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-rwxr-xr-xwqflask/utility/AJAX_table.py224
-rwxr-xr-xwqflask/utility/Plot.py2304
-rwxr-xr-xwqflask/utility/TDCell.py15
-rwxr-xr-xwqflask/utility/THCell.py16
-rwxr-xr-xwqflask/utility/svg.py133
-rwxr-xr-xwqflask/utility/webqtlUtil.py1459
6 files changed, 2073 insertions, 2078 deletions
diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py
index 963a530e..083d1c0d 100755
--- a/wqflask/utility/AJAX_table.py
+++ b/wqflask/utility/AJAX_table.py
@@ -39,115 +39,115 @@ import webqtlUtil
class AJAX_table:
- def __init__(self, fd):
- file = fd.formdata.getfirst("file", "")
- sort = fd.formdata.getfirst("sort", "")
- order = fd.formdata.getfirst("order", "up")
- cmd = fd.formdata.getfirst("cmd", "")
- tableID = fd.formdata.getfirst("tableID", "")
- addIndex = fd.formdata.getfirst("addIndex", "1")
- hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "")
- hiddenColumns = hiddenColumnsString.split(',')
-
- try:
- fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb')
- tblobj = cPickle.load(fp)
- fp.close()
-
- if cmd == 'addCorr':
- dbId = int(fd.formdata.getfirst("db"))
- dbFullName = fd.formdata.getfirst("dbname")
- trait = fd.formdata.getfirst("trait")
- form = fd.formdata.getfirst("form")
- ids = fd.formdata.getfirst("ids")
- vals = fd.formdata.getfirst("vals")
- ids = eval(ids)
- nnCorr = len(ids)
- vals = eval(vals)
-
- workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
- worksheet = workbook.add_worksheet()
-
- con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
- cursor = con.cursor()
-
- cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId)
- dbName, dbShortName = cursor.fetchone()
-
- tblobj['header'][0].append(
- THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"),
- text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1),
- )
-
- headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
- for i, item in enumerate(tblobj['header'][0]):
- if (i > 0):
- worksheet.write([8, i-1], item.text, headingStyle)
- worksheet.set_column([i-1, i-1], 2*len(item.text))
-
- for i, row in enumerate(tblobj['body']):
- ProbeSetId = row[1].text
- #XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData
- cursor.execute("""
- Select ProbeSetData.StrainId, ProbeSetData.Value
- From ProbeSetData, ProbeSetXRef, ProbeSet
- where ProbeSetXRef.ProbeSetFreezeId = %d AND
- ProbeSetXRef.DataId = ProbeSetData.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSet.Name = '%s'
- """ % (dbId, ProbeSetId))
- results = cursor.fetchall()
- vdict = {}
- for item in results:
- vdict[item[0]] = item[1]
- newvals = []
- for id in ids:
- if vdict.has_key(id):
- newvals.append(vdict[id])
- else:
- newvals.append(None)
- corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr)
- repr = '%0.4f' % corr
- row.append(
- TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr))
- )
-
- last_row=0
- for j, item in enumerate(tblobj['body'][i]):
- if (j > 0):
- worksheet.write([9+i, j-1], item.text)
- last_row = 9+i
- last_row += 1
-
- titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
- ##Write title Info
- # Modified by Hongqiang Li
- worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
- worksheet.write([1, 0], "Trait : %s" % trait, titleStyle)
- worksheet.write([2, 0], "Database : %s" % dbFullName, titleStyle)
- worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
- worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
- worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
- #Write footer info
- worksheet.write([1 + last_row, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
- worksheet.write([2 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
-
- cursor.close()
- workbook.close()
-
- objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb')
- cPickle.dump(tblobj, objfile)
- objfile.close()
- else:
- pass
-
- self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns))
-
- except:
- self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>"
-
- def __str__(self):
- return self.value
-
- def write(self):
- return str(self)
+ def __init__(self, fd):
+ file = fd.formdata.getfirst("file", "")
+ sort = fd.formdata.getfirst("sort", "")
+ order = fd.formdata.getfirst("order", "up")
+ cmd = fd.formdata.getfirst("cmd", "")
+ tableID = fd.formdata.getfirst("tableID", "")
+ addIndex = fd.formdata.getfirst("addIndex", "1")
+ hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "")
+ hiddenColumns = hiddenColumnsString.split(',')
+
+ try:
+ fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb')
+ tblobj = cPickle.load(fp)
+ fp.close()
+
+ if cmd == 'addCorr':
+ dbId = int(fd.formdata.getfirst("db"))
+ dbFullName = fd.formdata.getfirst("dbname")
+ trait = fd.formdata.getfirst("trait")
+ form = fd.formdata.getfirst("form")
+ ids = fd.formdata.getfirst("ids")
+ vals = fd.formdata.getfirst("vals")
+ ids = eval(ids)
+ nnCorr = len(ids)
+ vals = eval(vals)
+
+ workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
+ worksheet = workbook.add_worksheet()
+
+ con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
+ cursor = con.cursor()
+
+ cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId)
+ dbName, dbShortName = cursor.fetchone()
+
+ tblobj['header'][0].append(
+ THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"),
+ text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1),
+ )
+
+ headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
+ for i, item in enumerate(tblobj['header'][0]):
+ if (i > 0):
+ worksheet.write([8, i-1], item.text, headingStyle)
+ worksheet.set_column([i-1, i-1], 2*len(item.text))
+
+ for i, row in enumerate(tblobj['body']):
+ ProbeSetId = row[1].text
+ #XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData
+ cursor.execute("""
+ Select ProbeSetData.StrainId, ProbeSetData.Value
+ From ProbeSetData, ProbeSetXRef, ProbeSet
+ where ProbeSetXRef.ProbeSetFreezeId = %d AND
+ ProbeSetXRef.DataId = ProbeSetData.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSet.Name = '%s'
+ """ % (dbId, ProbeSetId))
+ results = cursor.fetchall()
+ vdict = {}
+ for item in results:
+ vdict[item[0]] = item[1]
+ newvals = []
+ for id in ids:
+ if vdict.has_key(id):
+ newvals.append(vdict[id])
+ else:
+ newvals.append(None)
+ corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr)
+ repr = '%0.4f' % corr
+ row.append(
+ TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr))
+ )
+
+ last_row=0
+ for j, item in enumerate(tblobj['body'][i]):
+ if (j > 0):
+ worksheet.write([9+i, j-1], item.text)
+ last_row = 9+i
+ last_row += 1
+
+ titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
+ ##Write title Info
+ # Modified by Hongqiang Li
+ worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
+ worksheet.write([1, 0], "Trait : %s" % trait, titleStyle)
+ worksheet.write([2, 0], "Database : %s" % dbFullName, titleStyle)
+ worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
+ worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
+ worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
+ #Write footer info
+ worksheet.write([1 + last_row, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
+ worksheet.write([2 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
+
+ cursor.close()
+ workbook.close()
+
+ objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb')
+ cPickle.dump(tblobj, objfile)
+ objfile.close()
+ else:
+ pass
+
+ self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns))
+
+ except:
+ self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>"
+
+ def __str__(self):
+ return self.value
+
+ def write(self):
+ return str(self)
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index e00b8e9e..04fe85bf 100755
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -39,1245 +39,1245 @@ from base import webqtlConfig
def cformat(d, rank=0):
- 'custom string format'
- strD = "%2.6f" % d
-
- if rank == 0:
- while strD[-1] in ('0','.'):
- if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
- break
- elif strD[-1] == '.':
- strD = strD[:-1]
- break
- else:
- strD = strD[:-1]
-
- else:
- strD = strD.split(".")[0]
-
- if strD == '-0.0':
- strD = '0.0'
- return strD
+ 'custom string format'
+ strD = "%2.6f" % d
+
+ if rank == 0:
+ while strD[-1] in ('0','.'):
+ if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
+ break
+ elif strD[-1] == '.':
+ strD = strD[:-1]
+ break
+ else:
+ strD = strD[:-1]
+
+ else:
+ strD = strD.split(".")[0]
+
+ if strD == '-0.0':
+ strD = '0.0'
+ return strD
def frange(start, end=None, inc=1.0):
- "A faster range-like function that does accept float increments..."
- if end == None:
- end = start + 0.0
- start = 0.0
- else:
- start += 0.0 # force it to be a float
- count = int((end - start) / inc)
- if start + count * inc != end:
- # Need to adjust the count. AFAICT, it always comes up one short.
- count += 1
- L = [start] * count
- for i in xrange(1, count):
- L[i] = start + i * inc
- return L
+ "A faster range-like function that does accept float increments..."
+ if end == None:
+ end = start + 0.0
+ start = 0.0
+ else:
+ start += 0.0 # force it to be a float
+ count = int((end - start) / inc)
+ if start + count * inc != end:
+ # Need to adjust the count. AFAICT, it always comes up one short.
+ count += 1
+ L = [start] * count
+ for i in xrange(1, count):
+ L[i] = start + i * inc
+ return L
def gammln(xx):
- cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5]
- x=xx-1.0
- tmp=x+5.5
- tmp -=(x+0.5)*log(tmp)
- ser=1.0
- for item in cof:
- x+=1.0
- ser+=item/x
+ cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5]
+ x=xx-1.0
+ tmp=x+5.5
+ tmp -=(x+0.5)*log(tmp)
+ ser=1.0
+ for item in cof:
+ x+=1.0
+ ser+=item/x
- return -tmp+log(2.50662827465*ser)
+ return -tmp+log(2.50662827465*ser)
def gser(a,x):
- gln=gammln(a)
- ITMAX=100
- EPS=3.0e-7
-
- if x<=0.0:
- gamser=0.0
- return [gamser,gln]
- else:
- ap=a
- sum=1.0/a
- dele=sum
- for i in range(1,ITMAX+1):
- ap+=1.0
- dele*=x/ap
- sum+=dele
- if abs(dele)<abs(sum)*EPS:
- gamser=sum*exp(-x+a*log(x)-gln)
- return [gamser,gln]
- return None
+ gln=gammln(a)
+ ITMAX=100
+ EPS=3.0e-7
+
+ if x<=0.0:
+ gamser=0.0
+ return [gamser,gln]
+ else:
+ ap=a
+ sum=1.0/a
+ dele=sum
+ for i in range(1,ITMAX+1):
+ ap+=1.0
+ dele*=x/ap
+ sum+=dele
+ if abs(dele)<abs(sum)*EPS:
+ gamser=sum*exp(-x+a*log(x)-gln)
+ return [gamser,gln]
+ return None
def gcf(a,x):
- ITMAX=100
- EPS=3.0e-7
- gold=0.0
- fac=1
- b1=1.0
- b0=0.0
- a0=1.0
- gln=gammln(a)
-
- a1=x
- for n in range(1,ITMAX+1):
- an=n+0.0
- ana=an-a
- a0=(a1+a0*ana)*fac
- b0=(b1+b0*ana)*fac
- anf=an*fac
- a1=x*a0+anf*a1
- b1=x*b0+anf*b1
- if (a1):
- fac=1.0/a1
- g=b1*fac
- if abs((g-gold)/g)<EPS:
- gammcf=exp(-x+a*log(x)-gln)*g
- return [gammcf,gln]
- gold=g
- return None
+ ITMAX=100
+ EPS=3.0e-7
+ gold=0.0
+ fac=1
+ b1=1.0
+ b0=0.0
+ a0=1.0
+ gln=gammln(a)
+
+ a1=x
+ for n in range(1,ITMAX+1):
+ an=n+0.0
+ ana=an-a
+ a0=(a1+a0*ana)*fac
+ b0=(b1+b0*ana)*fac
+ anf=an*fac
+ a1=x*a0+anf*a1
+ b1=x*b0+anf*b1
+ if (a1):
+ fac=1.0/a1
+ g=b1*fac
+ if abs((g-gold)/g)<EPS:
+ gammcf=exp(-x+a*log(x)-gln)*g
+ return [gammcf,gln]
+ gold=g
+ return None
def gammp(a,x):
- if x<0.0 or a<=0.0:
- return None
- if x<(a+1.0):
- a=gser(a,x)[0]
- return a
- else:
- a=gcf(a,x)[0]
- return 1.0-a
+ if x<0.0 or a<=0.0:
+ return None
+ if x<(a+1.0):
+ a=gser(a,x)[0]
+ return a
+ else:
+ a=gcf(a,x)[0]
+ return 1.0-a
def U(n):
- x=pow(0.5,1.0/n)
- m=[1-x]
- for i in range(2,n):
- a=(i-0.3175)/(n+0.365)
- m.append(a)
- m.append(x)
- return m
+ x=pow(0.5,1.0/n)
+ m=[1-x]
+ for i in range(2,n):
+ a=(i-0.3175)/(n+0.365)
+ m.append(a)
+ m.append(x)
+ return m
def erf(x):
- if x<0.0:
- return -gammp(0.5,x*x)
- else:
- return gammp(0.5,x*x)
+ if x<0.0:
+ return -gammp(0.5,x*x)
+ else:
+ return gammp(0.5,x*x)
def erfcc(x):
- z=abs(x)
- t=1.0/(1.0+0.5*z)
- ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
- if x>=0.0:
- return ans
- else:
- return 2.0-ans
+ z=abs(x)
+ t=1.0/(1.0+0.5*z)
+ ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
+ if x>=0.0:
+ return ans
+ else:
+ return 2.0-ans
def calMeanVar(data):
- n=len(data)
- if n<2:
- return None
- else:
- sum=reduce(lambda x,y:x+y,data,0.0)
- mean=sum/n
- z=data[:]
- for i in range(n):
- z[i]=z[i]-mean
- variance=reduce(lambda x,y:x+y*y,z,0.0)
- variance /= n-1
- variance =sqrt(variance)
- for i in range(n):
- z[i]=z[i]/variance
- return z
+ n=len(data)
+ if n<2:
+ return None
+ else:
+ sum=reduce(lambda x,y:x+y,data,0.0)
+ mean=sum/n
+ z=data[:]
+ for i in range(n):
+ z[i]=z[i]-mean
+ variance=reduce(lambda x,y:x+y*y,z,0.0)
+ variance /= n-1
+ variance =sqrt(variance)
+ for i in range(n):
+ z[i]=z[i]/variance
+ return z
def inverseCumul(p):
- #Coefficients in rational approximations.
- a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
+ #Coefficients in rational approximations.
+ a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
- b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
+ b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
- c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
+ c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
- d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
+ d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
- #Define break-points.
+ #Define break-points.
