diff options
4 files changed, 55 insertions, 56 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 32cdb9af..fa439b55 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -68,7 +68,7 @@ class MarkerRegression(object): self.vals.append(value) self.mapping_method = start_vars['method'] - if start_vars['manhattan_plot'] == "true": + if start_vars['manhattan_plot'] == "True": self.manhattan_plot = True else: self.manhattan_plot = False diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 01303b0f..b89f6b97 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -2066,63 +2066,62 @@ class MarkerRegression(object): if self.plotScale == "physic": this_chr = str(self.ChrList[self.selectedChr][0]) else: - this_chr = str(self.ChrList[self.selectedChr][1]+1) + this_chr = str(self.ChrList[self.selectedChr][1]+1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: #AdditiveCoordXY = [] #DominanceCoordXY = [] #for k, _locus in enumerate(_chr): - if 1 == 1: - Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale - #if self.plotScale == 'physic': - #Xc = startPosX + (_locus.Mb-startMb)*plotXScale - #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale - #else: - #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale - #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale - - # updated by NL 06-18-2011: - # fix the over limit LRS graph issue since genotype trait may give infinite LRS; - # for any lrs is over than 460(LRS max in this system), it will be reset to 460 - if 'lrs_value' in qtlresult: - if self.LRS_LOD == "LOD": - if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) - else: - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) + Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale + #if self.plotScale == 'physic': + #Xc = startPosX + (_locus.Mb-startMb)*plotXScale + #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale + #else: + #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale + #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale + + # updated by NL 06-18-2011: + # fix the over limit LRS graph issue since genotype trait may give infinite LRS; + # for any lrs is over than 460(LRS max in this system), it will be reset to 460 + if 'lrs_value' in qtlresult: + if self.LRS_LOD == "LOD": + if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) else: - if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max - else: - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max + Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR) else: - if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf': + if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max else: - if self.LRS_LOD == "LRS": - Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max - else: - Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max - #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf': - # Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max - #else: - # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max - - if self.manhattan_plot == True: - canvas.drawEllipse(Xc-1, Yc-1, Xc+1, Yc+1, fillColor=pid.black) + Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max + else: + if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf': + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max else: - LRSCoordXY.append((Xc, Yc)) - - if not self.multipleInterval and self.additiveChecked: - if additiveMax == 0.0: - additiveMax = 0.000001 - Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax - AdditiveCoordXY.append((Xc, Yc)) - # if not self.multipleInterval and INTERCROSS and self.additiveChecked: - # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax - # DominanceCoordXY.append((Xc, Yc)) - m += 1 - #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if self.LRS_LOD == "LRS": + Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max + else: + Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max + #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': + #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf': + # Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max + #else: + # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max + + if self.manhattan_plot == True: + canvas.drawEllipse(Xc-1, Yc-1, Xc+1, Yc+1, fillColor=pid.black) + else: + LRSCoordXY.append((Xc, Yc)) + + if not self.multipleInterval and self.additiveChecked: + if additiveMax == 0.0: + additiveMax = 0.000001 + Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax + AdditiveCoordXY.append((Xc, Yc)) + # if not self.multipleInterval and INTERCROSS and self.additiveChecked: + # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax + # DominanceCoordXY.append((Xc, Yc)) + m += 1 + #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) if self.manhattan_plot != True: canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index f3f33fad..7d34e88f 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -20,7 +20,7 @@ {% endfor %} <input type="hidden" name="maf"> <input type="hidden" name="selected_chr" value="{{ selectedChr }}"> - <input type="hidden" name="manhattan_plot"> + <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}"> <input type="hidden" name="num_perm" value="{{ nperm }}"> <input type="hidden" name="num_bootstrap" value="{{ nboot }}"> <input type="hidden" name="do_control" value="{{ doControl }}"> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 5d9b0278..067dfc67 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -66,11 +66,11 @@ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> <div class="col-xs-12 controls"> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="true"> + <input type="radio" name="manhattan_plot_pylmm" value="True"> Yes </label> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="false" checked=""> + <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> No </label> </div> @@ -160,11 +160,11 @@ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> <div class="col-xs-12 controls"> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_rqtl" value="true"> + <input type="radio" name="manhattan_plot_rqtl" value="True"> Yes </label> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_rqtl" value="false" checked=""> + <input type="radio" name="manhattan_plot_rqtl" value="False" checked=""> No </label> </div> @@ -242,11 +242,11 @@ <label style="text-align:left;" class="col-xs-12 control-label">Marker Regr.</label> <div class="col-xs-12 controls"> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="true"> + <input type="radio" name="manhattan_plot_reaper" value="True"> Yes </label> <label class="radio-inline"> - <input type="radio" name="manhattan_plot_reaper" value="false" checked=""> + <input type="radio" name="manhattan_plot_reaper" value="False" checked=""> No </label> </div> |