From c9b0ab18457929bd7ca458f7207e50fe14099d6a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 16:51:54 +0000
Subject: Removed the basicStatistics directory/contents because nothing there
was being used except corestats, which I moved to utility
Removed box plot code from Plot.py since we no longer use it either
---
wqflask/utility/Plot.py | 134 +-----------------------------------------------
1 file changed, 1 insertion(+), 133 deletions(-)
(limited to 'wqflask/utility/Plot.py')
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d60e2bb2..3a8b8dd5 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -36,11 +36,10 @@ from numarray import linear_algebra as la
from numarray import ones, array, dot, swapaxes
import reaper
-# sys.path.append("..") Never in a running webserver
-from basicStatistics import corestats
import svg
import webqtlUtil
+import corestats
from base import webqtlConfig
import utility.logger
@@ -315,137 +314,6 @@ def find_outliers(vals):
logger.debug(pf(locals()))
return upper_bound, lower_bound
-
-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)
-
def plotSecurity(canvas, text="12345"):
if not text:
return
--
cgit v1.2.3
From bd6d36ddb366a3ee427a0c237ebf8f672606ff19 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 18:13:59 +0000
Subject: Fixed issue that caused and error for certain types of mapping due to
variable not being initialized
Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them.
Also removed unused file AJAX_table.py and other unused code from several other files
---
wqflask/utility/AJAX_table.py | 155 ----
wqflask/utility/Plot.py | 854 +--------------------
wqflask/utility/after.py | 8 +-
wqflask/utility/benchmark.py | 2 +-
wqflask/utility/genofile_parser.py | 2 +-
wqflask/utility/logger.py | 2 +-
wqflask/utility/webqtlUtil.py | 132 +---
.../marker_regression/marker_regression_gn1.py | 5 +-
8 files changed, 10 insertions(+), 1150 deletions(-)
delete mode 100644 wqflask/utility/AJAX_table.py
(limited to 'wqflask/utility/Plot.py')
diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py
deleted file mode 100644
index d70acfcd..00000000
--- a/wqflask/utility/AJAX_table.py
+++ /dev/null
@@ -1,155 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import cPickle
-import os
-import MySQLdb
-import time
-import pyXLWriter as xl
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from THCell import THCell
-from TDCell import TDCell
-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()
-
- logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
-
- 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 = "The table is no longer available on this server"
-
- 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 3a8b8dd5..dbcee331 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -82,202 +82,6 @@ def frange(start, end=None, inc=1.0):
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
-
- 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)=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
-
-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]
-
- 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]
-
- d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
- #Define break-points.
-
- p_low = 0.02425
- p_high = 1 - p_low
-
- #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)
-
-
- #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)
-
- #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)
-
- 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
-
-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]
-
-def gpercentile(lst2, np):
- """Obsolete - use percentile in corestats instead"""
- 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 find_outliers(vals):
"""Calculates the upper and lower bounds of a set of sample/case values
@@ -314,34 +118,6 @@ def find_outliers(vals):
logger.debug(pf(locals()))
return upper_bound, lower_bound
-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
-
# 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):
@@ -429,542 +205,6 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
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
-
-#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
-
-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
-
-
# This function determines the scale of the plot
def detScaleOld(min,max):
if min>=max:
@@ -982,7 +222,7 @@ def detScaleOld(min,max):
high=c*ceil(max/c)
return [low,high,round((high-low)/c)]
-def detScale(min=0,max=0,bufferSpace=3):
+def detScale(min=0,max=0):
if min>=max:
return None
@@ -1019,57 +259,9 @@ def detScale(min=0,max=0,bufferSpace=3):
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
-
-
-
-
def bluefunc(x):
return 1.0 / (1.0 + exp(-10*(x-0.6)))
-
def redfunc(x):
return 1.0 / (1.0 + exp(10*(x-0.5)))
@@ -1098,52 +290,10 @@ def colorSpectrum(n=100):
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
-
-
-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
-
-
def _test():
import doctest
doctest.testmod()
if __name__=="__main__":
- _test()
+ _test()
\ No newline at end of file
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index a3bb85e9..b628a0a4 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -13,10 +13,4 @@ def after_this_request(f):
if not hasattr(g, 'after_request_callbacks'):
g.after_request_callbacks = []
g.after_request_callbacks.append(f)
- return f
-
-@app.after_request
-def call_after_request_callbacks(response):
- for callback in getattr(g, 'after_request_callbacks', ()):
- callback(response)
- return response
+ return f
\ No newline at end of file
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 8c97370d..8f1c916b 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -11,7 +11,7 @@ logger = getLogger(__name__ )
class Bench(object):
entries = collections.OrderedDict()
- def __init__(self, name=None, write_output=True):
+ def __init__(self, name=None, write_output=LOG_BENCH):
self.name = name
self.write_output = write_output
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 7149e560..af306731 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -72,7 +72,7 @@ class ConvertGenoFile(object):
yield row
def process_csv(self):
- for row_count, row in enumerate(self.process_rows()):
+ for row in self.process_rows():
row_items = row.split("\t")
this_marker = Marker()
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 128706df..510b1041 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -33,7 +33,7 @@ from pprint import pformat as pf
from inspect import stack
import datetime
-from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
+from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL
class GNLogger:
"""A logger class with some additional functionality, such as
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4fc978f5..2336e722 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -90,70 +90,6 @@ PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",
# Accessory Functions
#########################################
-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]
-
- 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]
-
- d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
- #Define break-points.