- p_low = 0.02425
- p_high = 1 - p_low
+ p_low = 0.02425
+ p_high = 1 - p_low
- #Rational approximation for lower region.
+ #Rational approximation for lower region.
- if p > 0 and p < p_low:
- q = sqrt(-2*log(p))
- x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
+ if p > 0 and p < p_low:
+ q = sqrt(-2*log(p))
+ x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
- #Rational approximation for central region.
+ #Rational approximation for central region.
- elif p>= p_low and p <= p_high:
- q = p - 0.5
- r = q*q
- x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
+ elif p>= p_low and p <= p_high:
+ q = p - 0.5
+ r = q*q
+ x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
- #Rational approximation for upper region.
+ #Rational approximation for upper region.
- elif p>p_high and p < 1:
- q = sqrt(-2*log(1-p))
- x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
+ elif p>p_high and p < 1:
+ q = sqrt(-2*log(1-p))
+ x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
- else:
- return None
+ else:
+ return None
- if p>0 and p < 1:
- e = 0.5 * erfcc(-x/sqrt(2)) - p
- u = e * sqrt(2*pi) * exp(x*x/2)
- x = x - u/(1 + x*u/2)
- return x
- else:
- return None
+ if p>0 and p < 1:
+ e = 0.5 * erfcc(-x/sqrt(2)) - p
+ u = e * sqrt(2*pi) * exp(x*x/2)
+ x = x - u/(1 + x*u/2)
+ return x
+ else:
+ return None
def gmean(lst):
- N = len(lst)
- if N == 0:
- return 0
- else:
- return (reduce(lambda x,y: x+y, lst, 0.0))/N
+ N = len(lst)
+ if N == 0:
+ return 0
+ else:
+ return (reduce(lambda x,y: x+y, lst, 0.0))/N
def gmedian(lst2):
- lst = lst2[:]
- N = len(lst)
- if N == 0:
- return 0
- else:
- lst.sort()
- if N % 2 == 0:
- return (lst[N/2]+lst[(N-2)/2])/2.0
- else:
- return lst[(N-1)/2]
+ lst = lst2[:]
+ N = len(lst)
+ if N == 0:
+ return 0
+ else:
+ lst.sort()
+ if N % 2 == 0:
+ return (lst[N/2]+lst[(N-2)/2])/2.0
+ else:
+ return lst[(N-1)/2]
def gpercentile(lst2, np):
- lst = lst2[:]
- N = len(lst)
- if N == 0 or np > 100 or np < 0:
- return None
- else:
- lst.sort()
- pNadd1 = (np/100.0)*N
- k = int(pNadd1)
- d = pNadd1 - k
- if k == 0:
- return lst[0]
- elif k >= N-1:
- return lst[N-1]
- else:
- return lst[k-1] + d*(lst[k] - lst[k-1])
+ lst = lst2[:]
+ N = len(lst)
+ if N == 0 or np > 100 or np < 0:
+ return None
+ else:
+ lst.sort()
+ pNadd1 = (np/100.0)*N
+ k = int(pNadd1)
+ d = pNadd1 - k
+ if k == 0:
+ return lst[0]
+ elif k >= N-1:
+ return lst[N-1]
+ else:
+ return lst[k-1] + d*(lst[k] - lst[k-1])
def findOutliers(vals):
- valsOnly = []
- dataXZ = vals[:]
- for i in range(len(dataXZ)):
- valsOnly.append(dataXZ[i][1])
-
- data = [('', valsOnly[:])]
-
- for item in data:
- itemvalue = item[1]
- nValue = len(itemvalue)
- catValue = []
-
- for item2 in itemvalue:
- try:
- tstrain, tvalue = item2
- except:
- tvalue = item2
- if nValue <= 4:
- continue
- else:
- catValue.append(tvalue)
-
- if catValue != []:
- lowHinge = gpercentile(catValue, 25)
- upHinge = gpercentile(catValue, 75)
- Hstep = 1.5*(upHinge - lowHinge)
-
- outlier = []
- extreme = []
-
- upperBound = upHinge + Hstep
- lowerBound = lowHinge - Hstep
-
- for item in catValue:
- if item >= upHinge + 2*Hstep:
- extreme.append(item)
- elif item >= upHinge + Hstep:
- outlier.append(item)
- else:
- pass
-
- for item in catValue:
- if item <= lowHinge - 2*Hstep:
- extreme.append(item)
- elif item <= lowHinge - Hstep:
- outlier.append(item)
- else:
- pass
- else:
- upperBound = 1000
- lowerBound = -1000
-
- return upperBound, lowerBound
+ valsOnly = []
+ dataXZ = vals[:]
+ for i in range(len(dataXZ)):
+ valsOnly.append(dataXZ[i][1])
+
+ data = [('', valsOnly[:])]
+
+ for item in data:
+ itemvalue = item[1]
+ nValue = len(itemvalue)
+ catValue = []
+
+ for item2 in itemvalue:
+ try:
+ tstrain, tvalue = item2
+ except:
+ tvalue = item2
+ if nValue <= 4:
+ continue
+ else:
+ catValue.append(tvalue)
+
+ if catValue != []:
+ lowHinge = gpercentile(catValue, 25)
+ upHinge = gpercentile(catValue, 75)
+ Hstep = 1.5*(upHinge - lowHinge)
+
+ outlier = []
+ extreme = []
+
+ upperBound = upHinge + Hstep
+ lowerBound = lowHinge - Hstep
+
+ for item in catValue:
+ if item >= upHinge + 2*Hstep:
+ extreme.append(item)
+ elif item >= upHinge + Hstep:
+ outlier.append(item)
+ else:
+ pass
+
+ for item in catValue:
+ if item <= lowHinge - 2*Hstep:
+ extreme.append(item)
+ elif item <= lowHinge - Hstep:
+ outlier.append(item)
+ else:
+ pass
+ else:
+ upperBound = 1000
+ lowerBound = -1000
+
+ return upperBound, lowerBound
def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- iValues = []
- for item in data:
- for item2 in item[1]:
- try:
- iValues.append(item2[1])
- except:
- iValues.append(item2)
-
- #draw frame
- max_Y = max(iValues)
- min_Y = min(iValues)
- scaleY = detScale(min_Y, max_Y)
- Yll = scaleY[0]
- Yur = scaleY[1]
- nStep = scaleY[2]
- stepY = (Yur - Yll)/nStep
- stepYPixel = plotHeight/(nStep)
- canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
-
- ##draw Y Scale
- YYY = Yll
- YCoord = plotHeight + yTopOffset
- scaleFont=pid.Font(ttf="cour",size=11,bold=1)
- for i in range(nStep+1):
- strY = cformat(d=YYY, rank=0)
- YCoord = max(YCoord, yTopOffset)
- canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
- canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont)
- YYY += stepY
- YCoord -= stepYPixel
-
- ##draw X Scale
- stepX = plotWidth/len(data)
- XCoord = xLeftOffset + 0.5*stepX
- YCoord = plotHeight + yTopOffset
- scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
- labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
- for item in data:
- itemname, itemvalue = item
- canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
- canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\
- YCoord +20,font=labelFont)
-
- nValue = len(itemvalue)
- catValue = []
- for item2 in itemvalue:
- try:
- tstrain, tvalue = item2
- except:
- tvalue = item2
- if nValue <= 4:
- canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
- else:
- catValue.append(tvalue)
- if catValue != []:
- catMean = gmean(catValue)
- catMedian = gmedian(catValue)
- lowHinge = gpercentile(catValue, 25)
- upHinge = gpercentile(catValue, 75)
- Hstep = 1.5*(upHinge - lowHinge)
-
- outlier = []
- extrem = []
-
- upperAdj = None
- for item in catValue:
- if item >= upHinge + 2*Hstep:
- extrem.append(item)
- elif item >= upHinge + Hstep:
- outlier.append(item)
- elif item > upHinge and item < upHinge + Hstep:
- if upperAdj == None or item > upperAdj:
- upperAdj = item
- else:
- pass
- lowerAdj = None
- for item in catValue:
- if item <= lowHinge - 2*Hstep:
- extrem.append(item)
- elif item <= lowHinge - Hstep:
- outlier.append(item)
- if item < lowHinge and item > lowHinge - Hstep:
- if lowerAdj == None or item < lowerAdj:
- lowerAdj = item
- else:
- pass
- canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
- XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
- canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
- XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
- if upperAdj != None:
- canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
- XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
- canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
- XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
- if lowerAdj != None:
- canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
- XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
- canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
- XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-
- outlierFont = pid.Font(ttf="cour",size=12,bold=0)
- if outlier != []:
- for item in outlier:
- yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
- #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
- canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
- if extrem != []:
- for item in extrem:
- yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
- #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
- canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
-
- canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
- color=pid.blue,size=3)
- #print (catMean, catMedian, cat25per, cat75per)
- pass
-
- XCoord += stepX
-
- labelFont=pid.Font(ttf="verdana",size=18,bold=0)
- canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \
- YCoord +40, font=labelFont)
- canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
- font=labelFont, angle =90)
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ iValues = []
+ for item in data:
+ for item2 in item[1]:
+ try:
+ iValues.append(item2[1])
+ except:
+ iValues.append(item2)
+
+ #draw frame
+ max_Y = max(iValues)
+ min_Y = min(iValues)
+ scaleY = detScale(min_Y, max_Y)
+ Yll = scaleY[0]
+ Yur = scaleY[1]
+ nStep = scaleY[2]
+ stepY = (Yur - Yll)/nStep
+ stepYPixel = plotHeight/(nStep)
+ canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
+
+ ##draw Y Scale
+ YYY = Yll
+ YCoord = plotHeight + yTopOffset
+ scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ for i in range(nStep+1):
+ strY = cformat(d=YYY, rank=0)
+ YCoord = max(YCoord, yTopOffset)
+ canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
+ canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont)
+ YYY += stepY
+ YCoord -= stepYPixel
+
+ ##draw X Scale
+ stepX = plotWidth/len(data)
+ XCoord = xLeftOffset + 0.5*stepX
+ YCoord = plotHeight + yTopOffset
+ scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
+ labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
+ for item in data:
+ itemname, itemvalue = item
+ canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
+ canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\
+ YCoord +20,font=labelFont)
+
+ nValue = len(itemvalue)
+ catValue = []
+ for item2 in itemvalue:
+ try:
+ tstrain, tvalue = item2
+ except:
+ tvalue = item2
+ if nValue <= 4:
+ canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
+ else:
+ catValue.append(tvalue)
+ if catValue != []:
+ catMean = gmean(catValue)
+ catMedian = gmedian(catValue)
+ lowHinge = gpercentile(catValue, 25)
+ upHinge = gpercentile(catValue, 75)
+ Hstep = 1.5*(upHinge - lowHinge)
+
+ outlier = []
+ extrem = []
+
+ upperAdj = None
+ for item in catValue:
+ if item >= upHinge + 2*Hstep:
+ extrem.append(item)
+ elif item >= upHinge + Hstep:
+ outlier.append(item)
+ elif item > upHinge and item < upHinge + Hstep:
+ if upperAdj == None or item > upperAdj:
+ upperAdj = item
+ else:
+ pass
+ lowerAdj = None
+ for item in catValue:
+ if item <= lowHinge - 2*Hstep:
+ extrem.append(item)
+ elif item <= lowHinge - Hstep:
+ outlier.append(item)
+ if item < lowHinge and item > lowHinge - Hstep:
+ if lowerAdj == None or item < lowerAdj:
+ lowerAdj = item
+ else:
+ pass
+ canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
+ XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
+ canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
+ XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
+ if upperAdj != None:
+ canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
+ XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
+ canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
+ XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
+ if lowerAdj != None:
+ canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
+ XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
+ canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
+ XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
+
+ outlierFont = pid.Font(ttf="cour",size=12,bold=0)
+ if outlier != []:
+ for item in outlier:
+ yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
+ #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
+ canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
+ if extrem != []:
+ for item in extrem:
+ yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
+ #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
+ canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
+
+ canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
+ color=pid.blue,size=3)
+ #print (catMean, catMedian, cat25per, cat75per)
+ pass
+
+ XCoord += stepX
+
+ labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+ canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \
+ YCoord +40, font=labelFont)
+ canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
+ font=labelFont, angle =90)
def plotSecurity(canvas, text="12345"):
- if not text:
- return
-
- plotWidth = canvas.size[0]
- plotHeight = canvas.size[1]
- if plotHeight<=0 or plotWidth<=0:
- return
-
- bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
- canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor)
-
- for i in range(30):
- randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
- scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50)))
- canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'),
- int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont,
- color=randomColor, angle=random.choice(range(-45, 50)))
-
- step = (plotWidth-20)/len(text)
- startX = 20
- for item in text:
- randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random())
- scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1)
- canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont,
- color=randomColor, angle=random.choice(range(-45, 50)))
- startX += step
+ if not text:
+ return
+
+ plotWidth = canvas.size[0]
+ plotHeight = canvas.size[1]
+ if plotHeight<=0 or plotWidth<=0:
+ return
+
+ bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
+ canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor)
+
+ for i in range(30):
+ randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
+ scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50)))
+ canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'),
+ int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont,
+ color=randomColor, angle=random.choice(range(-45, 50)))
+
+ step = (plotWidth-20)/len(text)
+ startX = 20
+ for item in text:
+ randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random())
+ scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1)
+ canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont,
+ color=randomColor, angle=random.choice(range(-45, 50)))
+ startX += step
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- if plotHeight<=0 or plotWidth<=0:
- return
-
- if len(data) < 2:
- return
-
- max_D = max(data)
- min_D = min(data)
- #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
- if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
- max_D=webqtlConfig.MAXLRS #maximum LRS value
-
- xLow, xTop, stepX = detScale(min_D, max_D)
-
- #reduce data
- step = ceil((xTop-xLow)/50.0)
- j = xLow
- dataXY = []
