="openPage(evt);")
else:
pass
px = mPlotWidth*item[0]/cLength
py = mPlotHeight*(1.0-item[1]/cLength)
l = svg.line("%2.1f" % (px-3*cordZOOM), "%2.1f" % py, "%2.1f" % (px+3*cordZOOM), "%2.1f" % py, ps=_probeset, mk=_marker)
g.addElement(l)
drawSpaceMain.addElement(g)
"""
#draw spectrum
i = 0
j = 0
middleoffsetX = 40
labelFont=pid.Font(ttf="tahoma",size=12,bold=0)
for dcolor in finecolors:
drawSpace.drawLine(xLeftOffset+ plotWidth + middleoffsetX -15 , plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth + middleoffsetX+15 , plotHeight + yTopOffset - i, color=dcolor)
if i % 50 == 0:
drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i, color=pid.black)
drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+5, font = labelFont)
j += 1
i += 1
drawSpace.drawLine(xLeftOffset+ plotWidth +middleoffsetX+15 ,plotHeight + yTopOffset - i+1, \
xLeftOffset+ plotWidth +middleoffsetX+20,plotHeight + yTopOffset - i+1, color=pid.black)
drawSpace.drawString("%1.1f" % -j , xLeftOffset+ plotWidth +middleoffsetX+25 ,plotHeight + yTopOffset - i+6, font = labelFont)
labelFont=pid.Font(ttf="tahoma",size=14,bold=1)
drawSpace.drawString("Log(pValue)" , xLeftOffset+ plotWidth +middleoffsetX+60 ,plotHeight + yTopOffset - 100, font = labelFont, angle =90)
labelFont=pid.Font(ttf="verdana",size=18,bold=0)
drawSpace.drawString(XLabel, xLeftOffset + (plotWidth -drawSpace.stringWidth(XLabel,font=labelFont))/2.0, plotHeight + yTopOffset +40, color=pid.blue, font=labelFont)
drawSpace.drawString(YLabel,xLeftOffset-60, plotHeight + yTopOffset-(plotHeight -drawSpace.stringWidth(YLabel,font=labelFont))/2.0, color=pid.blue, font=labelFont, angle =90)
"""
drawSpace.addElement(drawSpaceMain)
g= svg.group(id="dispBox", overflow="visible",
style="fill:white;stroke:orange;stroke-width:1;opacity:0.85;",
transform="translate(%d,650)" % (cWidth-40-300), visibility="hidden")
g.addElement(svg.rect(-80, -190, 300, 150, rx=10, ry=10))
g.addElement(svg.line(21, -40, 58, -40, style="stroke:white;"))
g.addElement(svg.polyline([[20, -40], [0, 0], [60, -40]]))
g.addElement(svg.text(-60, -160, "ProbeSet ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_probeset"))
g.addElement(svg.text(-60, -125, "Marker ", style="&colorText; &allText; &subtitleText; &strokeText;", id="_marker"))
drawSpace.addElement(g)
canvasSVG.setSVG(drawSpace) #set the svg of the drawing to the svg
return canvasSVG