-
- p_low = 0.02425
- p_high = 1 - p_low
-
- #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)
-
-
- #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)
-
- #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)
-
- 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 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
-
-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
-
def decodeEscape(str):
a = str
pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
@@ -952,72 +888,6 @@ def formatField(name):
#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
-
def natsort_key(string):
r = []
for c in string:
@@ -1027,4 +897,4 @@ def natsort_key(string):
except: r.append(c)
except:
r.append(c)
- return r
+ return r
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index c196b58b..632c2f8f 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1160,6 +1160,7 @@ class MarkerRegression(object):
else:
string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (self.dataset.group.name, self.ChrList[self.selectedChr][0])
+ string3 = ''
if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
if self.use_loco == "True":
string2 = 'Using GEMMA mapping method with LOCO and '
@@ -1170,7 +1171,7 @@ class MarkerRegression(object):
cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")])
string3 = cofactor_names
else:
- string2 += 'no cofactors.'
+ string2 += 'no cofactors'
string3 = ''
elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
string2 = 'Using R/qtl mapping method with '
@@ -1179,7 +1180,7 @@ class MarkerRegression(object):
else:
string2 += 'no control for other QTLs'
elif self.mapping_method == "plink":
- string2 = 'Using PLINK mapping method with no control for other QTLs.'
+ string2 = 'Using PLINK mapping method with no control for other QTLs'
else:
string2 = 'Using Haldane mapping function with '
if self.controlLocus and self.doControl != "false":
--
cgit v1.2.3
From 23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 23:07:33 +0000
Subject: Removed svg.py, which I know isn't used, and webqtlFormData, which
I'm pretty sure also isn't used any more.
Also removed some other unused code from the files listed
---
wqflask/base/webqtlFormData.py | 257 -----
wqflask/utility/Plot.py | 1 -
wqflask/utility/svg.py | 1068 --------------------
wqflask/utility/webqtlUtil.py | 88 --
wqflask/wqflask/correlation/show_corr_results.py | 52 -
.../marker_regression/marker_regression_gn1.py | 16 -
wqflask/wqflask/views.py | 80 +-
7 files changed, 22 insertions(+), 1540 deletions(-)
delete mode 100644 wqflask/base/webqtlFormData.py
delete mode 100644 wqflask/utility/svg.py
(limited to 'wqflask/utility/Plot.py')
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
deleted file mode 100644
index 1b41b2fc..00000000
--- a/wqflask/base/webqtlFormData.py
+++ /dev/null
@@ -1,257 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-from __future__ import print_function
-from pprint import pformat as pf
-
-import string
-import os
-
-import reaper
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from utility import webqtlUtil
-
-class webqtlFormData(object):
- 'Represents data from a WebQTL form page, needed to generate the next page'
-
- attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance'
- 'suggestive','significance','submitID','identification', 'enablevariance',
- 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
-
- #XZ: Attention! All attribute values must be picklable!
-
- def __init__(self,
- start_vars = None,
- req = None):
- # Todo: rework this whole thing
- for item in webqtlFormData.attrs:
- self.__dict__[item] = None
-
- for item in start_vars:
- self.__dict__[item] = start_vars[item]
-
- #Todo: This can't be good below...rework
- try:
- self.remote_ip = req.connection.remote_ip
- except:
- self.remote_ip = '1.2.3.4'
-
- self.ppolar = None
- self.mpolar = None
-
- if self.group:
- _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
-
- def set_number(stringy):
- return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
-
- self.nperm = set_number(self.nperm)
- self.nboot = set_number(self.nboot)
-
- if self.allsamplelist:
- self.allsamplelist = self.allsamplelist.split()
-
- if self.group == 'BXD300':
- self.group = 'BXD'
-
- def __getitem__(self, key):
- return self.__dict__[key]
-
- def get(self, key, default=None):
- if key in self.__dict__:
- return self.__dict__[key]
- else:
- return default
-
- def __str__(self):
- rstr = ''
- for item in self.attrs:
- if item != 'genotype':
- rstr += '%s:%s\n' % (item,str(getattr(self,item)))
- return rstr
-
-
- def readGenotype(self):
- '''read genotype from .geno file'''
- if self.group == 'BXD300':
- self.group = 'BXD'
-
- assert self.group, "self.group needs to be set"
-
- #genotype_1 is Dataset Object without parents and f1
- #genotype_2 is Dataset Object with parents and f1 (not for intercross)
-
- self.genotype_1 = reaper.Dataset()
-
- full_filename = locate(self.group + '.geno','genotype')
-
- # reaper barfs on unicode filenames, so here we ensure it's a string
- full_filename = str(full_filename)
- self.genotype_1.read(full_filename)
-
- print("Got to after read")
-
- try:
- # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group]
- except KeyError:
- _f1 = _f12 = _mat = _pat = None
-
- self.genotype_2 = self.genotype_1
- if self.genotype_1.type == "group" and _mat and _pat:
- self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
-
- #determine default genotype object
- if self.incparentsf1 and self.genotype_1.type != "intercross":
- self.genotype = self.genotype_2
- else:
- self.incparentsf1 = 0
- self.genotype = self.genotype_1
-
- self.samplelist = list(self.genotype.prgy)
- self.f1list = []
- self.parlist = []
-
- if _f1 and _f12:
- self.f1list = [_f1, _f12]
- if _mat and _pat:
- self.parlist = [_mat, _pat]
-
-
- def readData(self, samplelist, incf1=None):
- '''read user input data or from trait data and analysis form'''
-
- if incf1 == None:
- incf1 = []
-
- if not self.genotype:
- self.readGenotype()
- if not samplelist:
- if incf1:
- samplelist = self.f1list + self.samplelist
- else:
- samplelist = self.samplelist
-
- traitfiledata = getattr(self, "traitfile", None)
- traitpastedata = getattr(self, "traitpaste", None)