- Count = []
- while j <= xTop:
- dataXY.append(j)
- Count.append(0)
- j += step
-
- for i, item in enumerate(data):
- if item == float('inf') or item>webqtlConfig.MAXLRS:
- item = webqtlConfig.MAXLRS #maximum LRS value
- j = int((item-xLow)/step)
- Count[j] += 1
-
- yLow, yTop, stepY=detScale(0,max(Count))
-
- #draw data
- xScale = plotWidth/(xTop-xLow)
- yScale = plotHeight/(yTop-yLow)
- barWidth = xScale*step
-
- for i, count in enumerate(Count):
- if count:
- xc = (dataXY[i]-xLow)*xScale+xLeftOffset
- yc =-(count-yLow)*yScale+yTopOffset+plotHeight
- canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
-
- #draw drawing region
- canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-
- #draw scale
- scaleFont=pid.Font(ttf="cour",size=11,bold=1)
- x=xLow
- for i in range(stepX+1):
- xc=xLeftOffset+(x-xLow)*xScale
- canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
- strX = cformat(d=x, rank=0)
- canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
- x+= (xTop - xLow)/stepX
-
- y=yLow
- for i in range(stepY+1):
- yc=yTopOffset+plotHeight-(y-yLow)*yScale
- canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
- strY = "%d" %y
- canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
- y+= (yTop - yLow)/stepY
-
- #draw label
- labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
- if XLabel:
- canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
- yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
-
- if YLabel:
- canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
- font=labelFont,color=labelColor,angle=90)
-
- labelFont=pid.Font(ttf="verdana",size=16,bold=0)
- if title:
- canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
- 20,font=labelFont,color=labelColor)
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+
+ if len(data) < 2:
+ return
+
+ max_D = max(data)
+ min_D = min(data)
+ #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
+ if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
+ max_D=webqtlConfig.MAXLRS #maximum LRS value
+
+ xLow, xTop, stepX = detScale(min_D, max_D)
+
+ #reduce data
+ step = ceil((xTop-xLow)/50.0)
+ j = xLow
+ dataXY = []
+ Count = []
+ while j <= xTop:
+ dataXY.append(j)
+ Count.append(0)
+ j += step
+
+ for i, item in enumerate(data):
+ if item == float('inf') or item>webqtlConfig.MAXLRS:
+ item = webqtlConfig.MAXLRS #maximum LRS value
+ j = int((item-xLow)/step)
+ Count[j] += 1
+
+ yLow, yTop, stepY=detScale(0,max(Count))
+
+ #draw data
+ xScale = plotWidth/(xTop-xLow)
+ yScale = plotHeight/(yTop-yLow)
+ barWidth = xScale*step
+
+ for i, count in enumerate(Count):
+ if count:
+ xc = (dataXY[i]-xLow)*xScale+xLeftOffset
+ yc =-(count-yLow)*yScale+yTopOffset+plotHeight
+ canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
+
+ #draw drawing region
+ canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+
+ #draw scale
+ scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ x=xLow
+ for i in range(stepX+1):
+ xc=xLeftOffset+(x-xLow)*xScale
+ canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
+ strX = cformat(d=x, rank=0)
+ canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
+ x+= (xTop - xLow)/stepX
+
+ y=yLow
+ for i in range(stepY+1):
+ yc=yTopOffset+plotHeight-(y-yLow)*yScale
+ canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ strY = "%d" %y
+ canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ y+= (yTop - yLow)/stepY
+
+ #draw label
+ labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
+ if XLabel:
+ canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
+ yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
+
+ if YLabel:
+ canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
+ font=labelFont,color=labelColor,angle=90)
+
+ labelFont=pid.Font(ttf="verdana",size=16,bold=0)
+ if title:
+ canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
+ 20,font=labelFont,color=labelColor)
def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1):
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- if plotHeight<=0 or plotWidth<=0:
- return
-
- NNN = len(data)
- if NNN < 2 or NNN != len(label):
- return
- if variance and len(variance)!=NNN:
- variance = []
-
- Y2 = data[:]
- if variance:
- for i in range(NNN):
- if variance[i]:
- Y2 += [data[i]-variance[i]]
-
- #Y axis
- YLow, YTop, stepY = detScale(min(Y2), max(Y2))
- YScale = plotHeight/(YTop - YLow)
-
- if YLow < 0 and YTop > 0:
- drawZero = 1
- else:
- drawZero = 0
-
- #X axis
- X = range(NNN)
- Xll= 0
- Xur= NNN-1
-
-
- if drawZero:
- YZero = yTopOffset+plotHeight-YScale*(0-YLow)
- canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
- else:
- YZero = yTopOffset+plotHeight
- #draw data
- spaceWidth = barSpace
- if spaceWidth < 1:
- spaceWidth = 1
- barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
-
- xc= xLeftOffset
- scaleFont=pid.Font(ttf="verdana",size=11,bold=0)
- for i in range(NNN):
- yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
- canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
- if variance and variance[i]:
- varlen = variance[i]*YScale
- if yc-varlen < yTopOffset:
- topYd = yTopOffset
- else:
- topYd = yc-varlen
- canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
- canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
- canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
- strX = label[i]
- canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
- xc += barWidth + spaceWidth
-
- #draw drawing region
- canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-
- #draw Y scale
- scaleFont=pid.Font(ttf="cour",size=16,bold=1)
- y=YLow
- for i in range(stepY+1):
- yc=yTopOffset+plotHeight-(y-YLow)*YScale
- canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
- strY = cformat(d=y, rank=0)
- canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
- y+= (YTop - YLow)/stepY
-
- #draw label
- labelFont=pid.Font(ttf="verdana",size=17,bold=0)
- if XLabel:
- canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
-
- if YLabel:
- canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
-
- labelFont=pid.Font(ttf="verdana",size=18,bold=0)
- if title:
- canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
-
- return
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+
+ NNN = len(data)
+ if NNN < 2 or NNN != len(label):
+ return
+ if variance and len(variance)!=NNN:
+ variance = []
+
+ Y2 = data[:]
+ if variance:
+ for i in range(NNN):
+ if variance[i]:
+ Y2 += [data[i]-variance[i]]
+
+ #Y axis
+ YLow, YTop, stepY = detScale(min(Y2), max(Y2))
+ YScale = plotHeight/(YTop - YLow)
+
+ if YLow < 0 and YTop > 0:
+ drawZero = 1
+ else:
+ drawZero = 0
+
+ #X axis
+ X = range(NNN)
+ Xll= 0
+ Xur= NNN-1
+
+
+ if drawZero:
+ YZero = yTopOffset+plotHeight-YScale*(0-YLow)
+ canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
+ else:
+ YZero = yTopOffset+plotHeight
+ #draw data
+ spaceWidth = barSpace
+ if spaceWidth < 1:
+ spaceWidth = 1
+ barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
+
+ xc= xLeftOffset
+ scaleFont=pid.Font(ttf="verdana",size=11,bold=0)
+ for i in range(NNN):
+ yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
+ canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
+ if variance and variance[i]:
+ varlen = variance[i]*YScale
+ if yc-varlen < yTopOffset:
+ topYd = yTopOffset
+ else:
+ topYd = yc-varlen
+ canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
+ canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
+ canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
+ strX = label[i]
+ canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
+ xc += barWidth + spaceWidth
+
+ #draw drawing region
+ canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+
+ #draw Y scale
+ scaleFont=pid.Font(ttf="cour",size=16,bold=1)
+ y=YLow
+ for i in range(stepY+1):
+ yc=yTopOffset+plotHeight-(y-YLow)*YScale
+ canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ strY = cformat(d=y, rank=0)
+ canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ y+= (YTop - YLow)/stepY
+
+ #draw label
+ labelFont=pid.Font(ttf="verdana",size=17,bold=0)
+ if XLabel:
+ canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
+
+ if YLabel:
+ canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
+
+ labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+ if title:
+ canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
+
+ return
def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15):
- 'displayR : correlation scatter plot, loadings : loading plot'
-
- dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-
- #get ID font size
- idFontSize = int(idSize)
-
- #If filled is yes, set fill color
- if filled == "yes":
- fillColor = symbolColor
- else:
- fillColor = None
-
- if symbolSize == "large":
- sizeModifier = 7
- fontModifier = 12
- elif symbolSize == "medium":
- sizeModifier = 5
- fontModifier = 8
- elif symbolSize == "small":
- sizeModifier = 3
- fontModifier = 3
- else:
- sizeModifier = 1
- fontModifier = -1
-
- if rank == 0: # Pearson correlation
- bufferSpace = 0
- dataXPrimary = dataX
- dataYPrimary = dataY
- dataXAlt = dataXRanked #Values used just for printing the other corr type to the graph image
- dataYAlt = dataYRanked #Values used just for printing the other corr type to the graph image
- else: # Spearman correlation: Switching Ranked and Unranked X and Y values
- dataXPrimary = dataXRanked
- dataYPrimary = dataYRanked
- dataXAlt = dataX #Values used just for printing the other corr type to the graph image
- dataYAlt = dataY #Values used just for printing the other corr type to the graph image
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
- plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- if plotHeight<=0 or plotWidth<=0:
- return
- if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
- return
-
- max_X=max(dataXPrimary)
- min_X=min(dataXPrimary)
- max_Y=max(dataYPrimary)
- min_Y=min(dataYPrimary)
-
- #for some reason I forgot why I need to do this
- if loadingPlot:
- min_X = min(-0.1,min_X)
- max_X = max(0.1,max_X)
- min_Y = min(-0.1,min_Y)
- max_Y = max(0.1,max_Y)
-
- xLow, xTop, stepX=detScale(min_X,max_X)
- yLow, yTop, stepY=detScale(min_Y,max_Y)
- xScale = plotWidth/(xTop-xLow)
- yScale = plotHeight/(yTop-yLow)
-
- #draw drawing region
- canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace)
- canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1)
-
- #calculate data points
- data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
- xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-
- labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0)
-
- if loadingPlot:
- xZero = -xLow*xScale+xLeftOffset
- yZero = yTopOffset+plotHeight+yLow*yScale
- for point in xCoord:
- canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red)
- else:
- if connectdot:
- canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
- else:
- pass
-
- symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0)
-
- for i, item in enumerate(xCoord):
- if dataLabel and dataLabel[i] in specialCases:
- canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green)
- #canvas.drawCross(item[0],item[1],color=pid.blue,size=5)
- else:
- if symbolType == "vertRect":
- canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
- elif (symbolType == "circle" and filled != "yes"):
- canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
- elif (symbolType == "circle" and filled == "yes"):
- canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
- elif symbolType == "horiRect":
- canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
- elif (symbolType == "square"):
- canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
- elif (symbolType == "diamond" and filled != "yes"):
- canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
- elif (symbolType == "diamond" and filled == "yes"):
- canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
- elif symbolType == "4-star":
- canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
- elif symbolType == "3-star":
- canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
- else:
- canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2)
-
- if showLabel and dataLabel:
- if (symbolType == "vertRect" or symbolType == "diamond"):
- labelGap = 15
- elif (symbolType == "4-star" or symbolType == "3-star"):
- labelGap = 12
- else:
- labelGap = 11
- canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i],
- font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor)
-
- #draw scale
- scaleFont=pid.Font(ttf="cour",size=16,bold=1)
-
-
- x=xLow
- for i in range(stepX+1):
- xc=xLeftOffset+(x-xLow)*xScale
- if ((x == 0) & (rank == 1)):
- pass
- else:
- canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)
- strX = cformat(d=x, rank=rank)
- if ((strX == "0") & (rank == 1)):
- pass
- else:
- canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont)
- x+= (xTop - xLow)/stepX
-
- y=yLow
- for i in range(stepY+1):
- yc=yTopOffset+plotHeight-(y-yLow)*yScale
- if ((y == 0) & (rank == 1)):
- pass
- else:
- canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor)
- strY = cformat(d=y, rank=rank)
- if ((strY == "0") & (rank == 1)):
- pass
- else:
- canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont)
- y+= (yTop - yLow)/stepY
-
- #draw label
-
- labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0)
- titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0)
-
- if (rank == 1 and not title):
- canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0,
- 25,font=titleFont,color=labelColor)
- elif (rank == 0 and not title):
- canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0,
- 25,font=titleFont,color=labelColor)
-
- if XLabel:
- canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
- yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor)
-
- if YLabel:
- canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
- font=labelFont,color=labelColor,angle=90)
-
- labelFont=pid.Font(ttf="verdana",size=20,bold=0)
- if title:
- canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
- 20,font=labelFont,color=labelColor)
-
- if fitcurve:
- import sys
- sys.argv = [ "mod_python" ]
- #from numarray import linear_algebra as la
- #from numarray import ones, array, dot, swapaxes
- fitYY = array(dataYPrimary)
- fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
- AA = dot(fitXX,swapaxes(fitXX,0,1))
- BB = dot(fitXX,fitYY)
- bb = la.linear_least_squares(AA,BB)[0]
-
- xc1 = xLeftOffset
- yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
- if yc1 > yTopOffset+plotHeight:
- yc1 = yTopOffset+plotHeight
- xc1 = (yLow-bb[0])/bb[1]
- xc1=(xc1-xLow)*xScale+xLeftOffset
- elif yc1 < yTopOffset:
- yc1 = yTopOffset
- xc1 = (yTop-bb[0])/bb[1]
- xc1=(xc1-xLow)*xScale+xLeftOffset
- else:
- pass
-
- xc2 = xLeftOffset + plotWidth
- yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
- if yc2 > yTopOffset+plotHeight:
- yc2 = yTopOffset+plotHeight
- xc2 = (yLow-bb[0])/bb[1]
- xc2=(xc2-xLow)*xScale+xLeftOffset
- elif yc2 < yTopOffset:
- yc2 = yTopOffset
- xc2 = (yTop-bb[0])/bb[1]
- xc2=(xc2-xLow)*xScale+xLeftOffset
- else:
- pass
-
- canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor)
- if lineSize == "medium":
- canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
- if lineSize == "thick":
- canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
- canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor)
-
-
- if displayR:
- labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0)
- NNN = len(dataX)
- corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
- if NNN < 3:
- corrPValue = 1.0
- else:
- if abs(corr) >= 1.0:
- corrPValue = 0.0
- else:
- ZValue = 0.5*log((1.0+corr)/(1.0-corr))
- ZValue = ZValue*sqrt(NNN-3)
- corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
- NStr = "N = %d" % NNN
- strLenN = canvas.stringWidth(NStr,font=labelFont)
-
- if rank == 1:
- if corrPValue < 0.0000000000000001:
- corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr)
- else:
- corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue)
- else:
- if corrPValue < 0.0000000000000001:
- corrStr = "r = %1.3f P < 1.00 E-16" % (corr)
- else:
- corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue)
- strLen = canvas.stringWidth(corrStr,font=labelFont)
-
- canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor)
- canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor)
-
- return xCoord
+ 'displayR : correlation scatter plot, loadings : loading plot'
+
+ dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
+
+ #get ID font size
+ idFontSize = int(idSize)
+
+ #If filled is yes, set fill color
+ if filled == "yes":
+ fillColor = symbolColor
+ else:
+ fillColor = None
+
+ if symbolSize == "large":
+ sizeModifier = 7
+ fontModifier = 12
+ elif symbolSize == "medium":
+ sizeModifier = 5
+ fontModifier = 8
+ elif symbolSize == "small":
+ sizeModifier = 3
+ fontModifier = 3
+ else:
+ sizeModifier = 1
+ fontModifier = -1
+
+ if rank == 0: # Pearson correlation
+ bufferSpace = 0
+ dataXPrimary = dataX
+ dataYPrimary = dataY
+ dataXAlt = dataXRanked #Values used just for printing the other corr type to the graph image
+ dataYAlt = dataYRanked #Values used just for printing the other corr type to the graph image
+ else: # Spearman correlation: Switching Ranked and Unranked X and Y values
+ dataXPrimary = dataXRanked
+ dataYPrimary = dataYRanked
+ dataXAlt = dataX #Values used just for printing the other corr type to the graph image
+ dataYAlt = dataY #Values used just for printing the other corr type to the graph image
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+ if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
+ return
+
+ max_X=max(dataXPrimary)
+ min_X=min(dataXPrimary)
+ max_Y=max(dataYPrimary)
+ min_Y=min(dataYPrimary)
+
+ #for some reason I forgot why I need to do this
+ if loadingPlot:
+ min_X = min(-0.1,min_X)
+ max_X = max(0.1,max_X)
+ min_Y = min(-0.1,min_Y)
+ max_Y = max(0.1,max_Y)
+
+ xLow, xTop, stepX=detScale(min_X,max_X)
+ yLow, yTop, stepY=detScale(min_Y,max_Y)
+ xScale = plotWidth/(xTop-xLow)
+ yScale = plotHeight/(yTop-yLow)
+
+ #draw drawing region
+ canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace)
+ canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1)
+
+ #calculate data points
+ data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
+ xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
+
+ labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0)
+
+ if loadingPlot:
+ xZero = -xLow*xScale+xLeftOffset
+ yZero = yTopOffset+plotHeight+yLow*yScale
+ for point in xCoord:
+ canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red)
+ else:
+ if connectdot:
+ canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
+ else:
+ pass
+
+ symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0)
+
+ for i, item in enumerate(xCoord):
+ if dataLabel and dataLabel[i] in specialCases:
+ canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green)
+ #canvas.drawCross(item[0],item[1],color=pid.blue,size=5)
+ else:
+ if symbolType == "vertRect":
+ canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
+ elif (symbolType == "circle" and filled != "yes"):
+ canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
+ elif (symbolType == "circle" and filled == "yes"):
+ canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
+ elif symbolType == "horiRect":
+ canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
+ elif (symbolType == "square"):
+ canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
+ elif (symbolType == "diamond" and filled != "yes"):
+ canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
+ elif (symbolType == "diamond" and filled == "yes"):
+ canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
+ elif symbolType == "4-star":
+ canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
+ elif symbolType == "3-star":
+ canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
+ else:
+ canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2)
+
+ if showLabel and dataLabel:
+ if (symbolType == "vertRect" or symbolType == "diamond"):
+ labelGap = 15
+ elif (symbolType == "4-star" or symbolType == "3-star"):
+ labelGap = 12
+ else:
+ labelGap = 11
+ canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i],
+ font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor)
+
+ #draw scale
+ scaleFont=pid.Font(ttf="cour",size=16,bold=1)
+
+
+ x=xLow
+ for i in range(stepX+1):
+ xc=xLeftOffset+(x-xLow)*xScale
+ if ((x == 0) & (rank == 1)):
+ pass
+ else:
+ canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)
+ strX = cformat(d=x, rank=rank)
+ if ((strX == "0") & (rank == 1)):
+ pass
+ else:
+ canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont)
+ x+= (xTop - xLow)/stepX
+
+ y=yLow
+ for i in range(stepY+1):
+ yc=yTopOffset+plotHeight-(y-yLow)*yScale
+ if ((y == 0) & (rank == 1)):
+ pass
+ else:
+ canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor)
+ strY = cformat(d=y, rank=rank)
+ if ((strY == "0") & (rank == 1)):
+ pass
+ else:
+ canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont)
+ y+= (yTop - yLow)/stepY
+
+ #draw label
+
+ labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0)
+ titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0)
+
+ if (rank == 1 and not title):
+ canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0,
+ 25,font=titleFont,color=labelColor)
+ elif (rank == 0 and not title):
+ canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0,
+ 25,font=titleFont,color=labelColor)
+
+ if XLabel:
+ canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
+ yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor)
+
+ if YLabel:
+ canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
+ font=labelFont,color=labelColor,angle=90)
+
+ labelFont=pid.Font(ttf="verdana",size=20,bold=0)
+ if title:
+ canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
+ 20,font=labelFont,color=labelColor)
+
+ if fitcurve:
+ import sys
+ sys.argv = [ "mod_python" ]
+ #from numarray import linear_algebra as la
+ #from numarray import ones, array, dot, swapaxes
+ fitYY = array(dataYPrimary)
+ fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
+ AA = dot(fitXX,swapaxes(fitXX,0,1))
+ BB = dot(fitXX,fitYY)
+ bb = la.linear_least_squares(AA,BB)[0]
+
+ xc1 = xLeftOffset
+ yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
+ if yc1 > yTopOffset+plotHeight:
+ yc1 = yTopOffset+plotHeight
+ xc1 = (yLow-bb[0])/bb[1]
+ xc1=(xc1-xLow)*xScale+xLeftOffset
+ elif yc1 < yTopOffset:
+ yc1 = yTopOffset
+ xc1 = (yTop-bb[0])/bb[1]
+ xc1=(xc1-xLow)*xScale+xLeftOffset
+ else:
+ pass
+
+ xc2 = xLeftOffset + plotWidth
+ yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
+ if yc2 > yTopOffset+plotHeight:
+ yc2 = yTopOffset+plotHeight
+ xc2 = (yLow-bb[0])/bb[1]
+ xc2=(xc2-xLow)*xScale+xLeftOffset
+ elif yc2 < yTopOffset:
+ yc2 = yTopOffset
+ xc2 = (yTop-bb[0])/bb[1]
+ xc2=(xc2-xLow)*xScale+xLeftOffset
+ else:
+ pass
+
+ canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor)
+ if lineSize == "medium":
+ canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
+ if lineSize == "thick":
+ canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
+ canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor)
+
+
+ if displayR:
+ labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0)
+ NNN = len(dataX)
+ corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
+
+ if NNN < 3:
+ corrPValue = 1.0
+ else:
+ if abs(corr) >= 1.0:
+ corrPValue = 0.0
+ else:
+ ZValue = 0.5*log((1.0+corr)/(1.0-corr))
+ ZValue = ZValue*sqrt(NNN-3)
+ corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
+
+ NStr = "N = %d" % NNN
+ strLenN = canvas.stringWidth(NStr,font=labelFont)
+
+ if rank == 1:
+ if corrPValue < 0.0000000000000001:
+ corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr)
+ else:
+ corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue)
+ else:
+ if corrPValue < 0.0000000000000001:
+ corrStr = "r = %1.3f P < 1.00 E-16" % (corr)
+ else:
+ corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue)
+ strLen = canvas.stringWidth(corrStr,font=labelFont)
+
+ canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor)
+ canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor)
+
+ return xCoord
def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1):
- 'displayR : correlation scatter plot, loadings : loading plot'
-
- dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-
- # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation
- if rank == 0:
- dataXPrimary = dataX
- dataYPrimary = dataY
- dataXAlt = dataXRanked
- dataYAlt = dataYRanked
-
- else:
- dataXPrimary = dataXRanked
- dataYPrimary = dataYRanked
- dataXAlt = dataX
- dataYAlt = dataY
-
-
-
- xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
- plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset
- plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset
- if plotHeight<=0 or plotWidth<=0:
- return
- if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
- return
-
- max_X=max(dataXPrimary)
- min_X=min(dataXPrimary)
- max_Y=max(dataYPrimary)
- min_Y=min(dataYPrimary)
-
- #for some reason I forgot why I need to do this
- if loadingPlot:
- min_X = min(-0.1,min_X)
- max_X = max(0.1,max_X)
- min_Y = min(-0.1,min_Y)
- max_Y = max(0.1,max_Y)
-
- xLow, xTop, stepX=detScale(min_X,max_X)
- yLow, yTop, stepY=detScale(min_Y,max_Y)
- xScale = plotWidth/(xTop-xLow)
- yScale = plotHeight/(yTop-yLow)
-
- #draw drawing region
- r = svg.rect(xLeftOffset, yTopOffset, plotWidth, plotHeight, 'none', axesColor, 1)
- drawSpace.addElement(r)
-
- #calculate data points
- data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
- xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
- labelFontF = "verdana"
- labelFontS = 11
-
- if loadingPlot:
- xZero = -xLow*xScale+xLeftOffset
- yZero = yTopOffset+plotHeight+yLow*yScale
- for point in xCoord:
- drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1))
- else:
- if connectdot:
- pass
- #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
- else:
- pass
-
- for i, item in enumerate(xCoord):
- if dataLabel and dataLabel[i] in specialCases:
- drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5))
- #drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5)
- else:
- drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1))
- drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1))
- if showLabel and dataLabel:
- pass
- drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS,
- labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;"))
- #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i],
- # font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue)
-
- #draw scale
- #scaleFont=pid.Font(ttf="cour",size=14,bold=1)
- x=xLow
- for i in range(stepX+1):
- xc=xLeftOffset+(x-xLow)*xScale
- drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1))
- strX = cformat(d=x, rank=rank)
- drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle"))
- x+= (xTop - xLow)/stepX
-
- y=yLow
- for i in range(stepY+1):
- yc=yTopOffset+plotHeight-(y-yLow)*yScale
- drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1))
- strY = cformat(d=y, rank=rank)
- drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end"))
- y+= (yTop - yLow)/stepY
-
- #draw label
- labelFontF = "verdana"
- labelFontS = 17
- if XLabel:
- drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0,
- yTopOffset+plotHeight+yBottomOffset-10,XLabel,
- labelFontS, labelFontF, text_anchor="middle"))
-
- if YLabel:
- drawSpace.addElement(svg.text(xLeftOffset-50,
- yTopOffset+plotHeight/2,YLabel,
- labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50, yTopOffset+plotHeight/2)))
- #drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0,
- # font=labelFont,color=labelColor,angle=90)
-
-
- if fitcurve:
- sys.argv = [ "mod_python" ]
- #from numarray import linear_algebra as la
- #from numarray import ones, array, dot, swapaxes
- fitYY = array(dataYPrimary)
- fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
- AA = dot(fitXX,swapaxes(fitXX,0,1))
- BB = dot(fitXX,fitYY)
- bb = la.linear_least_squares(AA,BB)[0]
-
- xc1 = xLeftOffset
- yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
- if yc1 > yTopOffset+plotHeight:
- yc1 = yTopOffset+plotHeight
- xc1 = (yLow-bb[0])/bb[1]
- xc1=(xc1-xLow)*xScale+xLeftOffset
- elif yc1 < yTopOffset:
- yc1 = yTopOffset
- xc1 = (yTop-bb[0])/bb[1]
- xc1=(xc1-xLow)*xScale+xLeftOffset
- else:
- pass
-
- xc2 = xLeftOffset + plotWidth
- yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
- if yc2 > yTopOffset+plotHeight:
- yc2 = yTopOffset+plotHeight
- xc2 = (yLow-bb[0])/bb[1]
- xc2=(xc2-xLow)*xScale+xLeftOffset
- elif yc2 < yTopOffset:
- yc2 = yTopOffset
- xc2 = (yTop-bb[0])/bb[1]
- xc2=(xc2-xLow)*xScale+xLeftOffset
- else:
- pass
-
- drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
-
- if displayR:
- labelFontF = "trebuc"
- labelFontS = 14
- NNN = len(dataX)
-
- corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
- if NNN < 3:
- corrPValue = 1.0
- else:
- if abs(corr) >= 1.0:
- corrPValue = 0.0
- else:
- ZValue = 0.5*log((1.0+corr)/(1.0-corr))
- ZValue = ZValue*sqrt(NNN-3)
- corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
- NStr = "N of Cases=%d" % NNN
-
- if rank == 1:
- corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue)
- else:
- corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue)
-
- drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr,
- labelFontS, labelFontF, text_anchor="start"))
- drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr,
- labelFontS, labelFontF, text_anchor="end"))
- """
- """
- return
+ 'displayR : correlation scatter plot, loadings : loading plot'
+
+ dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
+
+ # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation
+ if rank == 0:
+ dataXPrimary = dataX
+ dataYPrimary = dataY
+ dataXAlt = dataXRanked
+ dataYAlt = dataYRanked
+
+ else:
+ dataXPrimary = dataXRanked
+ dataYPrimary = dataYRanked
+ dataXAlt = dataX
+ dataYAlt = dataY
+
+
+
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset
+ plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+ if len(dataXPrimary) < 1 or len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
+ return
+
+ max_X=max(dataXPrimary)
+ min_X=min(dataXPrimary)
+ max_Y=max(dataYPrimary)
+ min_Y=min(dataYPrimary)
+
+ #for some reason I forgot why I need to do this
+ if loadingPlot:
+ min_X = min(-0.1,min_X)
+ max_X = max(0.1,max_X)
+ min_Y = min(-0.1,min_Y)
+ max_Y = max(0.1,max_Y)
+
+ xLow, xTop, stepX=detScale(min_X,max_X)
+ yLow, yTop, stepY=detScale(min_Y,max_Y)
+ xScale = plotWidth/(xTop-xLow)
+ yScale = plotHeight/(yTop-yLow)
+
+ #draw drawing region
+ r = svg.rect(xLeftOffset, yTopOffset, plotWidth, plotHeight, 'none', axesColor, 1)
+ drawSpace.addElement(r)
+
+ #calculate data points
+ data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
+ xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
+ labelFontF = "verdana"
+ labelFontS = 11
+
+ if loadingPlot:
+ xZero = -xLow*xScale+xLeftOffset
+ yZero = yTopOffset+plotHeight+yLow*yScale
+ for point in xCoord:
+ drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1))
+ else:
+ if connectdot:
+ pass
+ #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
+ else:
+ pass
+
+ for i, item in enumerate(xCoord):
+ if dataLabel and dataLabel[i] in specialCases:
+ drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5))
+ #drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5)
+ else:
+ drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1))
+ drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1))
+ if showLabel and dataLabel:
+ pass
+ drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS,
+ labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;"))
+ #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i],
+ # font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue)
+
+ #draw scale
+ #scaleFont=pid.Font(ttf="cour",size=14,bold=1)
+ x=xLow
+ for i in range(stepX+1):
+ xc=xLeftOffset+(x-xLow)*xScale
+ drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1))
+ strX = cformat(d=x, rank=rank)
+ drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle"))
+ x+= (xTop - xLow)/stepX
+
+ y=yLow
+ for i in range(stepY+1):
+ yc=yTopOffset+plotHeight-(y-yLow)*yScale
+ drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1))
+ strY = cformat(d=y, rank=rank)
+ drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end"))
+ y+= (yTop - yLow)/stepY
+
+ #draw label
+ labelFontF = "verdana"
+ labelFontS = 17
+ if XLabel:
+ drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0,
+ yTopOffset+plotHeight+yBottomOffset-10,XLabel,
+ labelFontS, labelFontF, text_anchor="middle"))
+
+ if YLabel:
+ drawSpace.addElement(svg.text(xLeftOffset-50,
+ yTopOffset+plotHeight/2,YLabel,
+ labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50, yTopOffset+plotHeight/2)))
+ #drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0,
+ # font=labelFont,color=labelColor,angle=90)
+
+
+ if fitcurve:
+ sys.argv = [ "mod_python" ]
+ #from numarray import linear_algebra as la
+ #from numarray import ones, array, dot, swapaxes
+ fitYY = array(dataYPrimary)
+ fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
+ AA = dot(fitXX,swapaxes(fitXX,0,1))
+ BB = dot(fitXX,fitYY)
+ bb = la.linear_least_squares(AA,BB)[0]
+
+ xc1 = xLeftOffset
+ yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
+ if yc1 > yTopOffset+plotHeight:
+ yc1 = yTopOffset+plotHeight
+ xc1 = (yLow-bb[0])/bb[1]
+ xc1=(xc1-xLow)*xScale+xLeftOffset
+ elif yc1 < yTopOffset:
+ yc1 = yTopOffset
+ xc1 = (yTop-bb[0])/bb[1]
+ xc1=(xc1-xLow)*xScale+xLeftOffset
+ else:
+ pass
+
+ xc2 = xLeftOffset + plotWidth
+ yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
+ if yc2 > yTopOffset+plotHeight:
+ yc2 = yTopOffset+plotHeight
+ xc2 = (yLow-bb[0])/bb[1]
+ xc2=(xc2-xLow)*xScale+xLeftOffset
+ elif yc2 < yTopOffset:
+ yc2 = yTopOffset
+ xc2 = (yTop-bb[0])/bb[1]
+ xc2=(xc2-xLow)*xScale+xLeftOffset
+ else:
+ pass
+
+ drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
+
+ if displayR:
+ labelFontF = "trebuc"
+ labelFontS = 14
+ NNN = len(dataX)
+
+ corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
+
+ if NNN < 3:
+ corrPValue = 1.0
+ else:
+ if abs(corr) >= 1.0:
+ corrPValue = 0.0
+ else:
+ ZValue = 0.5*log((1.0+corr)/(1.0-corr))
+ ZValue = ZValue*sqrt(NNN-3)
+ corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
+
+ NStr = "N of Cases=%d" % NNN
+
+ if rank == 1:
+ corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue)
+ else:
+ corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue)
+
+ drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr,
+ labelFontS, labelFontF, text_anchor="start"))
+ drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr,
+ labelFontS, labelFontF, text_anchor="end"))
+ """
+ """
+ return
# This function determines the scale of the plot
def detScaleOld(min,max):
- if min>=max:
- return None
- elif min == -1.0 and max == 1.0:
- return [-1.2,1.2,12]
- else:
- a=max-min
- b=floor(log10(a))
- c=pow(10.0,b)
- if a < c*5.0:
- c/=2.0
- #print a,b,c
- low=c*floor(min/c)
- high=c*ceil(max/c)
- return [low,high,round((high-low)/c)]
+ if min>=max:
+ return None
+ elif min == -1.0 and max == 1.0:
+ return [-1.2,1.2,12]
+ else:
+ a=max-min
+ b=floor(log10(a))
+ c=pow(10.0,b)
+ if a < c*5.0:
+ c/=2.0
+ #print a,b,c
+ low=c*floor(min/c)
+ high=c*ceil(max/c)
+ return [low,high,round((high-low)/c)]
def detScale(min=0,max=0,bufferSpace=3):
- if min>=max:
- return None
- elif min == -1.0 and max == 1.0:
- return [-1.2,1.2,12]
- else:
- a=max-min
- if max != 0:
- max += 0.1*a
- if min != 0:
- if min > 0 and min < 0.1*a:
- min = 0.0
- else:
- min -= 0.1*a
- a=max-min
- b=floor(log10(a))
- c=pow(10.0,b)
- low=c*floor(min/c)
- high=c*ceil(max/c)
- n = round((high-low)/c)
- div = 2.0
- while n < 5 or n > 15:
- if n < 5:
- c /= div
- else:
- c *= div
- if div == 2.0:
- div =5.0
- else:
- div =2.0
- low=c*floor(min/c)
- high=c*ceil(max/c)
- n = round((high-low)/c)
-
- return [low,high,n]
+ if min>=max:
+ return None
+ elif min == -1.0 and max == 1.0:
+ return [-1.2,1.2,12]
+ else:
+ a=max-min
+ if max != 0:
+ max += 0.1*a
+ if min != 0:
+ if min > 0 and min < 0.1*a:
+ min = 0.0
+ else:
+ min -= 0.1*a
+ a=max-min
+ b=floor(log10(a))
+ c=pow(10.0,b)
+ low=c*floor(min/c)
+ high=c*ceil(max/c)
+ n = round((high-low)/c)
+ div = 2.0
+ while n < 5 or n > 15:
+ if n < 5:
+ c /= div
+ else:
+ c *= div
+ if div == 2.0:
+ div =5.0
+ else:
+ div =2.0
+ low=c*floor(min/c)
+ high=c*ceil(max/c)
+ n = round((high-low)/c)
+
+ return [low,high,n]
def colorSpectrumOld(n):
- if n == 1:
- return [pid.Color(1,0,0)]
- elif n == 2:
- return [pid.Color(1,0,0),pid.Color(0,0,1)]
- elif n == 3:
- return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
- else:
- step = 2.0/(n-1)
- red = 1.0
- green = 0.0
- blue = 0.0
- colors = [pid.Color(red,green,blue)]
- i = 1
- greenpeak = 0
- while i < n:
- if red >= step:
- red -= step
- green += step
- if green >= 1.0:
- greenpeak = 1
- blue += green -1.0
- green = 1.0
- else:
- red = 0.0
- if greenpeak:
- green -= step
- blue += step
- else:
- green += step
- if green >= 1.0:
- greenpeak = 1
- blue += green -1.0
- green = 2.0 -green
- elif green < 0.0:
- green = 0.0
- else:
- pass
- colors.append(pid.Color(red,green,blue))
- i += 1
- return colors
+ if n == 1:
+ return [pid.Color(1,0,0)]
+ elif n == 2:
+ return [pid.Color(1,0,0),pid.Color(0,0,1)]
+ elif n == 3:
+ return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
+ else:
+ step = 2.0/(n-1)
+ red = 1.0
+ green = 0.0
+ blue = 0.0
+ colors = [pid.Color(red,green,blue)]
+ i = 1
+ greenpeak = 0
+ while i < n:
+ if red >= step:
+ red -= step
+ green += step
+ if green >= 1.0:
+ greenpeak = 1
+ blue += green -1.0
+ green = 1.0
+ else:
+ red = 0.0
+ if greenpeak:
+ green -= step
+ blue += step
+ else:
+ green += step
+ if green >= 1.0:
+ greenpeak = 1
+ blue += green -1.0
+ green = 2.0 -green
+ elif green < 0.0:
+ green = 0.0
+ else:
+ pass
+ colors.append(pid.Color(red,green,blue))
+ i += 1
+ return colors
def bluefunc(x):
- return 1.0 / (1.0 + exp(-10*(x-0.6)))
+ return 1.0 / (1.0 + exp(-10*(x-0.6)))
def redfunc(x):
- return 1.0 / (1.0 + exp(10*(x-0.5)))
+ return 1.0 / (1.0 + exp(10*(x-0.5)))
def greenfunc(x):
- return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
+ return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
def colorSpectrum(n=100):
- multiple = 10
- if n == 1:
- return [pid.Color(1,0,0)]
- elif n == 2:
- return [pid.Color(1,0,0),pid.Color(0,0,1)]
- elif n == 3:
- return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
- N = n*multiple
- out = [None]*N;
- for i in range(N):
- x = float(i)/N
- out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
- out2 = [out[0]]
- step = N/float(n-1)
- j = 0
- for i in range(n-2):
- j += step
- out2.append(out[int(j)])
- out2.append(out[-1])
- return out2
+ multiple = 10
+ if n == 1:
+ return [pid.Color(1,0,0)]
+ elif n == 2:
+ return [pid.Color(1,0,0),pid.Color(0,0,1)]
+ elif n == 3:
+ return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
+ N = n*multiple
+ out = [None]*N;
+ for i in range(N):
+ x = float(i)/N
+ out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
+ out2 = [out[0]]
+ step = N/float(n-1)
+ j = 0
+ for i in range(n-2):
+ j += step
+ out2.append(out[int(j)])
+ out2.append(out[-1])
+ return out2
def colorSpectrumSVG(n=100):
- multiple = 10
- if n == 1:
- return ["rgb(255,0,0)"]
- elif n == 2:
- return ["rgb(255,0,0)","rgb(0,0,255)"]
- elif n == 3:
- return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"]
- N = n*multiple
- out = [None]*N;
- for i in range(N):
- x = float(i)/N
- out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255);
- out2 = [out[0]]
- step = N/float(n-1)
- j = 0
- for i in range(n-2):
- j += step
- out2.append(out[int(j)])
- out2.append(out[-1])
- return out2
+ multiple = 10
+ if n == 1:
+ return ["rgb(255,0,0)"]
+ elif n == 2:
+ return ["rgb(255,0,0)","rgb(0,0,255)"]
+ elif n == 3:
+ return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"]
+ N = n*multiple
+ out = [None]*N;
+ for i in range(N):
+ x = float(i)/N
+ out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255);
+ out2 = [out[0]]
+ step = N/float(n-1)
+ j = 0
+ for i in range(n-2):
+ j += step
+ out2.append(out[int(j)])
+ out2.append(out[-1])
+ return out2
def BWSpectrum(n=100):
- multiple = 10
- if n == 1:
- return [pid.Color(0,0,0)]
- elif n == 2:
- return [pid.Color(0,0,0),pid.Color(1,1,1)]
- elif n == 3:
- return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)]
-
- step = 1.0/n
- x = 0.0
- out = []
- for i in range(n):
- out.append(pid.Color(x,x,x));
- x += step
- return out
+ multiple = 10
+ if n == 1:
+ return [pid.Color(0,0,0)]
+ elif n == 2:
+ return [pid.Color(0,0,0),pid.Color(1,1,1)]
+ elif n == 3:
+ return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)]
+
+ step = 1.0/n
+ x = 0.0
+ out = []
+ for i in range(n):
+ out.append(pid.Color(x,x,x));
+ x += step
+ return out
diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py
index 76b9c5db..8de8e050 100755
--- a/wqflask/utility/TDCell.py
+++ b/wqflask/utility/TDCell.py
@@ -30,13 +30,12 @@
#
##########################################################
-
+
class TDCell:
- def __init__(self, html="", text="", val=0.0):
- self.html = html #html, for web page
- self.text = text #text value, for output to a text file
- self.val = val #sort by value
-
- def __str__(self):
- return self.text
+ def __init__(self, html="", text="", val=0.0):
+ self.html = html #html, for web page
+ self.text = text #text value, for output to a text file
+ self.val = val #sort by value
+ def __str__(self):
+ return self.text
diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py
index a96b9e49..dde221b5 100755
--- a/wqflask/utility/THCell.py
+++ b/wqflask/utility/THCell.py
@@ -32,13 +32,11 @@
class THCell:
- def __init__(self, html="", text="", sort=1, idx=-1):
- self.html = html #html, for web page
- self.text = text #Column text value
- self.sort = sort #0: not sortable, 1: yes
- self.idx = idx #sort by value
-
- def __str__(self):
- return self.text
-
+ def __init__(self, html="", text="", sort=1, idx=-1):
+ self.html = html #html, for web page
+ self.text = text #Column text value
+ self.sort = sort #0: not sortable, 1: yes
+ self.idx = idx #sort by value
+ def __str__(self):
+ return self.text
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index e49a6c3c..512bc9e6 100755
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -74,7 +74,7 @@ by using easy to use classes and methods usualy you start by creating a drawing
d.setSVG(s)
#and finaly you xmlify the drawing
d.toXml()
-
+
this results in the svg source of the drawing, which consists of a circle
on a white background. Its as easy as that;)
@@ -112,7 +112,7 @@ if sys.version_info[1]<2:
True=1
False=0
file=open
-
+
sys.setrecursionlimit=50
#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s)
#won't eat up too much processor time.
@@ -167,7 +167,7 @@ def _xypointlist(a):
def _viewboxlist(a):
"""formats a tuple"""
s=''
- for e in a:
+ for e in a:
s+=str(e)+' '
return s
@@ -178,7 +178,7 @@ def _pointlist(a):
class pathdata:
"""class used to create a pathdata object which can be used for a path.
although most methods are pretty straightforward it might be useful to look at the SVG specification."""
- #I didn't test the methods below.
+ #I didn't test the methods below.
def __init__(self,x=None,y=None):
self.path=[]
if x is not None and y is not None:
@@ -242,10 +242,10 @@ class pathdata:
self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
def __repr__(self):
return ' '.join(self.path)
-
-
+
+
class SVGelement:
"""SVGelement(type,attributes,elements,text,namespace,**args)
Creates a arbitrary svg element and is intended to be subclassed not used on its own.
