def _setOutputDevice(self, fn, height, width):
from proto.RSetup import r
if fn.endswith('.pdf'):
# self.LINE_HEIGHT = self.POINT_SIZE
r.pdf(fn,
height=height * 1.0 / 72,
width=width * 1.0 / 72,
pointsize=self.POINT_SIZE)
elif fn.endswith('.png'):
# if any(x > 800 for x in [width, height]):
# if self.HIGH_DEF_COLORS:
# picType = 'png16m'
# else:
# picType = 'png256'
#
# # self.LINE_HEIGHT = self.POINT_SIZE
# r.bitmap(fn, height=height, width=width, units='px', type=picType, pointsize=self.POINT_SIZE)
# else:
# self.LINE_HEIGHT = self.POINT_SIZE * 1.38 # for r.png(). Don't know why
r.png(filename=fn,
height=height,
width=width,
units='px',
pointsize=self.POINT_SIZE,
res=72,
type='cairo')
else:
raise ShouldNotOccurError
def openRFigure(self, h=600, w=800):
from proto.RSetup import r
r.png(filename=self.getDiskPath(True),
height=h,
width=w,
units='px',
pointsize=12,
res=72)
def makeTrackImage(cls, res, fn, main):
from proto.RSetup import r
resDictKey = 'Result'
POINT_SIZE = 12
LINE_HEIGHT = POINT_SIZE * 1.38
ensurePathExists(fn)
bmpFn = fn
width = 1000
height = 30 *min(100, len(res))
picType = 'png256'
r.png(filename=bmpFn, height=max([200, height]), width=width, units='px', pointsize=POINT_SIZE, res=72)
if resDictKey is not None:
xlab = res.getLabelHelpPair(resDictKey)[0]
else:
xlab = None
rCode = ''' par(mar=c(4.2, 0.2, 0.2, 14.2))\n
plot.new()\n
plot.window(xlim=c(0,%i),ylim=c(0,%i))\n
axis(1)\n
axis(4, at=((1:%i)*30)-21, lab=c(%s), las=1)\n
%s
'''
yFloor = 1
rectTemplate = 'rect(%f,%i,%f,%i, col="%s", border="%s")\n'
rectVals = []
globRes = res.getGlobalResult()
visRes = globRes.values()[0]
rawData = visRes.getAllTrackViews()
yLabels = []
maxVal = max([tv._bpSize() for tv in rawData])
halfMax = maxVal/2
for tv in rawData:
yLabels.append('"'+tv.genomeAnchor.chr+': %s"'% ':'.join(str(tv.genomeAnchor).split()[0].split(':')[1:]))
startArr, endArr = tv.startsAsNumpyArray(),tv.endsAsNumpyArray()
if tv.normalizeRows:
normalizer = 1000.0/tv._bpSize() if len(endArr)>0 else 0
maxVal = 1000
rectVals.append(rectTemplate % (0, yFloor+8, 1000, yFloor+8, 'lightgray', 'lightgray') )
rectVals += [rectTemplate % (start*normalizer, yFloor, end*normalizer, yFloor+15, 'red', 'red') for start, end in zip(startArr, endArr)]
else:
extra1=extra2 = 0
if tv.centerRows:
halfBin = tv._bpSize()/2
extra1 = halfMax-halfBin
extra2 = halfMax+halfBin
rectVals.append(rectTemplate % (0+extra1, yFloor+8, extra2 if tv.centerRows else tv._bpSize() , yFloor+5, 'lightgray', 'lightgray') )
rectVals += [rectTemplate % (start+extra1, yFloor, end+extra1, yFloor+15, 'red', 'red') for start, end in zip(startArr, endArr)]
yFloor+=30
if len(rectTemplate)>0:
rScript = rCode % (maxVal, height, len(yLabels), ','.join(yLabels), '\n'.join(rectVals))
r(rScript)