- variancefiledata = getattr(self, "variancefile", None)
- variancepastedata = getattr(self, "variancepaste", None)
- Nfiledata = getattr(self, "Nfile", None)
-
- #### Todo: Rewrite below when we get to someone submitting their own trait #####
-
- def to_float(item):
- try:
- return float(item)
- except ValueError:
- return None
-
- print("bottle samplelist is:", samplelist)
- if traitfiledata:
- tt = traitfiledata.split()
- values = map(webqtlUtil.StringAsFloat, tt)
- elif traitpastedata:
- tt = traitpastedata.split()
- values = map(webqtlUtil.StringAsFloat, tt)
- else:
- print("mapping formdataasfloat")
- #values = map(self.FormDataAsFloat, samplelist)
- values = [to_float(getattr(self, key)) for key in samplelist]
-
-
- if len(values) < len(samplelist):
- values += [None] * (len(samplelist) - len(values))
- elif len(values) > len(samplelist):
- values = values[:len(samplelist)]
-
- if variancefiledata:
- tt = variancefiledata.split()
- variances = map(webqtlUtil.StringAsFloat, tt)
- elif variancepastedata:
- tt = variancepastedata.split()
- variances = map(webqtlUtil.StringAsFloat, tt)
- else:
- variances = map(self.FormVarianceAsFloat, samplelist)
-
- if len(variances) < len(samplelist):
- variances += [None]*(len(samplelist) - len(variances))
- elif len(variances) > len(samplelist):
- variances = variances[:len(samplelist)]
-
- if Nfiledata:
- tt = string.split(Nfiledata)
- nsamples = map(webqtlUtil.IntAsFloat, tt)
- if len(nsamples) < len(samplelist):
- nsamples += [None]*(len(samplelist) - len(nsamples))
- else:
- nsamples = map(self.FormNAsFloat, samplelist)
-
- ##values, variances, nsamples is obsolete
- self.allTraitData = {}
- for i, _sample in enumerate(samplelist):
- if values[i] != None:
- self.allTraitData[_sample] = webqtlCaseData(
- _sample, values[i], variances[i], nsamples[i])
-
- def informativeStrains(self, samplelist=None, include_variances = None):
- '''if readData was called, use this to output informative samples (sample with values)'''
-
- if not samplelist:
- samplelist = self.samplelist
-
- samples = []
- values = []
- variances = []
-
- for sample in samplelist:
- if sample in self.allTraitData:
- _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
- if _val != None:
- if include_variances:
- if _var != None:
- samples.append(sample)
- values.append(_val)
- variances.append(_var)
- else:
- samples.append(sample)
- values.append(_val)
- variances.append(None)
-
- return samples, values, variances, len(samples)
-
- def FormVarianceAsFloat(self, key):
- try:
- return float(self.formdata.getfirst('V' + key))
- except:
- return None
-
- def FormNAsFloat(self, key):
- try:
- return int(self.formdata.getfirst('N' + key))
- except:
- return None
\ No newline at end of file
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index dbcee331..529cd117 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -37,7 +37,6 @@ from numarray import ones, array, dot, swapaxes
import reaper
-import svg
import webqtlUtil
import corestats
from base import webqtlConfig
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
deleted file mode 100644
index 512bc9e6..00000000
--- a/wqflask/utility/svg.py
+++ /dev/null
@@ -1,1068 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#!/usr/bin/env python
-##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
-##All rights reserved.
-##
-##Redistribution and use in source and binary forms, with or without modification,
-##are permitted provided that the following conditions are met:
-##
-##Redistributions of source code must retain the above copyright notice, this
-##list of conditions and the following disclaimer.
-##
-##Redistributions in binary form must reproduce the above copyright notice,
-##this list of conditions and the following disclaimer in the documentation and/or
-##other materials provided with the distribution.
-##
-##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
-##its contributors may be used to endorse or promote products derived from this
-##software without specific prior written permission.
-##
-##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
-##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-##Thanks to Gerald Rosennfellner for his help and useful comments.
-
-__doc__="""Use SVGdraw to generate your SVGdrawings.
-
-SVGdraw uses an object model drawing and a method toXML to create SVG graphics
-by using easy to use classes and methods usualy you start by creating a drawing eg
-
- d=drawing()
- #then you create a SVG root element
- s=svg()
- #then you add some elements eg a circle and add it to the svg root element
- c=circle()
- #you can supply attributes by using named arguments.
- c=circle(fill='red',stroke='blue')
- #or by updating the attributes attribute:
- c.attributes['stroke-width']=1
- s.addElement(c)
- #then you add the svg root element to the 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;)
-This module was created using the SVG specification of www.w3c.org and the
-O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
-is available from www.adobe.com"""
-
-__version__="1.0"
-
-# there are two possibilities to generate svg:
-# via a dom implementation and directly using text strings
-# the latter is way faster (and shorter in coding)
-# the former is only used in debugging svg programs
-# maybe it will be removed alltogether after a while
-# with the following variable you indicate whether to use the dom implementation
-# Note that PyXML is required for using the dom implementation.
-# It is also possible to use the standard minidom. But I didn't try that one.
-# Anyway the text based approach is about 60 times faster than using the full dom implementation.
-use_dom_implementation=0
-
-
-import exceptions
-if use_dom_implementation<>0:
- try:
- from xml.dom import implementation
- from xml.dom.ext import PrettyPrint
- except:
- raise exceptions.ImportError, "PyXML is required for using the dom implementation"
-#The implementation is used for the creating the XML document.
-#The prettyprint module is used for converting the xml document object to a xml file
-
-import sys
-assert sys.version_info[0]>=2
-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.
