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authorzsloan2016-04-06 18:21:04 +0000
committerzsloan2016-04-06 18:21:04 +0000
commitb1e0067c95efa7d2fffa0dd1230b917121869709 (patch)
tree771282c161a98c10677ef1710d231138a1104d6e
parent77bc01663a38b413d52d39de754b470a804afd97 (diff)
downloadgenenetwork2-b1e0067c95efa7d2fffa0dd1230b917121869709.tar.gz
Permutations (suggestive/significant lines, legend, and histogram) should now work for both R/qtl and qtl reaper mapping.
Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
-rw-r--r--[-rwxr-xr-x]wqflask/utility/Plot.py352
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py90
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py156
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js3
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html17
-rw-r--r--wqflask/wqflask/views.py2
6 files changed, 325 insertions, 295 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 51a57a6d..ad11a81e 100755..100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,10 +24,9 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-#import piddle as pid
-
from __future__ import print_function
+import piddle as pid
from pprint import pformat as pf
print("Lysol")
@@ -478,181 +477,180 @@ def plotSecurity(canvas, text="12345"):
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
-#def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
-#
-# xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-#
-# plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-# plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-# if plotHeight<=0 or plotWidth<=0:
-# return
-#
-# if len(data) < 2:
-# return
-#
-# max_D = max(data)
-# min_D = min(data)
-# #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
-# if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
-# max_D=webqtlConfig.MAXLRS #maximum LRS value
-#
-# xLow, xTop, stepX = detScale(min_D, max_D)
-#
-# #reduce data
-# step = ceil((xTop-xLow)/50.0)
-# j = xLow
-# dataXY = []
-# Count = []
-# while j <= xTop:
-# dataXY.append(j)
-# Count.append(0)
-# j += step
-#
-# for i, item in enumerate(data):
-# if item == float('inf') or item>webqtlConfig.MAXLRS:
-# item = webqtlConfig.MAXLRS #maximum LRS value
-# j = int((item-xLow)/step)
-# Count[j] += 1
-#
-# yLow, yTop, stepY=detScale(0,max(Count))
-#
-# #draw data
-# xScale = plotWidth/(xTop-xLow)
-# yScale = plotHeight/(yTop-yLow)
-# barWidth = xScale*step
-#
-# for i, count in enumerate(Count):
-# if count:
-# xc = (dataXY[i]-xLow)*xScale+xLeftOffset
-# yc =-(count-yLow)*yScale+yTopOffset+plotHeight
-# canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
-#
-# #draw drawing region
-# canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-#
-# #draw scale
-# scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-# x=xLow
-# for i in range(stepX+1):
-# xc=xLeftOffset+(x-xLow)*xScale
-# canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
-# strX = cformat(d=x, rank=0)
-# canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
-# x+= (xTop - xLow)/stepX
-#
-# y=yLow
-# for i in range(stepY+1):
-# yc=yTopOffset+plotHeight-(y-yLow)*yScale
-# canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-# strY = "%d" %y
-# canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-# y+= (yTop - yLow)/stepY
-#
-# #draw label
-# labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
-# if XLabel:
-# canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-# yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
-#
-# if YLabel:
-# canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-# font=labelFont,color=labelColor,angle=90)
-#
-# labelFont=pid.Font(ttf="verdana",size=16,bold=0)
-# if title:
-# canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-# 20,font=labelFont,color=labelColor)
-#
-#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 plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+
+ if len(data) < 2:
+ return
+
+ max_D = max(data)
+ min_D = min(data)
+ #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
+ if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
+ max_D=webqtlConfig.MAXLRS #maximum LRS value
+
+ xLow, xTop, stepX = detScale(min_D, max_D)
+
+ #reduce data
+ step = ceil((xTop-xLow)/50.0)