@@ -296,7 +296,7 @@ class SVGelement:
if self.cdata:
f.write('\n'+'\t'*(level+1)+'<![CDATA[')
for line in self.cdata.splitlines():
- f.write('\n'+'\t'*(level+2)+line)
+ f.write('\n'+'\t'*(level+2)+line)
f.write('\n'+'\t'*(level+1)+']]>\n')
if self.text:
if type(self.text)==type(''): #If the text is only text
@@ -305,13 +305,13 @@ class SVGelement:
f.write(str(self.text))
if self.elements:
f.write('\t'*level+'</'+self.type+'>\n')
- elif self.text:
+ elif self.text:
f.write('</'+self.type+'>\n')
elif self.cdata:
f.write('\t'*level+'</'+self.type+'>\n')
else:
f.write('/>\n')
-
+
class tspan(SVGelement):
"""ts=tspan(text='',**args)
@@ -330,12 +330,12 @@ class tspan(SVGelement):
def __repr__(self):
s="<tspan"
for key,value in self.attributes.items():
- s+= ' %s="%s"' % (key,value)
+ s+= ' %s="%s"' % (key,value)
s+='>'
s+=self.text
s+='</tspan>'
return s
-
+
class tref(SVGelement):
"""tr=tref(link='',**args)
@@ -350,12 +350,12 @@ class tref(SVGelement):
SVGelement.__init__(self,'tref',{'xlink:href':link},**args)
def __repr__(self):
s="<tref"
-
+
for key,value in self.attributes.items():
- s+= ' %s="%s"' % (key,value)
+ s+= ' %s="%s"' % (key,value)
s+='/>'
return s
-
+
class spannedtext:
"""st=spannedtext(textlist=[])
@@ -363,7 +363,7 @@ class spannedtext:
You can use it to add to a text element or path element. Don't add it directly
to a svg or a group element.
usage:
-
+
ts=tspan('this text is bold')
ts.attributes['font-weight']='bold'
tr=tref('#linktotext')
@@ -390,11 +390,11 @@ class spannedtext:
for element in self.textlist:
s+=str(element)
return s
-
+
class rect(SVGelement):
"""r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
-
- a rectangle is defined by a width and height and a xy pair
+
+ a rectangle is defined by a width and height and a xy pair
"""
def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args):
if width==None or height==None:
@@ -415,7 +415,7 @@ class rect(SVGelement):
self.attributes['stroke']=stroke
if stroke_width<>None:
self.attributes['stroke-width']=stroke_width
-
+
class ellipse(SVGelement):
"""e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
@@ -440,8 +440,8 @@ class ellipse(SVGelement):
self.attributes['stroke']=stroke
if stroke_width<>None:
self.attributes['stroke-width']=stroke_width
-
-
+
+
class circle(SVGelement):
"""c=circle(x,y,radius,fill,stroke,stroke_width,**args)
@@ -464,7 +464,7 @@ class circle(SVGelement):
class point(circle):
"""p=point(x,y,color)
-
+
A point is defined as a circle with a size 1 radius. It may be more efficient to use a
very small rectangle if you use many points because a circle is difficult to render.
"""
@@ -473,7 +473,7 @@ class point(circle):
class line(SVGelement):
"""l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
-
+
A line is defined by a begin x,y pair and an end x,y pair
"""
def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
@@ -490,10 +490,10 @@ class line(SVGelement):
self.attributes['stroke-width']=stroke_width
if stroke<>None:
self.attributes['stroke']=stroke
-
+
class polyline(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
+
a polyline is defined by a list of xy pairs
"""
def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
@@ -507,7 +507,7 @@ class polyline(SVGelement):
class polygon(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
+
a polygon is defined by a list of xy pairs
"""
def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
@@ -534,11 +534,11 @@ class path(SVGelement):
self.attributes['stroke-width']=stroke_width
if id<>None:
self.attributes['id']=id
-
-
+
+
class text(SVGelement):
"""t=text(x,y,text,font_size,font_family,**args)
-
+
a text element can bge used for displaying text on the screen
"""
def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
@@ -560,7 +560,7 @@ class text(SVGelement):
class textpath(SVGelement):
"""tp=textpath(text,link,**args)
- a textpath places a text on a path which is referenced by a link.
+ a textpath places a text on a path which is referenced by a link.
"""
def __init__(self,link,text=None,**args):
SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
@@ -589,7 +589,7 @@ class pattern(SVGelement):
class title(SVGelement):
"""t=title(text,**args)
-
+
a title is a text element. The text is displayed in the title bar
add at least one to the root svg element
"""
@@ -600,7 +600,7 @@ class title(SVGelement):
class description(SVGelement):
"""d=description(text,**args)
-
+
a description can be added to any element and is used for a tooltip
Add this element before adding other elements.
"""
@@ -648,7 +648,7 @@ class radialgradient(SVGelement):
self.attributes['fy']=fy
if id<>None:
self.attributes['id']=id
-
+
class stop(SVGelement):
"""st=stop(offset,stop_color,**args)
@@ -658,7 +658,7 @@ class stop(SVGelement):
SVGelement.__init__(self,'stop',{'offset':offset},**args)
if stop_color<>None:
self.attributes['stop-color']=stop_color
-
+
class style(SVGelement):
"""st=style(type,cdata=None,**args)
@@ -666,8 +666,8 @@ class style(SVGelement):
"""
def __init__(self,type,cdata=None,**args):
SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args)
-
-
+
+
class image(SVGelement):
"""im=image(url,width,height,x,y,**args)
@@ -686,7 +686,7 @@ class image(SVGelement):
self.attributes['x']=x
if y<>None:
self.attributes['y']=y
-
+
class cursor(SVGelement):
"""c=cursor(url,**args)
@@ -695,10 +695,10 @@ class cursor(SVGelement):
def __init__(self,url,**args):
SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
-
+
class marker(SVGelement):
"""m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
-
+
defines a marker which can be used as an endpoint for a line or other pathtypes
add an element to it which should be used as a marker.
"""
@@ -716,10 +716,10 @@ class marker(SVGelement):
self.attributes['markerWidth']=markerWidth
if markerHeight<>None:
self.attributes['markerHeight']=markerHeight
-
+
class group(SVGelement):
"""g=group(id,**args)
-
+
a group is defined by an id and is used to contain elements
g.addElement(SVGelement)
"""
@@ -736,14 +736,14 @@ class symbol(SVGelement):
display it by referencing its id.
sy.addElement(SVGelement)
"""
-
+
def __init__(self,id=None,viewBox=None,**args):
SVGelement.__init__(self,'symbol',**args)
if id<>None:
self.attributes['id']=id
if viewBox<>None:
self.attributes['viewBox']=_viewboxlist(viewBox)
-
+
class defs(SVGelement):
"""d=defs(**args)
@@ -762,10 +762,10 @@ class switch(SVGelement):
def __init__(self,**args):
SVGelement.__init__(self,'switch',**args)
-
+
class use(SVGelement):
"""u=use(link,x,y,width,height,**args)
-
+
references a symbol by linking to its id and its position, height and width
"""
def __init__(self,link,x=None,y=None,width=None,height=None,**args):
@@ -779,8 +779,8 @@ class use(SVGelement):
self.attributes['width']=width
if height<>None:
self.attributes['height']=height
-
-
+
+
class link(SVGelement):
"""a=link(url,**args)
@@ -789,7 +789,7 @@ class link(SVGelement):
"""
def __init__(self,link='',**args):
SVGelement.__init__(self,'a',{'xlink:href':link},**args)
-
+
class view(SVGelement):
"""v=view(id,**args)
@@ -807,11 +807,11 @@ class script(SVGelement):
"""
def __init__(self,type,cdata=None,**args):
SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
-
+
class animate(SVGelement):
"""an=animate(attribute,from,to,during,**args)
- animates an attribute.
+ animates an attribute.
"""
def __init__(self,attribute,fr=None,to=None,dur=None,**args):
SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
@@ -821,7 +821,7 @@ class animate(SVGelement):
self.attributes['to']=to
if dur<>None:
self.attributes['dur']=dur
-
+
class animateMotion(SVGelement):
"""an=animateMotion(pathdata,dur,**args)
@@ -836,7 +836,7 @@ class animateMotion(SVGelement):
class animateTransform(SVGelement):
"""antr=animateTransform(type,from,to,dur,**args)
-
+
transform an element from and to a value.
"""
def __init__(self,type=None,fr=None,to=None,dur=None,**args):
@@ -864,10 +864,10 @@ class animateColor(SVGelement):
if to<>None:
self.attributes['to']=to
if dur<>None:
- self.attributes['dur']=dur
+ self.attributes['dur']=dur
class set(SVGelement):
"""st=set(attribute,to,during,**args)
-
+
sets an attribute to a value for a
"""
def __init__(self,attribute,to=None,dur=None,**args):
@@ -878,10 +878,10 @@ class set(SVGelement):
self.attributes['dur']=dur
-
+
class svg(SVGelement):
"""s=svg(viewbox,width,height,**args)
-
+
a svg or element is the root of a drawing add all elements to a svg element.
You can have different svg elements in one svg file
s.addElement(SVGelement)
@@ -903,7 +903,7 @@ class svg(SVGelement):
if height<>None:
self.attributes['height']=height
self.namespace="http://www.w3.org/2000/svg"
-
+
class drawing:
"""d=drawing()
@@ -921,17 +921,17 @@ class drawing:
def setSVG(self,svg):
self.svg=svg
#Voeg een element toe aan de grafiek toe.
- if use_dom_implementation==0:
+ if use_dom_implementation==0:
def toXml(self, filename='',compress=False):
import cStringIO
xml=cStringIO.StringIO()
xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
if self.entity:
- xml.write(" [\n")
- for item in self.entity.keys():
- xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
- xml.write("]")
+ xml.write(" [\n")
+ for item in self.entity.keys():
+ xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
+ xml.write("]")
xml.write(">\n")
self.svg.toXml(0,xml)
if not filename:
@@ -964,7 +964,7 @@ class drawing:
compresses if filename ends with svgz or if compress is true
"""
doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
-
+
global root
#root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
#that is a bit messy.
@@ -1034,12 +1034,12 @@ class drawing:
print "SVG well formed"
if __name__=='__main__':
-
+
d=drawing()
s=svg((0,0,100,100))
r=rect(-100,-100,300,300,'cyan')
s.addElement(r)
-
+
t=title('SVGdraw Demo')
s.addElement(t)
g=group('animations')
@@ -1064,6 +1064,5 @@ if __name__=='__main__':
c=circle(i,j,1,'red','black',.5)
s.addElement(c)
d.setSVG(s)
-
- print d.toXml()
+ print d.toXml()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 6af7f846..6409e781 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -90,741 +90,741 @@ PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",
#########################################
def decodeEscape(str):
- a = str
- pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
- match = pattern.findall(a)
- matched = []
- for item in match:
- if item not in matched:
- a = a.replace(item, '%c' % eval("0x"+item[-2:]))
- matched.append(item)
- return a
-
+ a = str
+ pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
+ match = pattern.findall(a)
+ matched = []
+ for item in match:
+ if item not in matched:
+ a = a.replace(item, '%c' % eval("0x"+item[-2:]))
+ matched.append(item)
+ return a
+
def exportData(hddn, tdata, NP = None):
- for key in tdata.keys():
- _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
- if _val != None:
- hddn[key] = _val
- if _var != None:
- hddn['V'+key] = _var
- if NP and _N != None:
- hddn['N'+key] = _N
-
+ for key in tdata.keys():
+ _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
+ if _val != None:
+ hddn[key] = _val
+ if _var != None:
+ hddn['V'+key] = _var
+ if NP and _N != None:
+ hddn['N'+key] = _N
+
def genShortStrainName(RISet='', input_strainName=''):
- #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
- strainName = input_strainName
- if RISet != 'AXBXA':
- if RISet == 'BXD300':
- this_RISet = 'BXD'
- elif RISet == 'BDF2-2005':
- this_RISet = 'CASE05_'
- else:
- this_RISet = RISet
- strainName = string.replace(strainName,this_RISet,'')
- strainName = string.replace(strainName,'CASE','')
- try:
- strainName = "%02d" % int(strainName)
- except:
- pass
- else:
- strainName = string.replace(strainName,'AXB','A')
- strainName = string.replace(strainName,'BXA','B')
- try:
- strainName = strainName[0] + "%02d" % int(strainName[1:])
- except:
- pass
- return strainName
+ #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
+ strainName = input_strainName
+ if RISet != 'AXBXA':
+ if RISet == 'BXD300':
+ this_RISet = 'BXD'
+ elif RISet == 'BDF2-2005':
+ this_RISet = 'CASE05_'
+ else:
+ this_RISet = RISet
+ strainName = string.replace(strainName,this_RISet,'')
+ strainName = string.replace(strainName,'CASE','')
+ try:
+ strainName = "%02d" % int(strainName)
+ except:
+ pass
+ else:
+ strainName = string.replace(strainName,'AXB','A')
+ strainName = string.replace(strainName,'BXA','B')
+ try:
+ strainName = strainName[0] + "%02d" % int(strainName[1:])
+ except:
+ pass
+ return strainName
def toInt(in_str):
- "Converts an arbitrary string to an unsigned integer"
- start = -1
- end = -1
- for i, char in enumerate(in_str):
- if char >= '0' and char <= '9':
- if start < 0:
- start = i
- end = i+1
- else:
- if start >= 0:
- break
- if start < end:
- return int(in_str[start:end])
- else:
- return -1
+ "Converts an arbitrary string to an unsigned integer"
+ start = -1
+ end = -1
+ for i, char in enumerate(in_str):