-
-#the following code is pasted form xml.sax.saxutils
-#it makes it possible to run the code without the xml sax package installed
-#To make it possible to have in your text elements, it is necessary to escape the texts
-def _escape(data, entities={}):
- """Escape &, <, and > in a string of data.
-
- You can escape other strings of data by passing a dictionary as
- the optional entities parameter. The keys and values must all be
- strings; each key will be replaced with its corresponding value.
- """
- #data = data.replace("&", "&")
- data = data.replace("<", "<")
- data = data.replace(">", ">")
- for chars, entity in entities.items():
- data = data.replace(chars, entity)
- return data
-
-def _quoteattr(data, entities={}):
- """Escape and quote an attribute value.
-
- Escape &, <, and > in a string of data, then quote it for use as
- an attribute value. The \" character will be escaped as well, if
- necessary.
-
- You can escape other strings of data by passing a dictionary as
- the optional entities parameter. The keys and values must all be
- strings; each key will be replaced with its corresponding value.
- """
- data = _escape(data, entities)
- if '"' in data:
- if "'" in data:
- data = '"%s"' % data.replace('"', """)
- else:
- data = "'%s'" % data
- else:
- data = '"%s"' % data
- return data
-
-
-
-def _xypointlist(a):
- """formats a list of xy pairs"""
- s=''
- for e in a: #this could be done more elegant
- s+=str(e)[1:-1] +' '
- return s
-
-def _viewboxlist(a):
- """formats a tuple"""
- s=''
- for e in a:
- s+=str(e)+' '
- return s
-
-def _pointlist(a):
- """formats a list of numbers"""
- return str(a)[1:-1]
-
-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.
- def __init__(self,x=None,y=None):
- self.path=[]
- if x is not None and y is not None:
- self.path.append('M '+str(x)+' '+str(y))
- def closepath(self):
- """ends the path"""
- self.path.append('z')
- def move(self,x,y):
- """move to absolute"""
- self.path.append('M '+str(x)+' '+str(y))
- def relmove(self,x,y):
- """move to relative"""
- self.path.append('m '+str(x)+' '+str(y))
- def line(self,x,y):
- """line to absolute"""
- self.path.append('L '+str(x)+' '+str(y))
- def relline(self,x,y):
- """line to relative"""
- self.path.append('l '+str(x)+' '+str(y))
- def hline(self,x):
- """horizontal line to absolute"""
- self.path.append('H'+str(x))
- def relhline(self,x):
- """horizontal line to relative"""
- self.path.append('h'+str(x))
- def vline(self,y):
- """verical line to absolute"""
- self.path.append('V'+str(y))
- def relvline(self,y):
- """vertical line to relative"""
- self.path.append('v'+str(y))
- def bezier(self,x1,y1,x2,y2,x,y):
- """bezier with xy1 and xy2 to xy absolut"""
- self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
- def relbezier(self,x1,y1,x2,y2,x,y):
- """bezier with xy1 and xy2 to xy relative"""
- self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
- def smbezier(self,x2,y2,x,y):
- """smooth bezier with xy2 to xy absolut"""
- self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
- def relsmbezier(self,x2,y2,x,y):
- """smooth bezier with xy2 to xy relative"""
- self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
- def qbezier(self,x1,y1,x,y):
- """quadratic bezier with xy1 to xy absolut"""
- self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
- def relqbezier(self,x1,y1,x,y):
- """quadratic bezier with xy1 to xy relative"""
- self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
- def smqbezier(self,x,y):
- """smooth quadratic bezier to xy absolut"""
- self.path.append('T'+str(x)+','+str(y))
- def relsmqbezier(self,x,y):
- """smooth quadratic bezier to xy relative"""
- self.path.append('t'+str(x)+','+str(y))
- def ellarc(self,rx,ry,xrot,laf,sf,x,y):
- """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut"""
- self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
- def relellarc(self,rx,ry,xrot,laf,sf,x,y):
- """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative"""
- 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.
- This element is the base of every svg element it defines a class which resembles
- a xml-element. The main advantage of this kind of implementation is that you don't
- have to create a toXML method for every different graph object. Every element
- consists of a type, attribute, optional subelements, optional text and an optional
- namespace. Note the elements==None, if elements = None:self.elements=[] construction.
- This is done because if you default to elements=[] every object has a reference
- to the same empty list."""
- def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args):
- self.type=type
- if attributes==None:
- self.attributes={}
- else:
- self.attributes=attributes
- if elements==None:
- self.elements=[]
- else:
- self.elements=elements
- self.text=text
- self.namespace=namespace
- self.cdata=cdata
- for arg in args.keys():
- arg2 = arg.replace("__", ":")
- arg2 = arg2.replace("_", "-")
- self.attributes[arg2]=args[arg]
- def addElement(self,SVGelement):
- """adds an element to a SVGelement
-
- SVGelement.addElement(SVGelement)
- """
- self.elements.append(SVGelement)
-
- def toXml(self,level,f):
- f.write('\t'*level)
- f.write('<'+self.type)
- for attkey in self.attributes.keys():
- f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey])))
- if self.namespace:
- f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"')
- if self.elements or self.text or self.cdata:
- f.write('>')
- if self.elements:
- f.write('\n')
- for element in self.elements:
- element.toXml(level+1,f)
- if self.cdata:
- f.write('\n'+'\t'*(level+1)+'\n')
- if self.text:
- if type(self.text)==type(''): #If the text is only text
- f.write(_escape(str(self.text)))
- else: #If the text is a spannedtext class
- f.write(str(self.text))
- if self.elements:
- f.write('\t'*level+'\n')
- elif self.text:
- f.write('\n')
- elif self.cdata:
- f.write('\t'*level+'\n')
- else:
- f.write('/>\n')
-
-class tspan(SVGelement):
- """ts=tspan(text='',**args)
-
- a tspan element can be used for applying formatting to a textsection
- usage:
- ts=tspan('this text is bold')
- ts.attributes['font-weight']='bold'
- st=spannedtext()
- st.addtspan(ts)
- t=text(3,5,st)
- """
- def __init__(self,text=None,**args):
- SVGelement.__init__(self,'tspan',**args)
- if self.text<>None:
- self.text=text
- def __repr__(self):
- s="None:
- raise ValueError, 'height is required'
- if height<>None:
- raise ValueError, 'width is required'
- else:
- raise ValueError, 'both height and width are required'
- SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
- if x<>None:
- self.attributes['x']=x
- if y<>None:
- self.attributes['y']=y
- if fill<>None:
- self.attributes['fill']=fill
- if stroke<>None:
- 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)
-
- an ellipse is defined as a center and a x and y radius.
