ymax = shifty + sizey
if(ymin > shifty - sizey):
ymin = shifty - sizey
# calculate the scaling factor
scalex = (xmax - xmin) / (SHIFTX * 3)
scaley = (ymax - ymin) / (SHIFTY * 3)
# open the SVG file
nameset = combiName[j]
svgfilename = sys.argv[1] + '-flower'
#for k in range(len(nameset)):
# svgfilename += ('-' + nameset[k])
svgfilename += str(combiRank[j])
svgfilename += '.svg'
svgfile = svg.openFile(svgfilename)
# for each motif in the combination
for k in range(len(nameset)):
# search for the motif and specify its ID
nameid = -1
for i in range(len(motifName)):
if(motifName[i].find(nameset[k]) >= 0):
nameid = i
break
# calculate the size and color of the ellipsoid
sizeval = math.log(motifNgenes[nameid]) * sizecoef
if(motifApvalue[nameid] > significance):
colorval = -math.log(motifApvalue[nameid] / significance)
def main():
if len(sys.argv) < 2:
print 'Usage: # python %s resultfilename (target(csv)filename) (value(tab)filename)' % sys.argv[0]
quit()
# default values of sizes of petals
EWIDTH = 120
EHEIGHT = 50
MINWIDTH = 120
MINHEIGHT = 40
# shift from the origin(=upper-left end)
SHIFTX = 400
SHIFTY = 400
# coeffcient for the adjustment of petal position
PETALPOSCOEF = 0.8
# coefficient for the adjustment of torus size
TORUSSIZECOEF = 1.2
# coefficients for size calculation
sizecoef = 0.3
# add command line options
parser = OptionParser()
parser.add_option("--ewidth", "--EWIDTH", dest="EWIDTH", default="120")
parser.add_option("--eheight", "--EHEIGHT", dest="EHEIGHT", default="50")
parser.add_option("--minwidth", "--MINWIDTH", dest="MINWIDTH", default="120")
parser.add_option("--minheight", "--MINHEIGHT", dest="MINHEIGHT", default="40")
parser.add_option("--shiftx", "--SHIFTX", dest="SHIFTX", default="400")
parser.add_option("--shifty", "--SHIFTY", dest="SHIFTY", default="400")
parser.add_option("--petalposcoef", "--PETALPOSCOEF", dest="PETALPOSCOEF", default="0.8")
parser.add_option("--torussizecoef", "--TORUSSIZECOEF", dest="TORUSSIZECOEF", default="1.2")
(options, args) = parser.parse_args()
EWIDTH = int(options.EWIDTH)
EHEIGHT = int(options.EHEIGHT)
MINWIDTH = int(options.MINWIDTH)
MINHEIGHT = int(options.MINHEIGHT)
SHIFTX = int(options.SHIFTX)
SHIFTY = int(options.SHIFTY)
PETALPOSCOEF = float(options.PETALPOSCOEF)
TORUSSIZECOEF = float(options.TORUSSIZECOEF)
# read the result file
csvfname = ''
tabfname = ''
if len(sys.argv) > 3:
cfvfname = sys.argv[2]
tabfname = sys.argv[3]
significance = readfile.readResult(sys.argv[1], csvfname, tabfname)
colorvalMin = -math.log(1.0 / significance)
# for each combination
for j in range(len(combiName)):
# reset the end position values
xmin = 1.0e+30
xmax = -1.0e+30
ymin = 1.0e+30
ymax = -1.0e+30
# determine the scale of drawing
nameset = combiName[j]
for k in range(len(nameset)):
# search for the motif and specify its ID
nameid = -1
for i in range(len(motifName)):
if(motifName[i].find(nameset[k]) >= 0):
nameid = i
break
# calculate the end position values
sizeval = math.log(motifNgenes[nameid]) * sizecoef
rad = k * math.pi * 2 / len(combiName[j]) - math.pi * 0.5
sizex = EWIDTH * sizeval
