diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 30 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 116 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 1 |
4 files changed, 123 insertions, 66 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 112dcd5c..86fced39 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -103,10 +103,13 @@ class MarkerRegression(object): self.permCheck = False self.num_perm = int(start_vars['num_perm']) + self.LRSCheck = start_vars['LRSCheck'] + if "showGenes" in start_vars: self.showGenes = start_vars['showGenes'] else: self.showGenes = False + if "viewLegend" in start_vars: self.viewLegend = start_vars['viewLegend'] else: @@ -120,6 +123,7 @@ class MarkerRegression(object): except: self.num_perm = 0 + self.LRSCheck = self.score_type self.permCheck = "ON" self.showGenes = "ON" self.viewLegend = "ON" @@ -660,18 +664,18 @@ class MarkerRegression(object): if samples[i] in self.dataset.group.samplelist: trimmed_samples.append(samples[i]) trimmed_values.append(values[i]) - - self.lrs_array = genotype.permutation(strains = trimmed_samples, - 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)] + + 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['suggestive'] = self.suggestive self.json_data['significant'] = self.significant - #print("samples:", trimmed_samples) - if self.control_marker != "" and self.do_control == "true": reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values, @@ -706,14 +710,6 @@ class MarkerRegression(object): self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples, 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'] = [] diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 692e381b..45d98554 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -293,7 +293,7 @@ class MarkerRegression(object): self.graphHeight = self.GRAPH_DEFAULT_HEIGHT self.manhattan_plot = start_vars['manhattan_plot'] self.dominanceChecked = False - self.LRS_LOD = start_vars['score_type'] + self.LRS_LOD = start_vars['LRSCheck'] self.cutoff = start_vars['cutoff'] self.intervalAnalystChecked = False if 'additiveCheck' in start_vars.keys(): @@ -1108,7 +1108,6 @@ class MarkerRegression(object): if zoom == 2: fontZoom = 1.5 - labelFont=pid.Font(ttf="trebuc",size=12*fontZoom, bold=1) startPosY = 15 stepPosY = 12*fontZoom @@ -1146,10 +1145,8 @@ class MarkerRegression(object): lod = 1 if self.LRS_LOD == 'LOD': lod = self.LODFACTOR - 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) - - + canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black) + canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black) labelFont=pid.Font(ttf="verdana",size=12*fontZoom) labelColor = pid.black @@ -1865,46 +1862,66 @@ class MarkerRegression(object): #draw the LRS scale #We first determine whether or not we are using a sliding scale. - #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax. - #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment. - #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter. + #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max. + #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment. + #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter. #ZS: I'm not sure what this if statement is supposed to do. It appears to work correctly for both LOD and LRS if I just set lodm to 1.0 - #if self.LRS_LOD == 'LRS': - # lodm = self.LODFACTOR - #else: - # lodm = 1.0 - lodm = 1.0 + # if self.LRS_LOD == 'LRS': + # lodm = self.LODFACTOR + # else: + # lodm = 1.0 + #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD if self.lrsMax <= 0: #sliding scale - if self.LRS_LOD == "LRS" and "lrs_value" in self.qtlresults[0]: - LRSMax = max([result['lrs_value'] for result in self.qtlresults]) - #LRSMax = max(map(max, self.qtlresults)).lrs_value - else: - LRSMax = max([result['lod_score'] for result in self.qtlresults]) - #LRSMax = max(map(max, self.qtlresults)).lod_score - #genotype trait will give infinite LRS - LRSMax = min(LRSMax, webqtlConfig.MAXLRS) + if "lrs_value" in self.qtlresults[0]: + LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults]) + if self.LRS_LOD == "LOD": + LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR + if self.permChecked and self.nperm > 0 and not self.multipleInterval: + self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min(self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS) + else: + 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) + else: + pass + else: + LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults]) + if self.LRS_LOD == "LRS": + LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR + if self.permChecked and self.nperm > 0 and not self.multipleInterval: + self.significant = min(self.significant * self.LODFACTOR, webqtlConfig.MAXLRS) + self.suggestive = min(self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS) + else: + 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) + else: + pass + 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.significant, LRSMax) + LRS_LOD_Max = max(self.significant, LRS_LOD_Max) + + #genotype trait will give infinite