- """
- def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
- if rx==None or ry== None:
- if rx<>None:
- raise ValueError, 'rx is required'
- if ry<>None:
- raise ValueError, 'ry is required'
- else:
- raise ValueError, 'both rx and ry are required'
- SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
- if cx<>None:
- self.attributes['cx']=cx
- if cy<>None:
- self.attributes['cy']=cy
- if fill<>None:
- self.attributes['fill']=fill
- if stroke<>None:
- 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)
-
- The circle creates an element using a x, y and radius values eg
- """
- def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
- if r==None:
- raise ValueError, 'r is required'
- SVGelement.__init__(self,'circle',{'r':r},**args)
- if cx<>None:
- self.attributes['cx']=cx
- if cy<>None:
- self.attributes['cy']=cy
- if fill<>None:
- self.attributes['fill']=fill
- if stroke<>None:
- self.attributes['stroke']=stroke
- if stroke_width<>None:
- self.attributes['stroke-width']=stroke_width
-
-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.
- """
- def __init__(self,x,y,fill='black',**args):
- circle.__init__(self,x,y,1,fill,**args)
-
-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):
- SVGelement.__init__(self,'line',**args)
- if x1<>None:
- self.attributes['x1']=x1
- if y1<>None:
- self.attributes['y1']=y1
- if x2<>None:
- self.attributes['x2']=x2
- if y2<>None:
- self.attributes['y2']=y2
- if stroke_width<>None:
- 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):
- SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
- if fill<>None:
- self.attributes['fill']=fill
- if stroke_width<>None:
- self.attributes['stroke-width']=stroke_width
- if stroke<>None:
- self.attributes['stroke']=stroke
-
-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):
- SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
- if fill<>None:
- self.attributes['fill']=fill
- if stroke_width<>None:
- self.attributes['stroke-width']=stroke_width
- if stroke<>None:
- self.attributes['stroke']=stroke
-
-class path(SVGelement):
- """p=path(path,fill,stroke,stroke_width,**args)
-
- a path is defined by a path object and optional width, stroke and fillcolor
- """
- def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
- SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
- if stroke<>None:
- self.attributes['stroke']=stroke
- if fill<>None:
- self.attributes['fill']=fill
- if stroke_width<>None:
- 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):
- SVGelement.__init__(self,'text',**args)
- if x<>None:
- self.attributes['x']=x
- if y<>None:
- self.attributes['y']=y
- if font_size<>None:
- self.attributes['font-size']=font_size
- if font_family<>None:
- self.attributes['font-family']=font_family
- if text<>None:
- self.text=text
- if text_anchor<>None:
- self.attributes['text-anchor']=text_anchor
-
-
-class textpath(SVGelement):
- """tp=textpath(text,link,**args)
-
- 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)
- if text<>None:
- self.text=text
-
-class pattern(SVGelement):
- """p=pattern(x,y,width,height,patternUnits,**args)
-
- A pattern is used to fill or stroke an object using a pre-defined
- graphic object which can be replicated ("tiled") at fixed intervals
- in x and y to cover the areas to be painted.
- """
- def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
- SVGelement.__init__(self,'pattern',**args)
- if x<>None:
- self.attributes['x']=x
- if y<>None:
- self.attributes['y']=y
- if width<>None:
- self.attributes['width']=width
- if height<>None:
- self.attributes['height']=height
- if patternUnits<>None:
- self.attributes['patternUnits']=patternUnits
-
-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
- """
- def __init__(self,text=None,**args):
- SVGelement.__init__(self,'title',**args)
- if text<>None:
- self.text=text
-
-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.
- """
- def __init__(self,text=None,**args):
- SVGelement.__init__(self,'desc',**args)
- if text<>None:
- self.text=text
-
-class lineargradient(SVGelement):
- """lg=lineargradient(x1,y1,x2,y2,id,**args)
-
- defines a lineargradient using two xy pairs.
- stop elements van be added to define the gradient colors.
- """
- def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
- SVGelement.__init__(self,'linearGradient',**args)
- if x1<>None:
- self.attributes['x1']=x1
- if y1<>None:
- self.attributes['y1']=y1
- if x2<>None:
- self.attributes['x2']=x2
- if y2<>None:
- self.attributes['y2']=y2
- if id<>None:
- self.attributes['id']=id
-
-class radialgradient(SVGelement):
- """rg=radialgradient(cx,cy,r,fx,fy,id,**args)
-
- defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
- stop elements van be added to define the gradient colors.
