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authorzsloan2016-01-12 22:06:11 +0000
committerzsloan2016-01-12 22:06:11 +0000
commit8d5397590206a3bc5d32985c532bac354313f0b2 (patch)
tree91ced2966d2dde5c155a1d42f4605782132d2d95 /wqflask
parent5e8934baf749b8fee396813637035fbb7ece5b0e (diff)
downloadgenenetwork2-8d5397590206a3bc5d32985c532bac354313f0b2.tar.gz
Mapping works for rqtl and centimorgan scale
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py38
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js20
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html2
3 files changed, 38 insertions, 22 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index a0033bd2..23d5a631 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -517,10 +517,10 @@ class MarkerRegression(object):
################################################################
# Plots goes here
################################################################
- if self.plotScale != 'physic' or self.multipleInterval:
- showLocusForm = webqtlUtil.genRandStr("fm_")
- else:
- showLocusForm = ""
+ #if self.plotScale != 'physic' or self.multipleInterval:
+ # showLocusForm = webqtlUtil.genRandStr("fm_")
+ #else:
+ showLocusForm = ""
intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
@@ -1789,7 +1789,8 @@ class MarkerRegression(object):
edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
- HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
+ HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
+ #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
gifmap.areas.append(Areas)
##piddle bug
@@ -1947,21 +1948,32 @@ class MarkerRegression(object):
#DominanceCoordXY = []
#for k, _locus in enumerate(_chr):
if 1 == 1:
- if self.plotScale == 'physic':
+ Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+ #if self.plotScale == 'physic':
#Xc = startPosX + (_locus.Mb-startMb)*plotXScale
- Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
- else:
+ #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+ #else:
#Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
- Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
+ #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
# 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 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
+ if self.LRS_LOD == "LRS":
+ if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+ Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+ else:
+ Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
else:
- Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
+ if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
+ Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
+ else:
+ Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSMax
+ #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
+ #else:
+ # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
LRSCoordXY.append((Xc, Yc))
#if not self.multipleInterval and self.additiveChecked:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 721752dd..16eeb8df 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -180,7 +180,7 @@
$("#rqtl_geno_compute").on("click", (function(_this) {
return function() {
var form_data, url;
- $("#progress_bar_container").modal();
+ //$("#progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("rqtl_geno");
$('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
@@ -189,20 +189,22 @@
$('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
+ return submit_special(url);
+ //return do_ajax_post(url, form_data);
};
})(this));
$("#plink_compute").on("click", (function(_this) {
return function() {
var form_data, url;
- $("#static_progress_bar_container").modal();
+ //$("#static_progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("plink");
$('input[name=maf]').val($('input[name=maf_plink]').val());
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
+ return submit_special(url);
+ //return do_ajax_post(url, form_data);
};
})(this));
@@ -210,13 +212,14 @@
return function() {
var form_data, url;
console.log("RUNNING GEMMA");
- $("#static_progress_bar_container").modal();
+ //$("#static_progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("gemma");
$('input[name=maf]').val($('input[name=maf_gemma]').val());
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
+ return submit_special(url);
+ //return do_ajax_post(url, form_data);
};
})(this));
@@ -232,7 +235,7 @@
return function() {
var form_data, url;
console.log("In interval mapping");
- $("#progress_bar_container").modal();
+ //$("#progress_bar_container").modal();
url = "/interval_mapping";
$('input[name=method]').val("reaper");
$('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
@@ -240,7 +243,8 @@
$('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
+ return submit_special(url);
+ //return do_ajax_post(url, form_data);
};
})(this));
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index f5bec6ea..05623462 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -59,7 +59,7 @@
value="{{ marker.name }}" checked="checked">
</td>
<Td align="right">{{ loop.index }}</Td>
- {% if score_type == "LOD" %}
+ {% if LRS_LOD == "LOD" %}
<td>{{ '%0.2f' | format(marker.lod_score|float) }}</td>
{% else %}
<td>{{ '%0.2f' | format(marker.lrs_value|float) }}</td>