+ if char >= '0' and char <= '9':
+ if start < 0:
+ start = i
+ end = i+1
+ else:
+ if start >= 0:
+ break
+ if start < end:
+ return int(in_str[start:end])
+ else:
+ return -1
def transpose(m):
- 'transpose a matrix'
- n = len(m)
- return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
+ 'transpose a matrix'
+ n = len(m)
+ return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
def asymTranspose(m):
- 'transpose a matrix'
- t = max(map(len, m))
- n = len(m)
- m2 = [["-"]]*n
- for i in range(n):
- m2[i] = m[i] + [""]*(t- len(m[i]))
- return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
+ 'transpose a matrix'
+ t = max(map(len, m))
+ n = len(m)
+ m2 = [["-"]]*n
+ for i in range(n):
+ m2[i] = m[i] + [""]*(t- len(m[i]))
+ return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
- from random import choice
- _str = prefix[:]
- for i in range(length):
- _str += choice(chars)
- return _str
+ from random import choice
+ _str = prefix[:]
+ for i in range(length):
+ _str += choice(chars)
+ return _str
def generate_session():
- import sha
- return sha.new(str(time.time())).hexdigest()
+ import sha
+ return sha.new(str(time.time())).hexdigest()
def cvt2Dict(x):
- tmp = {}
- for key in x.keys():
- tmp[key] = x[key]
- return tmp
+ tmp = {}
+ for key in x.keys():
+ tmp[key] = x[key]
+ return tmp
def dump_session(session_obj, filename):
- "It seems mod python can only cPickle most basic data type"
- import cPickle
- session_file = open(filename, 'wb')
- #try:
- # pass
- #except:
- # pass
- cPickle.dump(session_obj, session_file)
- session_file.close()
-
+ "It seems mod python can only cPickle most basic data type"
+ import cPickle
+ session_file = open(filename, 'wb')
+ #try:
+ # pass
+ #except:
+ # pass
+ cPickle.dump(session_obj, session_file)
+ session_file.close()
+
def StringAsFloat(str):
- 'Converts string to float but catches any exception and returns None'
- try:
- return float(str)
- except:
- return None
-
+ 'Converts string to float but catches any exception and returns None'
+ try:
+ return float(str)
+ except:
+ return None
+
def IntAsFloat(str):
- 'Converts string to Int but catches any exception and returns None'
- try:
- return int(str)
- except:
- return None
-
+ 'Converts string to Int but catches any exception and returns None'
+ try:
+ return int(str)
+ except:
+ return None
+
def FloatAsFloat(flt):
- 'Converts float to string but catches any exception and returns None'
- try:
- return float("%2.3f" % flt)
- except:
- return None
+ 'Converts float to string but catches any exception and returns None'
+ try:
+ return float("%2.3f" % flt)
+ except:
+ return None
def RemoveZero(flt):
- 'Converts string to float but catches any exception and returns None'
- try:
- if abs(flt) < 1e-6:
- return None
- else:
- return flt
- except:
- return None
+ 'Converts string to float but catches any exception and returns None'
+ try:
+ if abs(flt) < 1e-6:
+ return None
+ else:
+ return flt
+ except:
+ return None
def SciFloat(d):
- 'Converts string to float but catches any exception and returns None'
+ 'Converts string to float but catches any exception and returns None'
- try:
- if abs(d) <= 1.0e-4:
- return "%1.2e" % d
- else:
- return "%1.5f" % d
- except:
- return None
+ try:
+ if abs(d) <= 1.0e-4:
+ return "%1.2e" % d
+ else:
+ return "%1.5f" % d
+ except:
+ return None
###To be removed
def FloatList2String(lst):
- 'Converts float list to string but catches any exception and returns None'
- tt=''
- try:
- for item in lst:
- if item == None:
- tt += 'X '
- else:
- tt += '%f ' % item
- return tt
- except:
- return ""
+ 'Converts float list to string but catches any exception and returns None'
+ tt=''
+ try:
+ for item in lst:
+ if item == None:
+ tt += 'X '
+ else:
+ tt += '%f ' % item
+ return tt
+ except:
+ return ""
def ListNotNull(lst):
- 'Determine if the elements in a list are all null'
- for item in lst:
- if item is not None:
- return 1
- return None
-
+ 'Determine if the elements in a list are all null'
+ for item in lst:
+ if item is not None:
+ return 1
+ return None
+
###To be removed
def FileDataProcess(str):
- 'Remove the description text from the input file if theres any'
- i=0
- while i<len(str):
- if str[i]<'\x7f' and str[i]>'\x20':
- break
- else:
- i+=1
- str=str[i:]
- str=string.join(string.split(str,'\000'),'')
- i=string.find(str,"*****")
- if i>-1:
- return str[i+5:]
- else:
- return str
+ 'Remove the description text from the input file if theres any'
+ i=0
+ while i<len(str):
+ if str[i]<'\x7f' and str[i]>'\x20':
+ break
+ else:
+ i+=1
+ str=str[i:]
+ str=string.join(string.split(str,'\000'),'')
+ i=string.find(str,"*****")
+ if i>-1:
+ return str[i+5:]
+ else:
+ return str
def rank(a,lst,offset=0):
- """Calculate the integer rank of a number in an array, can be used to calculate p-value"""
- n = len(lst)
- if n == 2:
- if a <lst[0]:
- return offset
- elif a > lst[1]:
- return offset + 2
- else:
- return offset +1
- elif n == 1:
- if a <lst[0]:
- return offset
- else:
- return offset +1
- elif n== 0:
- return offset
- else:
- mid = n/2
- if a < lst[mid]:
- return rank(a,lst[:mid-1],offset)
- else:
- return rank(a,lst[mid:],offset+mid)
+ """Calculate the integer rank of a number in an array, can be used to calculate p-value"""
+ n = len(lst)
+ if n == 2:
+ if a <lst[0]:
+ return offset
+ elif a > lst[1]:
+ return offset + 2
+ else:
+ return offset +1
+ elif n == 1:
+ if a <lst[0]:
+ return offset
+ else:
+ return offset +1
+ elif n== 0:
+ return offset
+ else:
+ mid = n/2
+ if a < lst[mid]:
+ return rank(a,lst[:mid-1],offset)
+ else:
+ return rank(a,lst[mid:],offset+mid)
def cmpScanResult(A,B):
- try:
- if A.LRS > B.LRS:
- return 1
- elif A.LRS == B.LRS:
- return 0
- else:
- return -1
- except:
- return 0
-
-
+ try:
+ if A.LRS > B.LRS:
+ return 1
+ elif A.LRS == B.LRS:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+
def cmpScanResult2(A,B):
- try:
- if A.LRS < B.LRS:
- return 1
- elif A.LRS == B.LRS:
- return 0
- else:
- return -1
- except:
- return 0
+ try:
+ if A.LRS < B.LRS:
+ return 1
+ elif A.LRS == B.LRS:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
def cmpOrder(A,B):
- try:
- if A[1] < B[1]:
- return -1
- elif A[1] == B[1]:
- return 0
- else:
- return 1
- except:
- return 0
+ try:
+ if A[1] < B[1]:
+ return -1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
def cmpOrder2(A,B):
- try:
- if A[-1] < B[-1]:
- return -1
- elif A[-1] == B[-1]:
- return 0
- else:
- return 1
- except:
- return 0
+ try:
+ if A[-1] < B[-1]:
+ return -1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
def calRank(xVals, yVals, N): ### Zach Sloan, February 4 2010
- """
- Returns a ranked set of X and Y values. These are used when generating
- a Spearman scatterplot. Bear in mind that this sets values equal to each
- other as the same rank.
- """
- XX = []
- YY = []
- X = [0]*len(xVals)
- Y = [0]*len(yVals)
- j = 0
-
- for i in range(len(xVals)):
-
- if xVals[i] != None and yVals[i] != None:
- XX.append((j, xVals[i]))
- YY.append((j, yVals[i]))
- j = j + 1
-
- NN = len(XX)
-
- XX.sort(cmpOrder2)
- YY.sort(cmpOrder2)
-
- j = 1
- rank = 0.0
-
- while j < NN:
-
- if XX[j][1] != XX[j-1][1]:
- X[XX[j-1][0]] = j
- j = j+1
-
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (XX[jt][1] != XX[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- X[XX[ji][0]] = rank
- if (jt == NN-1):
- if (XX[jt][1] == XX[j-1][1]):
- X[XX[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if X[XX[NN-1][0]] == 0:
- X[XX[NN-1][0]] = NN
-
- j = 1
- rank = 0.0
-
- while j < NN:
-
- if YY[j][1] != YY[j-1][1]:
- Y[YY[j-1][0]] = j
- j = j+1
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (YY[jt][1] != YY[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- Y[YY[ji][0]] = rank
- if (jt == NN-1):
- if (YY[jt][1] == YY[j-1][1]):
- Y[YY[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if Y[YY[NN-1][0]] == 0:
- Y[YY[NN-1][0]] = NN
-
- return (X,Y)
+ """
+ Returns a ranked set of X and Y values. These are used when generating
+ a Spearman scatterplot. Bear in mind that this sets values equal to each
+ other as the same rank.
+ """
+ XX = []
+ YY = []
+ X = [0]*len(xVals)
+ Y = [0]*len(yVals)
+ j = 0
+
+ for i in range(len(xVals)):
+
+ if xVals[i] != None and yVals[i] != None:
+ XX.append((j, xVals[i]))
+ YY.append((j, yVals[i]))
+ j = j + 1
+
+ NN = len(XX)
+
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+
+ j = 1
+ rank = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ return (X,Y)
def calCorrelationRank(xVals,yVals,N):
- """
- Calculated Spearman Ranked Correlation. The algorithm works
- by setting all tied ranks to the average of those ranks (for
- example, if ranks 5-10 all have the same value, each will be set
- to rank 7.5).
- """
-
- XX = []
- YY = []
- j = 0
-
- for i in range(len(xVals)):
- if xVals[i]!= None and yVals[i]!= None:
- XX.append((j,xVals[i]))
- YY.append((j,yVals[i]))
- j = j+1
-
- NN = len(XX)
- if NN <6:
- return (0.0,NN)
- XX.sort(cmpOrder2)
- YY.sort(cmpOrder2)
- X = [0]*NN
- Y = [0]*NN
-
- j = 1
- rank = 0.0
- t = 0.0
- sx = 0.0
-
- while j < NN:
-
- if XX[j][1] != XX[j-1][1]:
- X[XX[j-1][0]] = j
- j = j+1
-
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (XX[jt][1] != XX[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- X[XX[ji][0]] = rank
- t = jt-j
- sx = sx + (t*t*t-t)
- if (jt == NN-1):
- if (XX[jt][1] == XX[j-1][1]):
- X[XX[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if X[XX[NN-1][0]] == 0:
- X[XX[NN-1][0]] = NN
-
- j = 1
- rank = 0.0
- t = 0.0
- sy = 0.0
-
- while j < NN:
-
- if YY[j][1] != YY[j-1][1]:
- Y[YY[j-1][0]] = j
- j = j+1
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (YY[jt][1] != YY[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- Y[YY[ji][0]] = rank
- t = jt - j
- sy = sy + (t*t*t-t)
- if (jt == NN-1):
- if (YY[jt][1] == YY[j-1][1]):
- Y[YY[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if Y[YY[NN-1][0]] == 0:
- Y[YY[NN-1][0]] = NN
-
- D = 0.0
-
- for i in range(NN):
- D += (X[i]-Y[i])*(X[i]-Y[i])
-
- fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
- return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
+ """
+ Calculated Spearman Ranked Correlation. The algorithm works
+ by setting all tied ranks to the average of those ranks (for
+ example, if ranks 5-10 all have the same value, each will be set
+ to rank 7.5).
+ """
+
+ XX = []
+ YY = []
+ j = 0
+
+ for i in range(len(xVals)):
+ if xVals[i]!= None and yVals[i]!= None:
+ XX.append((j,xVals[i]))
+ YY.append((j,yVals[i]))
+ j = j+1
+
+ NN = len(XX)
+ if NN <6:
+ return (0.0,NN)
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+ X = [0]*NN
+ Y = [0]*NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sx = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ t = jt-j
+ sx = sx + (t*t*t-t)
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sy = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ t = jt - j
+ sy = sy + (t*t*t-t)
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ D = 0.0
+
+ for i in range(NN):
+ D += (X[i]-Y[i])*(X[i]-Y[i])
+
+ fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
+
+ return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
+
+
def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008
- """Calculates correlation ranks with data formatted from the text file.
- dbdata, userdata are lists of strings. N is an int. Returns a float.
- Used by correlationPage"""
- XX = []
- YY = []
- j = 0
- for i in range(N):
- if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
- XX.append((j,float(dbdata[i])))
- YY.append((j,float(userdata[i])))
- j += 1
- NN = len(XX)
- if NN <6:
- return (0.0,NN)
- XX.sort(cmpOrder2)
- YY.sort(cmpOrder2)
- X = [0]*NN
- Y = [0]*NN
-
- j = 1
- rank = 0.0
- t = 0.0
- sx = 0.0
-
- while j < NN:
-
- if XX[j][1] != XX[j-1][1]:
- X[XX[j-1][0]] = j
- j = j+1
-
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (XX[jt][1] != XX[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- X[XX[ji][0]] = rank
- t = jt-j
- sx = sx + (t*t*t-t)
- if (jt == NN-1):
- if (XX[jt][1] == XX[j-1][1]):
- X[XX[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if X[XX[NN-1][0]] == 0:
- X[XX[NN-1][0]] = NN
-
- j = 1
- rank = 0.0
- t = 0.0
- sy = 0.0
-
- while j < NN:
-
- if YY[j][1] != YY[j-1][1]:
- Y[YY[j-1][0]] = j
- j = j+1
- else:
- jt = j+1
- ji = j
- for jt in range(j+1, NN):
- if (YY[jt][1] != YY[j-1][1]):
- break
- rank = 0.5*(j+jt)
- for ji in range(j-1, jt):
- Y[YY[ji][0]] = rank
- t = jt - j
- sy = sy + (t*t*t-t)
- if (jt == NN-1):
- if (YY[jt][1] == YY[j-1][1]):
- Y[YY[NN-1][0]] = rank
- j = jt+1
-
- if j == NN:
- if Y[YY[NN-1][0]] == 0:
- Y[YY[NN-1][0]] = NN
-
- D = 0.0
-
- for i in range(NN):
- D += (X[i]-Y[i])*(X[i]-Y[i])
-
- fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
- return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
+ """Calculates correlation ranks with data formatted from the text file.
+ dbdata, userdata are lists of strings. N is an int. Returns a float.