- """
- def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
- SVGelement.__init__(self,'radialGradient',**args)
- if cx<>None:
- self.attributes['cx']=cx
- if cy<>None:
- self.attributes['cy']=cy
- if r<>None:
- self.attributes['r']=r
- if fx<>None:
- self.attributes['fx']=fx
- if fy<>None:
- self.attributes['fy']=fy
- if id<>None:
- self.attributes['id']=id
-
-class stop(SVGelement):
- """st=stop(offset,stop_color,**args)
-
- Puts a stop color at the specified radius
- """
- def __init__(self,offset,stop_color=None,**args):
- 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)
-
- Add a CDATA element to this element for defing in line stylesheets etc..
- """
- 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)
-
- adds an image to the drawing. Supported formats are .png, .jpg and .svg.
- """
- def __init__(self,url,x=None,y=None,width=None,height=None,**args):
- if width==None or height==None:
- if width<>None:
- raise ValueError, 'height is required'
- if height<>None:
- raise ValueError, 'width is required'
- else:
- raise ValueError, 'both height and width are required'
- SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
- if x<>None:
- self.attributes['x']=x
- if y<>None:
- self.attributes['y']=y
-
-class cursor(SVGelement):
- """c=cursor(url,**args)
-
- defines a custom cursor for a element or a drawing
- """
- 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.
- """
- def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
- SVGelement.__init__(self,'marker',**args)
- if id<>None:
- self.attributes['id']=id
- if viewBox<>None:
- self.attributes['viewBox']=_viewboxlist(viewBox)
- if refx<>None:
- self.attributes['refX']=refx
- if refy<>None:
- self.attributes['refY']=refy
- if markerWidth<>None:
- 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)
- """
- def __init__(self,id=None,**args):
- SVGelement.__init__(self,'g',**args)
- if id<>None:
- self.attributes['id']=id
-
-class symbol(SVGelement):
- """sy=symbol(id,viewbox,**args)
-
- defines a symbol which can be used on different places in your graph using
- the use element. A symbol is not rendered but you can use 'use' elements to
- 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)
-
- container for defining elements
- """
- def __init__(self,**args):
- SVGelement.__init__(self,'defs',**args)
-
-class switch(SVGelement):
- """sw=switch(**args)
-
- Elements added to a switch element which are "switched" by the attributes
- requiredFeatures, requiredExtensions and systemLanguage.
- Refer to the SVG specification for details.
- """
- 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):
- SVGelement.__init__(self,'use',{'xlink:href':link},**args)
- if x<>None:
- self.attributes['x']=x
- if y<>None:
- self.attributes['y']=y
-
- if width<>None:
- self.attributes['width']=width
- if height<>None:
- self.attributes['height']=height
-
-
-class link(SVGelement):
- """a=link(url,**args)
-
- a link is defined by a hyperlink. add elements which have to be linked
- a.addElement(SVGelement)
- """
- def __init__(self,link='',**args):
- SVGelement.__init__(self,'a',{'xlink:href':link},**args)
-
-class view(SVGelement):
- """v=view(id,**args)
-
- a view can be used to create a view with different attributes"""
- def __init__(self,id=None,**args):
- SVGelement.__init__(self,'view',**args)
- if id<>None:
- self.attributes['id']=id
-
-class script(SVGelement):
- """sc=script(type,type,cdata,**args)
-
- adds a script element which contains CDATA to the SVG drawing
-
- """
- 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.
- """
- def __init__(self,attribute,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
- if fr<>None:
- self.attributes['from']=fr
- if to<>None:
- self.attributes['to']=to
- if dur<>None:
- self.attributes['dur']=dur
-
-class animateMotion(SVGelement):
- """an=animateMotion(pathdata,dur,**args)
-
- animates a SVGelement over the given path in dur seconds
- """
- def __init__(self,pathdata,dur,**args):
- SVGelement.__init__(self,'animateMotion',**args)
- if pathdata<>None:
- self.attributes['path']=str(pathdata)
- if dur<>None:
- self.attributes['dur']=dur
-
-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):
- SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
- #As far as I know the attributeName is always transform
- if type<>None:
- self.attributes['type']=type
- if fr<>None:
- self.attributes['from']=fr
- if to<>None:
- self.attributes['to']=to
- if dur<>None:
- self.attributes['dur']=dur
-class animateColor(SVGelement):
- """ac=animateColor(attribute,type,from,to,dur,**args)
-
- Animates the color of a element
- """
- def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
- if type<>None:
- self.attributes['type']=type
- if fr<>None:
- self.attributes['from']=fr
- if to<>None:
- self.attributes['to']=to
- if dur<>None:
- 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):
- SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
- if to<>None:
- self.attributes['to']=to
- if dur<>None:
- 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)
-
- eg
- d=drawing()
- s=svg((0,0,100,100),'100%','100%')
- c=circle(50,50,20)
- s.addElement(c)
- d.setSVG(s)
- d.toXml()
- """
- def __init__(self,viewBox=None, width=None, height=None,**args):
- SVGelement.__init__(self,'svg',**args)
- if viewBox<>None:
- self.attributes['viewBox']=_viewboxlist(viewBox)
- if width<>None:
- self.attributes['width']=width
- if height<>None:
- self.attributes['height']=height
- self.namespace="http://www.w3.org/2000/svg"
-
-class drawing:
- """d=drawing()
-
- this is the actual SVG document. It needs a svg element as a root.
- Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG
- source to the screen or to a file
- d=drawing()
- d.addSVG(svg)
- d.toXml(optionalfilename)
- """
-
- def __init__(self, entity={}):
- self.svg=None
- self.entity = entity
- def setSVG(self,svg):
- self.svg=svg
- #Voeg een element toe aan de grafiek toe.
