diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 149 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 1 |
4 files changed, 91 insertions, 78 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 9f61ee3c..85404f58 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -144,7 +144,15 @@ class MarkerRegression(object): self.num_perm = 0 else: self.num_perm = int(start_vars['num_perm']) - self.additive = False + + if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON + if "additiveCheck" in start_vars: + self.additiveCheck = start_vars['additiveCheck'] + else: + self.additiveCheck = False + else: + self.additiveCheck = "ON" + self.control = start_vars['control_marker'] self.do_control = start_vars['do_control'] results = self.gen_reaper_results() @@ -666,8 +674,8 @@ class MarkerRegression(object): self.json_data['pos'] = [] self.json_data['lod.hk'] = [] self.json_data['markernames'] = [] - if self.additive: - self.json_data['additive'] = [] + #if self.additive: + # self.json_data['additive'] = [] #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary qtl_results = [] @@ -681,8 +689,8 @@ class MarkerRegression(object): self.json_data['pos'].append(reaper_locus.Mb) self.json_data['lod.hk'].append(qtl.lrs) self.json_data['markernames'].append(reaper_locus.name) - if self.additive: - self.json_data['additive'].append(qtl.additive) + #if self.additive: + # self.json_data['additive'].append(qtl.additive) locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb} qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb, "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance} diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index b53d5b1e..e3466bef 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -121,10 +121,10 @@ class MarkerRegression(object): SIGNIFICANT_WIDTH = 5 SUGGESTIVE_WIDTH = 5 ADDITIVE_COLOR_POSITIVE = pid.green - ADDITIVE_COLOR_NEGATIVE = pid.red + ADDITIVE_COLOR_NEGATIVE = pid.orange ADDITIVE_COLOR = ADDITIVE_COLOR_POSITIVE DOMINANCE_COLOR_POSITIVE = pid.darkviolet - DOMINANCE_COLOR_NEGATIVE = pid.orange + DOMINANCE_COLOR_NEGATIVE = pid.red ## BEGIN HaplotypeAnalyst HAPLOTYPE_POSITIVE = pid.green @@ -279,11 +279,14 @@ class MarkerRegression(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.manhattan_plot = start_vars['manhattan_plot'] - self.additiveChecked = False self.dominanceChecked = False self.LRS_LOD = start_vars['score_type'] self.cutoff = start_vars['cutoff'] self.intervalAnalystChecked = False + if 'additiveCheck' in start_vars.keys(): + self.additiveChecked = start_vars['additiveCheck'] + else: + self.additiveChecked = False if 'viewLegend' in start_vars.keys(): self.legendChecked = start_vars['viewLegend'] else: @@ -585,8 +588,8 @@ class MarkerRegression(object): ################################################################ btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.') - if (self.additiveChecked): - btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar) + #if (self.additiveChecked): + # btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar) 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.') @@ -1920,7 +1923,7 @@ class MarkerRegression(object): if self.multipleInterval: lrsEdgeWidth = 1 else: - #additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0])) + additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults)) #if INTERCROSS: # dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0])) #else: @@ -1993,77 +1996,77 @@ class MarkerRegression(object): else: LRSCoordXY.append((Xc, Yc)) - #if not self.multipleInterval and self.additiveChecked: - # if additiveMax == 0.0: - # additiveMax = 0.000001 - # Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax - # AdditiveCoordXY.append((Xc, Yc)) - #if not self.multipleInterval and INTERCROSS and self.additiveChecked: - # Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax - # DominanceCoordXY.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)) - lineWidth = 1 - if not self.multipleInterval and self.additiveChecked: - plusColor = self.ADDITIVE_COLOR_POSITIVE - minusColor = self.ADDITIVE_COLOR_NEGATIVE - for k, aPoint in enumerate(AdditiveCoordXY): - if k > 0: - Xc0, Yc0 = AdditiveCoordXY[k-1] - Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 - Xcm = Xc - else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 - if Yc0 < yZero: - canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - elif (Yc0-yZero)*(Yc-yZero) > 0: - if Yc < yZero: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - minYc = min(Yc-yZero, Yc0-yZero) - if minYc < 0: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if not self.multipleInterval and INTERCROSS and self.dominanceChecked: - plusColor = self.DOMINANCE_COLOR_POSITIVE - minusColor = self.DOMINANCE_COLOR_NEGATIVE - for k, aPoint in enumerate(DominanceCoordXY): - if k > 0: - Xc0, Yc0 = DominanceCoordXY[k-1] - Xc, Yc = aPoint - if (Yc0-yZero)*(Yc-yZero) < 0: - if Xc == Xc0: #genotype , locus distance is 0 - Xcm = Xc - else: - Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 - if Yc0 < yZero: - canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - elif (Yc0-yZero)*(Yc-yZero) > 0: - if Yc < yZero: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - minYc = min(Yc-yZero, Yc0-yZero) - if minYc < 0: - canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - else: - canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + lineWidth = 1 + if not self.multipleInterval and self.additiveChecked: + plusColor = self.ADDITIVE_COLOR_POSITIVE + minusColor = self.ADDITIVE_COLOR_NEGATIVE + for k, aPoint in enumerate(AdditiveCoordXY): + if k > 0: + Xc0, Yc0 = AdditiveCoordXY[k-1] + Xc, Yc = aPoint + if (Yc0-yZero)*(Yc-yZero) < 0: + if Xc == Xc0: #genotype , locus distance is 0 + Xcm = Xc + else: + Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + if Yc0 < yZero: + canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + elif (Yc0-yZero)*(Yc-yZero) > 0: + if Yc < yZero: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + minYc = min(Yc-yZero, Yc0-yZero) + if minYc < 0: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if not self.multipleInterval and INTERCROSS and self.dominanceChecked: + plusColor = self.DOMINANCE_COLOR_POSITIVE + minusColor = self.DOMINANCE_COLOR_NEGATIVE + for k, aPoint in enumerate(DominanceCoordXY): + if k > 0: + Xc0, Yc0 = DominanceCoordXY[k-1] + Xc, Yc = aPoint + if (Yc0-yZero)*(Yc-yZero) < 0: + if Xc == Xc0: #genotype , locus distance is 0 + Xcm = Xc + else: + Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + if Yc0 < yZero: + canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + elif (Yc0-yZero)*(Yc-yZero) > 0: + if Yc < yZero: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + minYc = min(Yc-yZero, Yc0-yZero) + if minYc < 0: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) if self.manhattan_plot != True: diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 3be9ad01..550173fc 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -68,6 +68,7 @@ </table> </div> <div class="col-xs-4" style="padding: 0px;"> + <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> <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> <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span><br> <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index de04a758..98c75710 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -357,6 +357,7 @@ def marker_regression_page(): 'startMb', 'endMb', 'graphWidth', + 'additiveCheck', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', |