LRS + LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS) else: - LRSMax = self.lrsMax*lodm + LRS_LOD_Max = self.lrsMax - if LRSMax/lodm > 100: + if LRS_LOD_Max > 100: LRSScale = 20.0 - elif LRSMax/lodm > 20: + elif LRS_LOD_Max > 20: LRSScale = 5.0 - elif LRSMax/lodm > 7.5: + elif LRS_LOD_Max > 7.5: LRSScale = 2.5 else: LRSScale = 1.0 - LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale) + LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale) #make sure the user's value appears on the y-axis - #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460 - LRSAxisList.append(round(LRSMax/lodm)) + #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460 + LRSAxisList.append(round(LRS_LOD_Max)) #draw the "LRS" or "LOD" string to the left of the axis LRSScaleFont=pid.Font(ttf="verdana", size=16*zoom, bold=0) @@ -1915,17 +1932,17 @@ class MarkerRegression(object): yZero - 150 - 300*(zoom - 1), font=LRSLODFont, color=pid.black, angle=90) for item in LRSAxisList: - if LRSMax == 0.0: - LRSMax = 0.000001 - yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh + if LRS_LOD_Max == 0.0: + LRS_LOD_Max = 0.000001 + yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom) scaleStr = "%2.1f" % item #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) if self.permChecked and self.nperm > 0 and not self.multipleInterval: - significantY = yZero - self.significant*LRSHeightThresh/LRSMax - suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax + significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max + suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max startPosX = xLeftOffset #"Significant" and "Suggestive" Drawing Routine @@ -2025,21 +2042,30 @@ class MarkerRegression(object): # 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 self.LRS_LOD == "LRS": - if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax + 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) else: - Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax + 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 else: if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf': - Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax + Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max else: - Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSMax + 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/LRSMax + # Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max #else: - # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax + # 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) diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 8ec8a104..11c0f859 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -61,6 +61,20 @@ </td> </tr> <tr> + <td><b>Units: </b></td> + <td style="padding: 5px;"> + <label class="radio-inline"> + <input type="radio" name="LRSCheck" value="LRS" {% if LRS_LOD == "LRS" %}checked{% endif %}>LRS + </label> + <label class="radio-inline"> + <input type="radio" name="LRSCheck" value="LOD" {% if LRS_LOD == "LOD" %}checked{% endif %}>LOD + </label> + <a href="http://genenetwork.org/glossary.html#LOD" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + </td> + </tr> + <tr> <td><b>Width: </b></td> <td> <input type="text" name="graphWidth" value="{% if graphWidth is defined %}{{ graphWidth }}{% else %}1600{% endif %}" size="5"><span style="font-size: 11px;"> pixels (minimum=900)</span> @@ -70,13 +84,25 @@ </div> <div class="col-xs-4" style="padding: 0px;"> {% 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> + <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 + <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <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> + <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 + <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <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> + <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 + <a href="http://genenetwork.org/glossary.html#additive" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <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> <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> @@ -151,12 +177,20 @@ class="checkbox edit_sample_checkbox" value="{{ marker.name }}" checked="checked"> </td> - <Td align="right">{{ loop.index }}</Td> + <td align="right">{{ loop.index }}</td> {% if LRS_LOD == "LOD" %} + {% if 'lod_score' in marker %} <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td> {% else %} + <td>{{ '%0.2f' | format(marker.lrs_value|float / 4.16) }}</td> + {% endif %} + {% else %} + {% if 'lod_score' in marker %} + <td>{{ '%0.2f' | format(marker.lod_score|float * 4.16) }}</td> + {% else %} <td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td> {% endif %} + {% endif %} <td>{{marker.chr}}</td> <td>{{ '%0.6f' | format(marker.Mb|float) }}</td> <td> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index acfc5fc6..2e846066 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -354,6 +354,7 @@ def marker_regression_page(): 'num_bootstrap', 'bootCheck', 'bootstrap_results', + 'LRSCheck', 'maf', 'manhattan_plot', 'control_marker', |