- if use_dom_implementation==0:
- def toXml(self, filename='',compress=False):
- import cStringIO
- xml=cStringIO.StringIO()
- xml.write("\n")
- xml.write("\n" % (item, self.entity[item]))
- xml.write("]")
- xml.write(">\n")
- self.svg.toXml(0,xml)
- if not filename:
- if compress:
- import gzip
- f=cStringIO.StringIO()
- zf=gzip.GzipFile(fileobj=f,mode='wb')
- zf.write(xml.getvalue())
- zf.close()
- f.seek(0)
- return f.read()
- else:
- return xml.getvalue()
- else:
- if filename[-4:]=='svgz':
- import gzip
- f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
- f.write(xml.getvalue())
- f.close()
- else:
- f=file(filename,'w')
- f.write(xml.getvalue())
- f.close()
-
- else:
- def toXml(self,filename='',compress=False):
- """drawing.toXml() ---->to the screen
- drawing.toXml(filename)---->to the file
- writes a svg drawing to the screen or to a file
- 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.
- root=implementation.createDocument(None,None,doctype)
- #Create the xml document.
- global appender
- def appender(element,elementroot):
- """This recursive function appends elements to an element and sets the attributes
- and type. It stops when alle elements have been appended"""
- if element.namespace:
- e=root.createElementNS(element.namespace,element.type)
- else:
- e=root.createElement(element.type)
- if element.text:
- textnode=root.createTextNode(element.text)
- e.appendChild(textnode)
- for attribute in element.attributes.keys(): #in element.attributes is supported from python 2.2
- e.setAttribute(attribute,str(element.attributes[attribute]))
- if element.elements:
- for el in element.elements:
- e=appender(el,e)
- elementroot.appendChild(e)
- return elementroot
- root=appender(self.svg,root)
- if not filename:
- import cStringIO
- xml=cStringIO.StringIO()
- PrettyPrint(root,xml)
- if compress:
- import gzip
- f=cStringIO.StringIO()
- zf=gzip.GzipFile(fileobj=f,mode='wb')
- zf.write(xml.getvalue())
- zf.close()
- f.seek(0)
- return f.read()
- else:
- return xml.getvalue()
- else:
- try:
- if filename[-4:]=='svgz':
- import gzip
- import cStringIO
- xml=cStringIO.StringIO()
- PrettyPrint(root,xml)
- f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
- f.write(xml.getvalue())
- f.close()
- else:
- f=open(filename,'w')
- PrettyPrint(root,f)
- f.close()
- except:
- print "Cannot write SVG file: " + filename
- def validate(self):
- try:
- import xml.parsers.xmlproc.xmlval
- except:
- raise exceptions.ImportError,'PyXml is required for validating SVG'
- svg=self.toXml()
- xv=xml.parsers.xmlproc.xmlval.XMLValidator()
- try:
- xv.feed(svg)
- except:
- raise "SVG is not well formed, see messages above"
- else:
- 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')
- e=ellipse(0,0,5,2)
- g.addElement(e)
- c=circle(0,0,1,'red')
- g.addElement(c)
- pd=pathdata(0,-10)
- for i in range(6):
- pd.relsmbezier(10,5,0,10)
- pd.relsmbezier(-10,5,0,10)
- an=animateMotion(pd,10)
- an.attributes['rotate']='auto-reverse'
- an.attributes['repeatCount']="indefinite"
- g.addElement(an)
- s.addElement(g)
- for i in range(20,120,20):
- u=use('#animations',i,0)
- s.addElement(u)
- for i in range(0,120,20):
- for j in range(5,105,10):
- c=circle(i,j,1,'red','black',.5)
- s.addElement(c)
- d.setSVG(s)
-
- print d.toXml()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 2336e722..94dd7cbf 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -34,9 +34,6 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
-
-
-
# NL, 07/27/2010. moved from webqtlForm.py
#Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
ParInfo ={
@@ -64,43 +61,10 @@ ParInfo ={
'SXM':['SMF1', 'MSF1', 'Steptoe','Morex']
}
-
-# NL, 07/27/2010. moved from template.py
-IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py
-IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py
-
-IMGASC = HT.Image("/images/sortup.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-
-"""
-IMGASC = HT.Image("/images/sortup_icon.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0)
-"""
-
-PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0)
-
#########################################
# Accessory Functions
#########################################
-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
-
def exportData(hddn, tdata, NP = None):
for key in tdata.keys():
_val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
@@ -136,37 +100,6 @@ def genShortStrainName(RISet='', input_strainName=''):
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
-
-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]))]
-
-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]))]
-
def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
from random import choice
_str = prefix[:]
@@ -174,27 +107,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
_str += choice(chars)
return _str
-def generate_session():
- import sha
- return sha.new(str(time.time())).hexdigest()
-
-def cvt2Dict(x):
- 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()
-
def StringAsFloat(str):
'Converts string to float but catches any exception and returns None'
try:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 73072423..abf9fc89 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -296,60 +296,8 @@ class CorrelationResults(object):
if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
self.do_tissue_correlation_for_trait_list()
- #print("self.correlation_results: ", pf(self.correlation_results))
-
self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
- #XZ, 09/18/2008: get all information about the user selected database.
- #target_db_name = fd.corr_dataset
- #self.target_db_name = start_vars['corr_dataset']
-
- # Zach said this is ok
- # Auth if needed
- #try:
- # auth_user_for_db(self.db, self.cursor, self.target_db_name, self.privilege, self.userName)
- #except AuthException as e:
- # detail = [e.message]
- # return self.error(detail)
-
- #XZ, 09/18/2008: filter out the strains that have no value.