+ j = xLow
+ dataXY = []
+ Count = []
+ while j <= xTop:
+ dataXY.append(j)
+ Count.append(0)
+ j += step
+
+ for i, item in enumerate(data):
+ if item == float('inf') or item>webqtlConfig.MAXLRS:
+ item = webqtlConfig.MAXLRS #maximum LRS value
+ j = int((item-xLow)/step)
+ Count[j] += 1
+
+ yLow, yTop, stepY=detScale(0,max(Count))
+
+ #draw data
+ xScale = plotWidth/(xTop-xLow)
+ yScale = plotHeight/(yTop-yLow)
+ barWidth = xScale*step
+
+ for i, count in enumerate(Count):
+ if count:
+ xc = (dataXY[i]-xLow)*xScale+xLeftOffset
+ yc =-(count-yLow)*yScale+yTopOffset+plotHeight
+ canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
+
+ #draw drawing region
+ canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+
+ #draw scale
+ scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ x=xLow
+ for i in range(int(stepX)+1):
+ xc=xLeftOffset+(x-xLow)*xScale
+ canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
+ strX = cformat(d=x, rank=0)
+ canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
+ x+= (xTop - xLow)/stepX
+
+ y=yLow
+ for i in range(int(stepY)+1):
+ yc=yTopOffset+plotHeight-(y-yLow)*yScale
+ canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ strY = "%d" %y
+ canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ y+= (yTop - yLow)/stepY
+
+ #draw label
+ labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
+ if XLabel:
+ canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
+ yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
+
+ if YLabel:
+ canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
+ font=labelFont,color=labelColor,angle=90)
+
+ labelFont=pid.Font(ttf="verdana",size=16,bold=0)
+ if title:
+ canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
+ 20,font=labelFont,color=labelColor)
+
+def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1):
+ xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
+ plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
+ plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
+ if plotHeight<=0 or plotWidth<=0:
+ return
+
+ NNN = len(data)
+ if NNN < 2 or NNN != len(label):
+ return
+ if variance and len(variance)!=NNN:
+ variance = []
+
+ Y2 = data[:]
+ if variance:
+ for i in range(NNN):
+ if variance[i]:
+ Y2 += [data[i]-variance[i]]
+
+ #Y axis
+ YLow, YTop, stepY = detScale(min(Y2), max(Y2))
+ YScale = plotHeight/(YTop - YLow)
+
+ if YLow < 0 and YTop > 0:
+ drawZero = 1
+ else:
+ drawZero = 0
+
+ #X axis
+ X = range(NNN)
+ Xll= 0
+ Xur= NNN-1
+
+
+ if drawZero:
+ YZero = yTopOffset+plotHeight-YScale*(0-YLow)
+ canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
+ else:
+ YZero = yTopOffset+plotHeight
+ #draw data
+ spaceWidth = barSpace
+ if spaceWidth < 1:
+ spaceWidth = 1
+ barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
+
+ xc= xLeftOffset
+ scaleFont=pid.Font(ttf="verdana",size=11,bold=0)
+ for i in range(NNN):
+ yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
+ canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
+ if variance and variance[i]:
+ varlen = variance[i]*YScale
+ if yc-varlen < yTopOffset:
+ topYd = yTopOffset
+ else:
+ topYd = yc-varlen
+ canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
+ canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
+ canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
+ strX = label[i]
+ canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
+ xc += barWidth + spaceWidth
+
+ #draw drawing region
+ canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+
+ #draw Y scale
+ scaleFont=pid.Font(ttf="cour",size=16,bold=1)
+ y=YLow
+ for i in range(stepY+1):
+ yc=yTopOffset+plotHeight-(y-YLow)*YScale
+ canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ strY = cformat(d=y, rank=0)
+ canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ y+= (YTop - YLow)/stepY
+
+ #draw label
+ labelFont=pid.Font(ttf="verdana",size=17,bold=0)
+ if XLabel:
+ canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
+
+ if YLabel:
+ canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
+
+ labelFont=pid.Font(ttf="verdana",size=18,bold=0)
+ if title:
+ canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
+
+ return
+
#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'