+ Used by correlationPage"""
+ XX = []
+ YY = []
+ j = 0
+ for i in range(N):
+ if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
+ XX.append((j,float(dbdata[i])))
+ YY.append((j,float(userdata[i])))
+ j += 1
+ NN = len(XX)
+ if NN <6:
+ return (0.0,NN)
+ XX.sort(cmpOrder2)
+ YY.sort(cmpOrder2)
+ X = [0]*NN
+ Y = [0]*NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sx = 0.0
+
+ while j < NN:
+
+ if XX[j][1] != XX[j-1][1]:
+ X[XX[j-1][0]] = j
+ j = j+1
+
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (XX[jt][1] != XX[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ X[XX[ji][0]] = rank
+ t = jt-j
+ sx = sx + (t*t*t-t)
+ if (jt == NN-1):
+ if (XX[jt][1] == XX[j-1][1]):
+ X[XX[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if X[XX[NN-1][0]] == 0:
+ X[XX[NN-1][0]] = NN
+
+ j = 1
+ rank = 0.0
+ t = 0.0
+ sy = 0.0
+
+ while j < NN:
+
+ if YY[j][1] != YY[j-1][1]:
+ Y[YY[j-1][0]] = j
+ j = j+1
+ else:
+ jt = j+1
+ ji = j
+ for jt in range(j+1, NN):
+ if (YY[jt][1] != YY[j-1][1]):
+ break
+ rank = 0.5*(j+jt)
+ for ji in range(j-1, jt):
+ Y[YY[ji][0]] = rank
+ t = jt - j
+ sy = sy + (t*t*t-t)
+ if (jt == NN-1):
+ if (YY[jt][1] == YY[j-1][1]):
+ Y[YY[NN-1][0]] = rank
+ j = jt+1
+
+ if j == NN:
+ if Y[YY[NN-1][0]] == 0:
+ Y[YY[NN-1][0]] = NN
+
+ D = 0.0
+
+ for i in range(NN):
+ D += (X[i]-Y[i])*(X[i]-Y[i])
+
+ fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
+
+ return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
def calCorrelation(dbdata,userdata,N):
- X = []
- Y = []
- for i in range(N):
- if dbdata[i]!= None and userdata[i]!= None:
- X.append(dbdata[i])
- Y.append(userdata[i])
- NN = len(X)
- if NN <6:
- return (0.0,NN)
- sx = reduce(lambda x,y:x+y,X,0.0)
- sy = reduce(lambda x,y:x+y,Y,0.0)
- meanx = sx/NN
- meany = sy/NN
- xyd = 0.0
- sxd = 0.0
- syd = 0.0
- for i in range(NN):
- xyd += (X[i] - meanx)*(Y[i]-meany)
- sxd += (X[i] - meanx)*(X[i] - meanx)
- syd += (Y[i] - meany)*(Y[i] - meany)
- try:
- corr = xyd/(sqrt(sxd)*sqrt(syd))
- except:
- corr = 0
- return (corr,NN)
+ X = []
+ Y = []
+ for i in range(N):
+ if dbdata[i]!= None and userdata[i]!= None:
+ X.append(dbdata[i])
+ Y.append(userdata[i])
+ NN = len(X)
+ if NN <6:
+ return (0.0,NN)
+ sx = reduce(lambda x,y:x+y,X,0.0)
+ sy = reduce(lambda x,y:x+y,Y,0.0)
+ meanx = sx/NN
+ meany = sy/NN
+ xyd = 0.0
+ sxd = 0.0
+ syd = 0.0
+ for i in range(NN):
+ xyd += (X[i] - meanx)*(Y[i]-meany)
+ sxd += (X[i] - meanx)*(X[i] - meanx)
+ syd += (Y[i] - meany)*(Y[i] - meany)
+ try:
+ corr = xyd/(sqrt(sxd)*sqrt(syd))
+ except:
+ corr = 0
+ return (corr,NN)
def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008
- """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings. N is an int. Returns a float
- Used by correlationPage"""
- X = []
- Y = []
- for i in range(N):
- #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
- # X.append(float(dbdata[i]))
- # Y.append(float(userdata[i]))
- if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
- continue
- else:
- X.append(float(dbdata[i]))
- Y.append(float(userdata[i]))
- NN = len(X)
- if NN <6:
- return (0.0,NN)
- sx = sum(X)
- sy = sum(Y)
- meanx = sx/float(NN)
- meany = sy/float(NN)
- xyd = 0.0
- sxd = 0.0
- syd = 0.0
- for i in range(NN):
- x1 = X[i]-meanx
- y1 = Y[i]-meany
- xyd += x1*y1
- sxd += x1**2
- syd += y1**2
- try:
- corr = xyd/(sqrt(sxd)*sqrt(syd))
- except:
- corr = 0
- return (corr,NN)
+ """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings. N is an int. Returns a float
+ Used by correlationPage"""
+ X = []
+ Y = []
+ for i in range(N):
+ #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
+ # X.append(float(dbdata[i]))
+ # Y.append(float(userdata[i]))
+ if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
+ continue
+ else:
+ X.append(float(dbdata[i]))
+ Y.append(float(userdata[i]))
+ NN = len(X)
+ if NN <6:
+ return (0.0,NN)
+ sx = sum(X)
+ sy = sum(Y)
+ meanx = sx/float(NN)
+ meany = sy/float(NN)
+ xyd = 0.0
+ sxd = 0.0
+ syd = 0.0
+ for i in range(NN):
+ x1 = X[i]-meanx
+ y1 = Y[i]-meany
+ xyd += x1*y1
+ sxd += x1**2
+ syd += y1**2
+ try:
+ corr = xyd/(sqrt(sxd)*sqrt(syd))
+ except:
+ corr = 0
+ return (corr,NN)
def readLineCSV(line): ### dcrowell July 2008
- """Parses a CSV string of text and returns a list containing each element as a string.
- Used by correlationPage"""
- returnList = line.split('","')
- returnList[-1]=returnList[-1][:-2]
- returnList[0]=returnList[0][1:]
- return returnList
+ """Parses a CSV string of text and returns a list containing each element as a string.
+ Used by correlationPage"""
+ returnList = line.split('","')
+ returnList[-1]=returnList[-1][:-2]
+ returnList[0]=returnList[0][1:]
+ return returnList
def cmpCorr(A,B):
- try:
- if abs(A[1]) < abs(B[1]):
- return 1
- elif abs(A[1]) == abs(B[1]):
- return 0
- else:
- return -1
- except:
- return 0
+ try:
+ if abs(A[1]) < abs(B[1]):
+ return 1
+ elif abs(A[1]) == abs(B[1]):
+ return 0
+ else:
+ return -1
+ except:
+ return 0
def cmpLitCorr(A,B):
- try:
- if abs(A[3]) < abs(B[3]): return 1
- elif abs(A[3]) == abs(B[3]):
- if abs(A[1]) < abs(B[1]): return 1
- elif abs(A[1]) == abs(B[1]): return 0
- else: return -1
- else: return -1
- except:
- return 0
+ try:
+ if abs(A[3]) < abs(B[3]): return 1
+ elif abs(A[3]) == abs(B[3]):
+ if abs(A[1]) < abs(B[1]): return 1
+ elif abs(A[1]) == abs(B[1]): return 0
+ else: return -1
+ else: return -1
+ except:
+ return 0
def cmpPValue(A,B):
- try:
- if A.corrPValue < B.corrPValue:
- return -1
- elif A.corrPValue == B.corrPValue:
- if abs(A.corr) > abs(B.corr):
- return -1
- elif abs(A.corr) < abs(B.corr):
- return 1
- else:
- return 0
- else:
- return 1
- except:
- return 0
+ try:
+ if A.corrPValue < B.corrPValue:
+ return -1
+ elif A.corrPValue == B.corrPValue:
+ if abs(A.corr) > abs(B.corr):
+ return -1
+ elif abs(A.corr) < abs(B.corr):
+ return 1
+ else:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
def cmpEigenValue(A,B):
- try:
- if A[0] > B[0]:
- return -1
- elif A[0] == B[0]:
- return 0
- else:
- return 1
- except:
- return 0
+ try:
+ if A[0] > B[0]:
+ return -1
+ elif A[0] == B[0]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
def cmpLRSFull(A,B):
- try:
- if A[0] < B[0]:
- return -1
- elif A[0] == B[0]:
- return 0
- else:
- return 1
- except:
- return 0
+ try:
+ if A[0] < B[0]:
+ return -1
+ elif A[0] == B[0]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
def cmpLRSInteract(A,B):
- try:
- if A[1] < B[1]:
- return -1
- elif A[1] == B[1]:
- return 0
- else:
- return 1
- except:
- return 0
-
-
+ try:
+ if A[1] < B[1]:
+ return -1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
+
def cmpPos(A,B):
- try:
- try:
- AChr = int(A.chr)
- except:
- AChr = 20
- try:
- BChr = int(B.chr)
- except:
- BChr = 20
- if AChr > BChr:
- return 1
- elif AChr == BChr:
- if A.mb > B.mb:
- return 1
- if A.mb == B.mb:
- return 0
- else:
- return -1
- else:
- return -1
- except:
- return 0
-
+ try:
+ try:
+ AChr = int(A.chr)
+ except:
+ AChr = 20
+ try:
+ BChr = int(B.chr)
+ except:
+ BChr = 20
+ if AChr > BChr:
+ return 1
+ elif AChr == BChr:
+ if A.mb > B.mb:
+ return 1
+ if A.mb == B.mb:
+ return 0
+ else:
+ return -1
+ else:
+ return -1
+ except:
+ return 0
+
def cmpGenoPos(A,B):
- try:
- A1 = A.chr
- B1 = B.chr
- try:
- A1 = int(A1)
- except:
- A1 = 25
- try:
- B1 = int(B1)
- except:
- B1 = 25
- if A1 > B1:
- return 1
- elif A1 == B1:
- if A.mb > B.mb:
- return 1
- if A.mb == B.mb:
- return 0
- else:
- return -1
- else:
- return -1
- except:
- return 0
+ try:
+ A1 = A.chr
+ B1 = B.chr
+ try:
+ A1 = int(A1)
+ except:
+ A1 = 25
+ try:
+ B1 = int(B1)
+ except:
+ B1 = 25
+ if A1 > B1:
+ return 1
+ elif A1 == B1:
+ if A.mb > B.mb:
+ return 1
+ if A.mb == B.mb:
+ return 0
+ else:
+ return -1
+ else:
+ return -1
+ except:
+ return 0
#XZhou: Must use "BINARY" to enable case sensitive comparison.
def authUser(name,password,db, encrypt=None):
- try:
- if encrypt:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
- else:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
- db.execute(query)
- records = db.fetchone()
- if not records:
- raise ValueError
- return records#(privilege,id,name,password,grpName)
- except:
- return (None, None, None, None, None)
+ try:
+ if encrypt:
+ query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
+ else:
+ query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
+ db.execute(query)
+ records = db.fetchone()
+ if not records:
+ raise ValueError
+ return records#(privilege,id,name,password,grpName)
+ except:
+ return (None, None, None, None, None)
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
@@ -840,9 +840,9 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users)
class VisualizeException(Exception):
def __init__(self, message):
- self.message = message
+ self.message = message
def __str__(self):
- return self.message
+ return self.message
# safeConvert : (string -> A) -> A -> A
# to convert a string to type A, using the supplied default value
@@ -852,12 +852,12 @@ def safeConvert(f, value, default):
return f(value)
except:
return default
-
+
# safeFloat : string -> float -> float
# to convert a string to a float safely
def safeFloat(value, default):
return safeConvert(float, value, default)
-
+
# safeInt: string -> int -> int
# to convert a string to an int safely
def safeInt(value, default):
@@ -878,7 +878,7 @@ def yesNoToInt(value):
if value == "yes":
return 1
elif value == "no":
- return 0
+ return 0
else:
return None
@@ -890,79 +890,79 @@ def intToYesNo(value):
elif value == 0:
return "no"
else:
- return None
-
+ return None
+
def formatField(name):
- name = name.replace("_", " ")
- name = name.title()
- #name = name.replace("Mb Mm6", "Mb");
- return name.replace("Id", "ID")
+ name = name.replace("_", " ")
+ name = name.title()
+ #name = name.replace("Mb Mm6", "Mb");
+ return name.replace("Id", "ID")
#XZ, 03/27/2009: This function is very specific.
#It is used by AJAX_table.py, correlationPage.py and dataPage.py
def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]):
- header = tblobj['header']
- body = tblobj['body']
- field, order = sortby
-
- #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
- hiddenColumnsString = ",".join(hiddenColumns)
-
- tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
-
- hiddenColumnIdx = [] #indices of columns to hide
- idx = -1
- last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
- for row in header:
- hr = HT.TR()
- for i, item in enumerate(row):
- if (item.text == '') or (item.text not in hiddenColumns):
- if item.sort and item.text:
- down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)
- up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
- if item.text == field:
- idx = item.idx
- last_idx = idx
- if order == 'up':
- up = IMGASCON
- elif order == 'down':
- down = IMGDESCON
- item.html.append(HT.Div(up, down, style="float: bottom;"))
- hr.append(item.html)
- else:
- hiddenColumnIdx.append(i)
- tbl.append(hr)
-
- for i, row in enumerate(body):
- for j, item in enumerate(row):
- if order == 'down':
- if (item.val == '' or item.val == 'x' or item.val == 'None'):
- item.val = 0
- if order == 'up':
- if (item.val == '' or item.val == 'x' or item.val == 'None'):
- item.val = 'zzzzz'
-
- if idx >= 0:
- if order == 'down':
- body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
- elif order == 'up':
- body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
- else:
- pass
-
- for i, row in enumerate(body):
- hr = HT.TR(Id = row[0].text)
- for j, item in enumerate(row):
- if (j not in hiddenColumnIdx):
- if j == 0:
- if addIndex == "1":
- item.html.contents = [i+1] + item.html.contents
- hr.append(item.html)
- tbl.append(hr)
-
- return tbl
+ header = tblobj['header']
+ body = tblobj['body']
+ field, order = sortby
+
+ #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
+ hiddenColumnsString = ",".join(hiddenColumns)
+
+ tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
+
+ hiddenColumnIdx = [] #indices of columns to hide
+ idx = -1
+ last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
+ for row in header:
+ hr = HT.TR()
+ for i, item in enumerate(row):
+ if (item.text == '') or (item.text not in hiddenColumns):
+ if item.sort and item.text:
+ down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)
+ up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
+ if item.text == field:
+ idx = item.idx
+ last_idx = idx
+ if order == 'up':
+ up = IMGASCON
+ elif order == 'down':
+ down = IMGDESCON
+ item.html.append(HT.Div(up, down, style="float: bottom;"))
+ hr.append(item.html)
+ else:
+ hiddenColumnIdx.append(i)
+ tbl.append(hr)
+
+ for i, row in enumerate(body):
+ for j, item in enumerate(row):
+ if order == 'down':
+ if (item.val == '' or item.val == 'x' or item.val == 'None'):
+ item.val = 0
+ if order == 'up':
+ if (item.val == '' or item.val == 'x' or item.val == 'None'):
+ item.val = 'zzzzz'
+
+ if idx >= 0:
+ if order == 'down':
+ body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
+ elif order == 'up':
+ body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
+ else:
+ pass
+
+ for i, row in enumerate(body):
+ hr = HT.TR(Id = row[0].text)
+ for j, item in enumerate(row):
+ if (j not in hiddenColumnIdx):
+ if j == 0:
+ if addIndex == "1":
+ item.html.contents = [i+1] + item.html.contents
+ hr.append(item.html)
+ tbl.append(hr)
+
+ return tbl
def natsort_key(string):
r = []
@@ -974,4 +974,3 @@ def natsort_key(string):
except:
r.append(c)
return r
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 20:11:18 +0000