diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 20 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 4 |
5 files changed, 120 insertions, 34 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 6ce35a6c..f08e47ca 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -80,6 +80,8 @@ class MarkerRegression(object): 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 @@ -130,7 +132,7 @@ class MarkerRegression(object): self.num_perm = 0 else: self.num_perm = start_vars['num_perm'] - self.control = start_vars['control_marker'] + 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'] @@ -143,17 +145,35 @@ class MarkerRegression(object): if start_vars['num_perm'] == "": self.num_perm = 0 else: - self.num_perm = int(start_vars['num_perm']) + self.num_perm = int(start_vars['num_perm']) 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 else: + try: + if int(start_vars['num_bootstrap']) > 0: + self.bootCheck = "ON" + self.num_bootstrap = int(start_vars['num_bootstrap']) + 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.control = start_vars['control_marker'] + self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] results = self.gen_reaper_results() elif self.mapping_method == "plink": @@ -447,7 +467,7 @@ class MarkerRegression(object): def create_covariates(self, cross): ro.globalenv["the_cross"] = cross ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix - userinputS = self.control.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user + userinputS = self.control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS) #print("Marker names of selected covariates:", covariate_names) ro.r('covnames <- c(' + covariate_names + ')') @@ -656,14 +676,40 @@ class MarkerRegression(object): #print("samples:", trimmed_samples) - if self.control != "" and self.do_control == "true": - #print("CONTROL IS:", self.control) + if self.control_marker != "" and self.do_control == "true": reaper_results = genotype.regression(strains = trimmed_samples, - trait = trimmed_values, - control = str(self.control)) + trait = trimmed_values, + control = str(self.control_marker)) + if self.bootCheck: + control_geno = [] + control_geno2 = [] + _FIND = 0 + for _chr in genotype: + for _locus in _chr: + if _locus.name == self.control_marker: + control_geno2 = _locus.genotype + _FIND = 1 + break + if _FIND: + break + if control_geno2: + _prgy = list(genotype.prgy) + for _strain in trimmed_samples: + _idx = _prgy.index(_strain) + control_geno.append(control_geno2[_idx]) + + self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples, + trait = trimmed_values, + control = control_geno, + nboot = self.num_bootstrap) else: reaper_results = genotype.regression(strains = trimmed_samples, - trait = trimmed_values) + trait = trimmed_values) + + if self.bootCheck: + self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples, + trait = trimmed_values, + nboot = self.num_bootstrap) 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 739dc569..99f0ac99 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -227,24 +227,34 @@ class MarkerRegression(object): 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']) + else: + self.nboot = 0 if (start_vars['num_perm'] == "") or (start_vars['num_perm'] < 1): self.permChecked = False else: self.permChecked = True #self.permChecked = fd.formdata.getvalue('permCheck', True) - #self.bootChecked = fd.formdata.getvalue('bootCheck', '') - self.bootChecked = False #ZS: For now setting to False, I'll add this option later once rest of figure works + + if 'bootCheck' in start_vars.keys(): + self.bootChecked = start_vars['bootCheck'] + else: + self.bootChecked = False + 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: self.doControl = "false" - if 'control' in start_vars.keys(): - self.controlLocus = start_vars['control'] + if 'control_marker' in start_vars.keys(): + self.controlLocus = start_vars['control_marker'] else: self.controlLocus = "" - - #self.controlLocus = fd.formdata.getvalue('controlLocus', '') #try: self.selectedChr = int(start_vars['selected_chr']) @@ -795,8 +805,8 @@ class MarkerRegression(object): plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) #draw bootstap - #if self.bootChecked and not self.multipleInterval: - # self.drawBootStrapResult(canvas, fd.nboot, drawAreaHeight, plotXScale, offset=newoffset) + if self.bootChecked and not self.multipleInterval: + self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: @@ -843,17 +853,31 @@ class MarkerRegression(object): BootCoord = [] i = 0 startX = xLeftOffset - for j, _chr in enumerate(self.genotype): - BootCoord.append( []) - for _locus in _chr: - if self.plotScale == 'physic': - Xc = startX + (_locus.Mb-self.startMb)*plotXScale - else: - Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale - BootCoord[-1].append([Xc, self.bootResult[i]]) - i += 1 - startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale - + + if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes + for j, _chr in enumerate(self.genotype): + BootCoord.append( []) + for _locus in _chr: + if self.plotScale == 'physic': + Xc = startX + (_locus.Mb-self.startMb)*plotXScale + else: + Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale + BootCoord[-1].append([Xc, self.bootResult[i]]) + i += 1 + startX += (self.ChrLengthDistList[j] + self.GraphInterval)*plotXScale + else: + for j, _chr in enumerate(self.genotype): + if _chr.name == self.ChrList[self.selectedChr][0]: + BootCoord.append( []) + for _locus in _chr: + if _chr.name == self.ChrList[self.selectedChr][0]: + if self.plotScale == 'physic': + Xc = startX + (_locus.Mb-self.startMb)*plotXScale + else: + Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale + BootCoord[-1].append([Xc, self.bootResult[i]]) + i += 1 + #reduce bootResult if self.selectedChr > -1: maxBootBar = 80.0 @@ -1134,7 +1158,7 @@ class MarkerRegression(object): string1 = 'Mapping for Dataset: %s, mapping on All Chromosomes' % self.dataset.group.name else: string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (self.dataset.group.name, self.ChrList[self.selectedChr][0]) - if self.controlLocus: + if self.controlLocus and self.doControl != "false": string2 = 'Using %s as control' % self.controlLocus else: string2 = 'Using Haldane mapping function with no control for other QTLs' diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 107b1869..88fb0e89 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -22,6 +22,7 @@ <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_bootstrap" value="{{ nboot }}"> <input type="hidden" name="do_control" value="{{ doControl }}"> <input type="hidden" name="control_marker" value="{{ controlLocus }}"> <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}"> @@ -69,6 +70,7 @@ </div> <div class="col-xs-4" style="padding: 0px;"> {% if mapping_method == "reaper" %} + <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="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> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 6252f6f4..620a4631 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -188,6 +188,12 @@ </div> </div> <div class="mapping_method_fields form-group"> + <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> + <input name="num_bootstrap" value="2000" type="text" class="form-control"> + </div> + </div> + <div class="mapping_method_fields form-group"> <label for="control_for" class="col-xs-3 control-label">Control for</label> <div style="margin-left: 20px;" class="col-xs-4 controls"> {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} @@ -204,12 +210,15 @@ No </label> </div> - </div> -<!-- + </div> + +<!-- <div class="mapping_method_fields form-group"> - <label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - <input name="mapping_bootstraps" value="2000" type="text" class="form-control"> + <label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap Test (n=2000)</label> + <div class="col-xs-4 controls"> + <label> + <input type="checkbox" name="bootCheck" id="bootCheck"> Bootstrap Test (n=2000) + </label> </div> </div> @@ -228,6 +237,7 @@ </div> --> + <div class="mapping_method_fields form-group"> <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> <div class="col-xs-12 controls"> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 98c75710..9d0fd131 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -348,6 +348,10 @@ def marker_regression_page(): 'score_type', 'suggestive', 'num_perm', + 'permCheck', + 'num_bootstrap', + 'bootCheck', + 'bootstrap_results', 'maf', 'manhattan_plot', 'control_marker', |