#
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index f08e47ca..112dcd5c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -79,10 +79,8 @@ class MarkerRegression(object):
self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
self.score_type = "LRS" #ZS: LRS or LOD
self.mapping_scale = "physic"
- self.num_perm = 0
self.bootstrap_results = []
-
#ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
if "selected_chr" in start_vars:
@@ -99,6 +97,12 @@ class MarkerRegression(object):
if "haplotypeAnalystCheck" in start_vars:
self.haplotypeAnalystCheck = start_vars['haplotypeAnalystCheck']
if "startMb" in start_vars: #ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load
+ if "permCheck" in start_vars:
+ self.permCheck = "ON"
+ else:
+ self.permCheck = False
+ self.num_perm = int(start_vars['num_perm'])
+
if "showGenes" in start_vars:
self.showGenes = start_vars['showGenes']
else:
@@ -108,6 +112,15 @@ class MarkerRegression(object):
else:
self.viewLegend = False
else:
+ try:
+ if int(start_vars['num_perm']) > 0:
+ self.num_perm = int(start_vars['num_perm'])
+ else:
+ self.num_perm = 0
+ except:
+ self.num_perm = 0
+
+ self.permCheck = "ON"
self.showGenes = "ON"
self.viewLegend = "ON"
@@ -120,45 +133,32 @@ class MarkerRegression(object):
with Bench("Getting markers from csv"):
marker_obs = get_markers_from_csv(included_markers, p_values, self.dataset.group.name)
results = marker_obs
- #self.dataset.group.get_specified_markers(markers = included_markers)
- #self.dataset.group.markers.add_pvalues(p_values)
- #results = self.dataset.group.markers.markers
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
self.score_type = "LOD"
self.mapping_scale = "morgan"
- if start_vars['num_perm'] == "":
- self.num_perm = 0
- else:
- self.num_perm = start_vars['num_perm']
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
self.method = start_vars['mapmethod_rqtl_geno']
self.model = start_vars['mapmodel_rqtl_geno']
-
if start_vars['pair_scan'] == "true":
self.pair_scan = True
-
results = self.run_rqtl_geno()
- elif self.mapping_method == "reaper":
- if start_vars['num_perm'] == "":
- self.num_perm = 0
- else:
- self.num_perm = int(start_vars['num_perm'])
-
+ elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
- if "bootCheck" in start_vars:
- self.bootCheck = "ON"
- self.num_bootstrap = int(start_vars['num_bootstrap'])
- else:
- self.bootCheck = False
- self.num_bootstrap = int(start_vars['num_bootstrap'])
if "additiveCheck" in start_vars:
self.additiveCheck = start_vars['additiveCheck']
else:
self.additiveCheck = False
+
+ if "bootCheck" in start_vars:
+ self.bootCheck = "ON"
+ else:
+ self.bootCheck = False
+ self.num_bootstrap = int(start_vars['num_bootstrap'])
else:
+ self.additiveCheck = "ON"
try:
if int(start_vars['num_bootstrap']) > 0:
self.bootCheck = "ON"
@@ -166,12 +166,9 @@ class MarkerRegression(object):
else:
self.bootCheck = False
self.num_bootstrap = 0
- #ZS: If some string that can't be converted to int is input for num_bootstrap
except:
- self.num_bootstrap = 0
self.bootCheck = False
-
- self.additiveCheck = "ON"
+ self.num_bootstrap = 0
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
@@ -180,10 +177,8 @@ class MarkerRegression(object):
results = self.run_plink()
elif self.mapping_method == "pylmm":
print("RUNNING PYLMM")
- self.num_perm = start_vars['num_perm']
- if self.num_perm != "":
- if int(self.num_perm) > 0:
- self.run_permutations(str(temp_uuid))
+ if self.num_perm > 0:
+ self.run_permutations(str(temp_uuid))
results = self.gen_data(str(temp_uuid))
else:
print("RUNNING NOTHING")
@@ -449,11 +444,11 @@ class MarkerRegression(object):
else:
print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=self.model, method=self.method)
- if int(self.num_perm) > 0: # Do permutation (if requested by user)
+ if self.num_perm > 0 and self.permCheck == "ON": # Do permutation (if requested by user)
if self.do_control == "true":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm), model=self.model, method=self.method)
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = self.num_perm, model=self.model, method=self.method)
else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm), model=self.model, method=self.method)
