aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/trait.py15
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py13
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html2
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html2
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html77
-rw-r--r--wqflask/wqflask/templates/search_result_page.html2
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) {
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:00:51 +0000