- #self.sample_names, vals, vars, N = fd.informativeStrains(sample_list)
-
- #print("samplenames is:", pf(self.sample_names))
- #CF - If less than a minimum number of strains/cases in common, don't calculate anything
- #if len(self.sample_names) < self.corr_min_informative:
- # detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)]
- # self.error(heading=None, detail=detail)
-
- #correlation_method = self.CORRELATION_METHODS[self.method]
- #rankOrder = self.RANK_ORDERS[self.method]
-
- # CF - Number of results returned
- # Todo: Get rid of self.returnNumber
-
- #self.record_count = 0
-
- #myTrait = get_custom_trait(fd, self.cursor)
-
-
- # We will not get Literature Correlations if there is no GeneId because there is nothing
- # to look against
- #self.geneid = self.this_trait.geneid
-
- # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
- #self.trait_symbol = myTrait.symbol
-
-
- #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
- #self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.dataset.group.species, self.geneid)
-
- #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)'
- #self.tissue_probeset_freeze_id = 1
-
- #traitList = self.correlate()
-
- #print("Done doing correlation calculation")
-
############################################################################################################################################
def get_formatted_corr_type(self):
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 632c2f8f..81da8976 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -190,21 +190,6 @@ class MarkerRegression(object):
self.js_data = start_vars['js_data']
self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
- #ZS: Think I can just get all this from dataset object now
- #RISet and Species
- #if not fd.genotype:
- # fd.readGenotype()
- #
- #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
- #
- #if ((fd.parentsf14regression == 'on') and fd.genotype_2):
- # fd.genotype = fd.genotype_2
- #else:
- # fd.genotype = fd.genotype_1
- #fd.strainlist = list(fd.genotype.prgy)
- #
- #self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
-
if self.dataset.group.species == "rat":
self._ucscDb = "rn3"
elif self.dataset.group.species == "mouse":
@@ -212,7 +197,6 @@ class MarkerRegression(object):
else:
self._ucscDb = ""
-
#####################################
# Options
#####################################
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3c2cca94..8ff359a7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -57,7 +57,6 @@ from utility import temp_data
from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
from utility.helper_functions import get_species_groups
-from base import webqtlFormData
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility.benchmark import Bench
@@ -163,62 +162,37 @@ def css(filename):
def twitter(filename):
return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)
-#@app.route("/data_sharing")
-#def data_sharing_page():
-# logger.info("In data_sharing")
-# fd = webqtlFormData.webqtlFormData(request.args)
-# logger.info("1Have fd")
-# sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-# info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
-# logger.info("type(htmlfilelist):", type(htmlfilelist))
-# htmlfilelist = htmlfilelist.encode("utf-8")
-# #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-# logger.info("1 Made it to rendering")
-# return render_template("data_sharing.html",
-# info=info,
-# htmlfilelist=htmlfilelist)
-
-
@app.route("/search", methods=('GET',))
def search_page():
logger.info("in search_page")
logger.info(request.url)
- if 'info_database' in request.args:
- logger.info("Going to sharing_info_page")
- template_vars = sharing_info_page()
- if template_vars.redirect_url:
- logger.info("Going to redirect")
- return flask.redirect(template_vars.redirect_url)
- else:
- return render_template("data_sharing.html", **template_vars.__dict__)
+ result = None
+ if USE_REDIS:
+ with Bench("Trying Redis cache"):
+ key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
+ logger.debug("key is:", pf(key))
+ result = Redis.get(key)
+ if result:
+ logger.info("Redis cache hit on search results!")
+ result = pickle.loads(result)
else:
- result = None
- if USE_REDIS:
- with Bench("Trying Redis cache"):
- key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
- logger.debug("key is:", pf(key))
- result = Redis.get(key)
- if result:
- logger.info("Redis cache hit on search results!")
- result = pickle.loads(result)
- else:
- logger.info("Skipping Redis cache (USE_REDIS=False)")
+ logger.info("Skipping Redis cache (USE_REDIS=False)")
- logger.info("request.args is", request.args)
- the_search = search_results.SearchResultPage(request.args)
- result = the_search.__dict__
- valid_search = result['search_term_exists']
+ logger.info("request.args is", request.args)
+ the_search = search_results.SearchResultPage(request.args)
+ result = the_search.__dict__
+ valid_search = result['search_term_exists']
- logger.debugf("result", result)
+ logger.debugf("result", result)
- if USE_REDIS and valid_search:
- Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*60)
+ if USE_REDIS and valid_search:
+ Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*60)
- if valid_search:
- return render_template("search_result_page.html", **result)
- else:
- return render_template("search_error.html")
+ if valid_search:
+ return render_template("search_result_page.html", **result)
+ else:
+ return render_template("search_error.html")
@app.route("/gsearch", methods=('GET',))
def gsearchact():
@@ -741,7 +715,6 @@ def network_graph_page():
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
logger.info(request.url)
- #fd = webqtlFormData.webqtlFormData(request.form)
template_vars = show_corr_results.CorrelationResults(request.form)
return render_template("correlation_page.html", **template_vars.__dict__)
@@ -777,15 +750,6 @@ def submit_bnw():
template_vars = get_bnw_input(request.form)
return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
-# Todo: Can we simplify this? -Sam
-def sharing_info_page():
- """Info page displayed when the user clicks the "Info" button next to the dataset selection"""
- logger.info("In sharing_info_page")
- logger.info(request.url)
- fd = webqtlFormData.webqtlFormData(request.args)
- template_vars = SharingInfoPage.SharingInfoPage(fd)
- return template_vars
-
# Take this out or secure it before putting into production
@app.route("/get_temp_data")
def get_temp_data():
--
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