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = self.num_perm, model=self.model, method=self.method)
self.process_rqtl_perm_results(perm_data_frame) # Functions that sets the thresholds for the webinterface
@@ -531,10 +526,11 @@ class MarkerRegression(object):
def process_rqtl_perm_results(self, results):
perm_vals = []
- for line in str(results).split("\n")[1:(int(self.num_perm)+1)]:
+ for line in str(results).split("\n")[1:(self.num_perm+1)]:
#print("R/qtl permutation line:", line.split())
perm_vals.append(float(line.split()[1]))
+ self.perm_output = perm_vals
self.suggestive = np.percentile(np.array(perm_vals), 67)
self.significant = np.percentile(np.array(perm_vals), 95)
@@ -666,8 +662,8 @@ class MarkerRegression(object):
trimmed_values.append(values[i])
self.lrs_array = genotype.permutation(strains = trimmed_samples,
- trait = trimmed_values,
- nperm= self.num_perm)
+ trait = trimmed_values,
+ nperm= self.num_perm)
self.suggestive = self.lrs_array[int(self.num_perm*0.37-1)]
self.significant = self.lrs_array[int(self.num_perm*0.95-1)]
@@ -699,17 +695,25 @@ class MarkerRegression(object):
control_geno.append(control_geno2[_idx])
self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- control = control_geno,
- nboot = self.num_bootstrap)
+ trait = trimmed_values,
+ control = control_geno,
+ nboot = self.num_bootstrap)
else:
reaper_results = genotype.regression(strains = trimmed_samples,
trait = trimmed_values)
if self.bootCheck:
self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- nboot = self.num_bootstrap)
+ trait = trimmed_values,
+ nboot = self.num_bootstrap)
+
+ if self.num_perm < 100:
+ self.suggestive = 0
+ self.significant = 0
+ else:
+ self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm)
+ self.suggestive = self.perm_output[int(self.num_perm*0.37-1)]
+ self.significant = self.perm_output[int(self.num_perm*0.95-1)]
self.json_data['chr'] = []
self.json_data['pos'] = []
@@ -823,7 +827,7 @@ class MarkerRegression(object):
#print("self.num_perm:", self.num_perm)
- for permutation in range(int(self.num_perm)):
+ for permutation in range(self.num_perm):
pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
np.random.shuffle(pheno_vector)
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 99f0ac99..b8307aaa 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -220,33 +220,32 @@ class MarkerRegression(object):
else:
self.plotScale = "physic"
- #self.plotScale = fd.formdata.getvalue('scale', 'physic')
- #if self.plotScale == 'physic' and not fd.genotype.Mbmap: #ZS: Not sure where "Mbmap" is stored, if at all; should be fine without this though
- # self.plotScale = 'morgan'
- if start_vars['num_perm'] != "":
- self.nperm = int(start_vars['num_perm'])
- else:
- self.nperm = 0
- if 'num_bootstrap' in start_vars.keys():
- self.nboot = int(start_vars['num_bootstrap'])
+ if 'permCheck' in start_vars.keys():
+ self.permChecked = start_vars['permCheck']
else:
- self.nboot = 0
- if (start_vars['num_perm'] == "") or (start_vars['num_perm'] < 1):
self.permChecked = False
+ if start_vars['num_perm'] > 0:
+ self.nperm = int(start_vars['num_perm'])
+ if self.permChecked:
+ self.perm_output = start_vars['perm_output']
+ self.suggestive = start_vars['suggestive']
+ self.significant = start_vars['significant']
else:
- self.permChecked = True
- #self.permChecked = fd.formdata.getvalue('permCheck', True)
-
+ self.nperm = 0
+
if 'bootCheck' in start_vars.keys():
self.bootChecked = start_vars['bootCheck']
else:
self.bootChecked = False
+ if 'num_bootstrap' in start_vars.keys():
+ self.nboot = int(start_vars['num_bootstrap'])
+ else:
+ self.nboot = 0
if 'bootstrap_results' in start_vars.keys():
self.bootResult = start_vars['bootstrap_results']
else:
self.bootResult = []
-
if 'do_control' in start_vars.keys():
self.doControl = start_vars['do_control']
else:
@@ -593,9 +592,9 @@ class MarkerRegression(object):
else:
showLocusForm = intImg
- if self.permChecked and not self.multipleInterval and 0<self.nperm:
- perm_histogram = self.drawPermutationHistogram()
- perm_text_file = self.permutationTextFile()
+ if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm:
+ self.perm_filename = self.drawPermutationHistogram()