sizey = EHEIGHT * sizeval
shiftx = (math.cos(rad) * (sizex - EHEIGHT * 2)) + SHIFTX
shifty = (math.sin(rad) * (sizex - EHEIGHT * 2)) + SHIFTY
if(xmax < shiftx + sizex):
xmax = shiftx + sizex
if(xmin > shiftx - sizex):
xmin = shiftx - sizex
if(ymax < shifty + sizey):
ymax = shifty + sizey
if(ymin > shifty - sizey):
ymin = shifty - sizey
# calculate the scaling factor
scalex = (xmax - xmin) / (SHIFTX * 3)
scaley = (ymax - ymin) / (SHIFTY * 3)
# open the SVG file
nameset = combiName[j]
svgfilename = sys.argv[1] + '-flower'
#for k in range(len(nameset)):
# svgfilename += ('-' + nameset[k])
svgfilename += str(combiRank[j])
svgfilename += '.svg'
svgfile = svg.openFile(svgfilename)
# for each motif in the combination
for k in range(len(nameset)):
# search for the motif and specify its ID
nameid = -1
for i in range(len(motifName)):
if(motifName[i].find(nameset[k]) >= 0):
nameid = i
break
# calculate the size and color of the ellipsoid
sizeval = math.log(motifNgenes[nameid]) * sizecoef
if(motifApvalue[nameid] > significance):
colorval = -math.log(motifApvalue[nameid] / significance)
if(colorval < colorvalMin):
colorval = colorvalMin
if(motifApvalue[nameid] <= significance):
colorval = motifApvalue[nameid] / significance
# initialize variables before calculating the shape of the ellipsoid
rad = k * math.pi * 2 / len(combiName[j]) - math.pi * 0.5
sizex = EWIDTH * sizeval * scalex
sizey = EHEIGHT * sizeval * scaley
if(sizex < MINWIDTH):
sizex = MINWIDTH
if(sizey < MINHEIGHT):
sizey = MINHEIGHT
shiftx = (math.cos(rad) * (sizex - EHEIGHT * PETALPOSCOEF)) + SHIFTX
shifty = (math.sin(rad) * (sizex - EHEIGHT * PETALPOSCOEF)) + SHIFTY
annox = (math.cos(rad) * (sizex * 2 - EHEIGHT * PETALPOSCOEF)) + SHIFTX
annoy = (math.sin(rad) * (sizex * 2 - EHEIGHT * PETALPOSCOEF)) + SHIFTY
# draw a motif
svg.drawMotif(sizex, sizey, shiftx, shifty, rad, colorval, svgfile)
svg.annotateMotif(motifName[nameid], motifApvalue[nameid],
annox, annoy, svgfile)
# draw the combination
colorval = combiApvalue[j] / significance
size = EHEIGHT * scalex * TORUSSIZECOEF
if(size < MINHEIGHT):
size = MINHEIGHT
svg.drawMotif(size, size, SHIFTX, SHIFTY, 0.0, colorval, svgfile)
svg.annotateMotif("", combiApvalue[j], SHIFTX-30, SHIFTY-5, svgfile)
# close the SVG file
svg.closeFile(svgfile)
ymax = shifty + sizey
if (ymin > shifty - sizey):
ymin = shifty - sizey
# calculate the scaling factor
scalex = (xmax - xmin) / (SHIFTX * 3)
scaley = (ymax - ymin) / (SHIFTY * 3)
# open the SVG file
nameset = combiName[j]
svgfilename = sys.argv[1] + '-flower'
#for k in range(len(nameset)):
# svgfilename += ('-' + nameset[k])
svgfilename += str(combiRank[j])
svgfilename += '.svg'
svgfile = svg.openFile(svgfilename)
# for each motif in the combination
for k in range(len(nameset)):
# search for the motif and specify its ID
nameid = -1
for i in range(len(motifName)):
if (motifName[i].find(nameset[k]) >= 0):
nameid = i
break
# calculate the size and color of the ellipsoid
sizeval = math.log(motifNgenes[nameid]) * sizecoef
if (motifApvalue[nameid] > significance):
colorval = -math.log(motifApvalue[nameid] / significance)
