diff options
| -rw-r--r-- | wqflask/base/trait.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_gene.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/gsearch_pheno.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 77 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 2 |
7 files changed, 78 insertions, 35 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index f18481a8..900e050c 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -322,7 +322,7 @@ class GeneralTrait(object): #phenotype traits, then display the pre-publication description instead #of the post-publication description if self.confidential: - self.description_display = "" + self.description_display = self.pre_publication_description #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( # privilege=self.dataset.privilege, @@ -330,11 +330,11 @@ class GeneralTrait(object): # authorized_users=self.authorized_users): # # description = self.pre_publication_description - - if description: - self.description_display = description.strip() else: - self.description_display = "" + if description: + self.description_display = description.strip() + else: + self.description_display = "" if not self.year.isdigit(): self.pubmed_text = "N/A" @@ -612,7 +612,10 @@ class GeneralTrait(object): if self.probe_target_description: formatted += "; " + self.probe_target_description elif self.dataset.type == 'Publish': - formatted = self.post_publication_description + if self.confidential: + formatted = self.pre_publication_description + else: + formatted = self.post_publication_description else: formatted = "Not available" return formatted.capitalize() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 89af856e..a53afd5a 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -702,8 +702,6 @@ class MarkerRegression(object): control = control_geno, nboot = self.num_bootstrap) else: - # reaper_results = genotype.regression(strains = self.samples, - # trait = self.vals) reaper_results = genotype.regression(strains = trimmed_samples, trait = trimmed_values) diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 4f52bd55..f902afb7 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -810,7 +810,7 @@ class MarkerRegression(object): #draw bootstap #if self.bootChecked and not self.multipleInterval: - # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset) + # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb) # Draw clickable region and gene band if selected if self.plotScale == 'physic' and self.selectedChr > -1: @@ -857,7 +857,7 @@ class MarkerRegression(object): BootCoord = [] i = 0 startX = xLeftOffset - + if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes for j, _chr in enumerate(self.genotype): BootCoord.append( []) @@ -876,7 +876,7 @@ class MarkerRegression(object): for _locus in _chr: if _chr.name == self.ChrList[self.selectedChr][0]: if self.plotScale == 'physic': - Xc = startX + (_locus.Mb-self.startMb)*plotXScale + Xc = startX + (_locus.Mb-startMb)*plotXScale else: Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale BootCoord[-1].append([Xc, self.bootResult[i]]) @@ -1017,7 +1017,7 @@ class MarkerRegression(object): else: locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale break - if locPixel >= 0: + if locPixel >= 0 and self.plotScale == 'physic': traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12)) canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1) @@ -1762,6 +1762,7 @@ class MarkerRegression(object): strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=megabaseLabelFont, color=pid.black) pass else: + strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont) + 8 ChrAInfo = [] preLpos = -1 distinctCount = 0.0 @@ -1847,6 +1848,10 @@ class MarkerRegression(object): if j == 0: canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor) startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale + + centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0) + canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2, + strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black) canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index a50157ce..2d970b36 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -93,7 +93,7 @@ {% block js %} <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> + <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index b28a34df..be4981bb 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -86,7 +86,7 @@ {% block js %} <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script> + <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index c5cb278c..7454b650 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -169,14 +169,16 @@ </div> </form> - <div style="width:48%;"> - {% if selectedChr == -1 %} + {% if selectedChr == -1 %} + <div style="width:{% if 'additive' in trimmed_markers[0] %}50%{% else %}35%{% endif %};"> <h2>Results</h2> + <div id="table_container" style="background-color: #eeeeee; border: 1px solid black;"> <table id="qtl_results" class="table table-hover table-striped"> <thead> <tr> <th></th> - <th>Index</th> + <th>Row</th> + <th>Locus</th> <th>{{ LRS_LOD }}</th> <th>Chr</th> {% if plotScale == "centimorgan" %} @@ -184,7 +186,12 @@ {% else %} <th>Mb</th> {% endif %} - <th>Locus</th> + {% if 'additive' in trimmed_markers[0] %} + <th>Add Eff</th> + {% endif %} + {% if 'dominance' in trimmed_markers[0] %} + <th>Dom Eff</th> + {% endif %} </tr> </thead> <tbody> @@ -196,6 +203,7 @@ value="{{ marker.name }}" checked="checked"> </td> <td align="right">{{ loop.index }}</td> + <td>{{ marker.name }}</td> {% if LRS_LOD == "LOD" %} {% if 'lod_score' in marker %} <td>{{ '%0.2f' | format(marker.lod_score|float) }}</td> @@ -211,13 +219,22 @@ {% endif %} <td>{{marker.chr}}</td> <td>{{ '%0.6f' | format(marker.Mb|float) }}</td> - <td>{{ marker.name }}</td> + {% if 'additive' in marker %} + <td>{{ '%0.3f' | format(marker.additive|float) }}</td> + {% endif %} + {% if 'dominance' in marker %} + <td>{{ '%0.2f' | format(marker.dominance|float) }}</td> + {% endif %} </tr> {% endfor %} </tbody> </table> - {% else %} + </div> + </div> + {% else %} + <div> <h2>Interval Analyst</h2> + <div id="table_container" style="background-color: #eeeeee; border: 1px solid black;"> <table id="interval_analyst" class="table table-hover table-striped"> <thead> <tr> @@ -236,8 +253,9 @@ {% endfor %} </tbody> </table> - {% endif %} + </div> </div> + {% endif %} </div> <!-- End of body --> @@ -251,7 +269,7 @@ <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script> <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script> + <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> @@ -274,26 +292,35 @@ <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); - $('#qtl_results').dataTable( { + $('#qtl_results').DataTable( { "columns": [ - { "type": "natural", "sWidth": "10%", "bSortable": false }, + { "type": "natural", "width": "5%", "bSortable": false }, + { "type": "natural", "width": "6%" }, + { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural", "sWidth": "30%"} + { "type": "natural" } ], - "order": [[1, "asc"]], + "order": [[1, "asc" ]], "buttons": [ - 'csv' + { + extend: 'csvHtml5', + text: 'Download CSV', + title: 'search_results', + fieldBoundary: '"', + exportOptions: { + columns: [1, 2, 3, 4, 5, 6, 7, 8] + } + } ], "sDom": "RZBtir", "iDisplayLength": -1, - "autoWidth": true, "bDeferRender": true, "bSortClasses": false, - "scrollY": "700px", - "scrollCollapse": true, + "scrollY": true, + "scrollCollapse": false, "paging": false } ); @@ -302,12 +329,24 @@ "targets": 0, "sortable": false }], - "order": [[3, "asc"]], - "sDom": "RZtir", + "order": [[3, "asc" ]], + "buttons": [ + { + extend: 'csvHtml5', + text: 'Download CSV', + title: 'search_results', + fieldBoundary: '"', + exportOptions: { + columns: [1, 2, 3, 4, 5, 6, 7, 8, 9] + } + } + ], + "sDom": "RZBtir", "iDisplayLength": -1, - "autoWidth": true, "bDeferRender": true, "bSortClasses": false, + "scrollY": true, + "scrollCollapse": false, "paging": false } ); diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 4ba2d802..523037f8 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -163,7 +163,6 @@ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> - <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/1.4.1/js/dataTables.scroller.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> @@ -171,7 +170,6 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.min.js"></script> - <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.js"></script> <script type="text/javascript" charset="utf-8"> function getValue(x) { |