+ #perm_text_file = self.permutationTextFile()
################################################################
# footnote goes here
@@ -608,12 +607,12 @@ class MarkerRegression(object):
if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
- if self.permChecked and not self.multipleInterval and 0 < self.nperm:
- TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
- #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
- else:
- TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
- #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
+ #if self.permChecked and not self.multipleInterval and 0 < self.nperm:
+ # TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
+ # #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
+ #else:
+ TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
+ #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
if geneTable:
@@ -683,7 +682,7 @@ class MarkerRegression(object):
fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime()))
fpText.write("Trait ID: %s\n" % self.this_trait.name)
fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive)
- fpText.write("Significant LRS = %0.2f\n" % self.significance)
+ fpText.write("Significant LRS = %0.2f\n" % self.significant)
"""
if self.this_trait.symbol and self.this_trait.chr and self.this_trait.mb:
writeSymbol, writeChromosome, writeMb = self.this_trait.symbol, self.this_trait.chr, self.this_trait.mb
@@ -720,7 +719,7 @@ class MarkerRegression(object):
else:
lrs_lod = marker['lod_score']
- P_value = self.calculatePValue(lrs_lod, self.LRSArray)
+ P_value = self.calculatePValue(lrs_lod, self.perm_output)
#if _dominance:
# fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
@@ -1139,7 +1138,7 @@ class MarkerRegression(object):
canvas.drawLine(startPosX+54,startPosY,startPosX+67,startPosY,color=self.HAPLOTYPE_RECOMBINATION, width=4)
canvas.drawString('Haplotypes (Pat, Mat, Het, Unk)',startPosX+76,startPosY+5,font=labelFont,color=pid.black)
- if self.permChecked:
+ if self.permChecked and self.nperm > 0:
startPosY += stepPosY
startPosX = xLeftOffset
canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
@@ -1147,7 +1146,7 @@ class MarkerRegression(object):
lod = 1
if self.LRS_LOD == 'LOD':
lod = self.LODFACTOR
- canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significance/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
+ canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant/lod),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive/lod),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
@@ -1884,10 +1883,10 @@ class MarkerRegression(object):
#LRSMax = max(map(max, self.qtlresults)).lod_score
#genotype trait will give infinite LRS
LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
- if self.permChecked and not self.multipleInterval:
- self.significance = min(self.significance, webqtlConfig.MAXLRS)
+ if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+ self.significant = min(self.significant, webqtlConfig.MAXLRS)
self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
- LRSMax = max(self.significance, LRSMax)
+ LRSMax = max(self.significant, LRSMax)
else:
LRSMax = self.lrsMax*lodm
@@ -1922,34 +1921,46 @@ class MarkerRegression(object):
#Draw the LRS/LOD Y axis label
canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
-
- #"Significant" and "Suggestive" Drawing Routine
- # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
- if self.permChecked and not self.multipleInterval:
- significantY = yZero - self.significance*LRSHeightThresh/LRSMax
+ if self.permChecked and self.nperm > 0 and not self.multipleInterval:
+ significantY = yZero - self.significant*LRSHeightThresh/LRSMax
suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax
startPosX = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
- canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
+
+ #"Significant" and "Suggestive" Drawing Routine
+ # ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
+
+ #ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
+ def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
+ rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
+ canvas.drawLine(start_pos_x+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
- canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
+ canvas.drawLine(start_pos_x+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
- sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
- sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2)
+ sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
+ sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2)
if self.LRS_LOD == 'LRS':
sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
- sig_title = "Significant LRS = %0.2f" % self.significance
+ sig_title = "Significant LRS = %0.2f" % self.significant
else:
sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
- sig_title = "Significant LOD = %0.2f" % (self.significance/4.61)
+ sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
gifmap.areas.append(Areas1)
gifmap.areas.append(Areas2)
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
+ start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale
+ return start_pos_x
+
+ for i, _chr in enumerate(self.genotype):
+ if self.selectedChr != -1:
+ if _chr.name == self.ChrList[self.selectedChr][0]:
+ startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0])
+ break
+ else:
+ continue
+ else:
+ startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i])
if self.multipleInterval:
lrsEdgeWidth = 1
@@ -2217,17 +2228,17 @@ class MarkerRegression(object):
if self.multipleInterval:
self.suggestive = 0
- self.significance = 0
+ self.significant = 0
if self.selectedChr > -1:
self.genotype.chromosome = [self.genotype[self.selectedChr]]
else:
#single interval mapping
try:
self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
- self.significance = float(fd.formdata.getvalue('permSignificance'))
+ self.significant = float(fd.formdata.getvalue('permSignificance'))
except:
self.suggestive = None
- self.significance = None
+ self.significant = None
_strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
@@ -2258,21 +2269,21 @@ class MarkerRegression(object):
return "The control marker you selected is not in the genofile."
if weightedRegression:
- self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
+ self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals,
variance = _vars, nperm=self.nperm)
else:
- self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
+ self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals,
nperm=self.nperm)
- if self.significance and self.suggestive:
+ if self.significant and self.suggestive:
pass
else:
if self.nperm < 100:
self.suggestive = 0
- self.significance = 0
+ self.significant = 0
else:
- self.suggestive = self.LRSArray[int(self.nperm*0.37-1)]
- self.significance = self.LRSArray[int(self.nperm*0.95-1)]
+ self.suggestive = self.perm_output[int(self.nperm*0.37-1)]
+ self.significant = self.perm_output[int(self.nperm*0.95-1)]
#calculating bootstrap
#from now on, genotype could only contain a single chromosome
@@ -2443,7 +2454,7 @@ class MarkerRegression(object):
controlsForm.append(controlsTable)
controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden"))
- controlsForm.append(HT.Input(name="permSignificance", value=self.significance, type="hidden"))
+ controlsForm.append(HT.Input(name="permSignificance", value=self.significant, type="hidden"))
## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below
## END HaplotypeAnalyst
@@ -2504,26 +2515,27 @@ class MarkerRegression(object):
# Permutation Graph
#########################################
myCanvas = pid.PILCanvas(size=(400,300))
- #plotBar(myCanvas,10,10,390,290,LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test',identification=fd.identification)
- Plot.plotBar(myCanvas, self.LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test')
+ Plot.plotBar(myCanvas, self.perm_output, XLabel='LRS', YLabel='Frequency', title=' Histogram of Permutation Test')
filename= webqtlUtil.genRandStr("Reg_")
myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif')
- img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
-
+
+ return filename
+
+ # img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
- self.suggestive = self.LRSArray[int(self.nperm*0.37-1)]
- self.significant = self.LRSArray[int(self.nperm*0.95-1)]
- self.highlysignificant = self.LRSArray[int(self.nperm*0.99-1)]
+ # self.suggestive = self.perm_output[int(self.nperm*0.37-1)]
+ # self.significant = self.perm_output[int(self.nperm*0.95-1)]
+ # self.highlysignificant = self.perm_output[int(self.nperm*0.99-1)]
- permutationHeading = HT.Paragraph('Histogram of Permutation Test')
- permutationHeading.__setattr__("class","title")
+ # permutationHeading = HT.Paragraph('Histogram of Permutation Test')
+ # permutationHeading.__setattr__("class","title")
- permutation = HT.TableLite()
- permutation.append(HT.TR(HT.TD(img)),
- HT.TR(HT.TD('')),
- HT.TR(HT.TD('Total of %d permutations'%self.nperm)))
+ # permutation = HT.TableLite()
+ # permutation.append(HT.TR(HT.TD(img)),
+ # HT.TR(HT.TD('')),
+ # HT.TR(HT.TD('Total of %d permutations'%self.nperm)))
- return permutation
+ # return permutation
def permutationTextFile(self):
filename= webqtlUtil.genRandStr("Reg_")
@@ -2531,14 +2543,14 @@ class MarkerRegression(object):
fpText.write('Suggestive LRS (p = 0.63) = %3.2f\n'%self.suggestive)
fpText.write('Significant LRS (p = 0.05) = %3.2f\n'%self.significant)
fpText.write('Highly Significant LRS (p = 0.01) = %3.2f\n\n'%self.highlysignificant)
- fpText.write('%s Permutations\n\n' % str(len(self.LRSArray)))
+ fpText.write('%s Permutations\n\n' % str(len(self.perm_output)))
LRSInfo =HT.Paragraph('&nbsp;&nbsp;&nbsp;&nbsp;Suggestive LRS = %3.2f\n'%self.suggestive,
HT.BR(),
'&nbsp;&nbsp;&nbsp;&nbsp;Significant LRS =%3.2f\n'%self.significant,
HT.BR(),
'&nbsp;&nbsp;&nbsp;&nbsp;Highly Significant LRS =%3.2f\n' % self.highlysignificant)
- for lrs_value in self.LRSArray:
+ for lrs_value in self.perm_output:
fpText.write(str(lrs_value) + "\n")
textUrl = HT.Href(text = 'Download Permutation Results', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 68744aa9..519d1304 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -228,9 +228,10 @@
//$("#progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("reaper");
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+ $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
$('input[name=control_marker]').val($('input[name=control_reaper]').val());
$('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
$('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
$('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
form_data = $('#trait_data_form').serialize();
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 88fb0e89..8ec8a104 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -21,7 +21,7 @@
<input type="hidden" name="maf">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot">
- <input type="hidden" name="num_perm">
+ <input type="hidden" name="num_perm" value="{{ nperm }}">
<input type="hidden" name="num_bootstrap" value="{{ nboot }}">
<input type="hidden" name="do_control" value="{{ doControl }}">
<input type="hidden" name="control_marker" value="{{ controlLocus }}">
@@ -69,8 +69,13 @@
</table>
</div>
<div class="col-xs-4" style="padding: 0px;">
- {% if mapping_method == "reaper" %}
+ {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
+ <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test <br>
+ {% endif %}
+ {% if mapping_method == "reaper" and nboot > 0 %}
<input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test <br>
+ {% endif %}
+ {% if mapping_method == "reaper" %}
<input type="checkbox" name="additiveCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if additiveChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Allele Effects<br>
{% endif %}
<input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br>
@@ -98,6 +103,14 @@
<div class="qtlcharts">
{{ gifmap|safe }}
<img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+ {% if additiveChecked|upper == "ON" %}
+ <br>
+ <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
+ {% endif %}
+ {% if permChecked|upper == "ON" %}
+ <br><br>
+ <img src="/static/output/{{ perm_filename }}.gif">
+ {% endif %}
</div>
</div>
{% if mapping_method != "gemma" %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9d0fd131..acfc5fc6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -347,8 +347,10 @@ def marker_regression_page():
'mapping_scale',
'score_type',
'suggestive',
+ 'significant',
'num_perm',
'permCheck',
+ 'perm_output',
'num_bootstrap',
'bootCheck',
'bootstrap_results',