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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py31
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py18
-rw-r--r--wqflask/wqflask/static/new/javascript/create_interval_map.coffee2
-rw-r--r--wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee1
-rw-r--r--wqflask/wqflask/static/new/javascript/create_manhattan_plot.js2
-rwxr-xr-xwqflask/wqflask/static/new/javascript/marker_regression.coffee3
-rwxr-xr-xwqflask/wqflask/static/new/javascript/marker_regression.js2
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee2
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js2
9 files changed, 49 insertions, 14 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1524143e..539bc995 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -61,6 +61,8 @@ class MarkerRegression(object):
self.mapping_method = start_vars['method']
self.maf = start_vars['maf'] # Minor allele frequency
+ self.suggestive = ""
+ self.significant = ""
#print("self.maf:", self.maf)
self.dataset.group.get_markers()
@@ -103,6 +105,9 @@ class MarkerRegression(object):
self.json_data['lod.hk'] = []
self.json_data['markernames'] = []
+ self.json_data['suggestive'] = self.suggestive
+ self.json_data['significant'] = self.significant
+
#Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
self.qtl_results = []
for qtl in self.filtered_markers:
@@ -293,24 +298,42 @@ class MarkerRegression(object):
r_string = 'scanone(the_cross, pheno.col="the_pheno", n.perm='+self.num_perm+', addcovar=covariates, intcovar=covariates[,'+ str(len(control_markers)) +'])'
print("r_string:", r_string)
- if self.num_perm > 0:
+ if int(self.num_perm) > 0:
thresholds = robjects.r(r_string)
- print("thresholds:", thresholds)
-
+ self.suggestive, self.significant = self.process_rqtl_perm_results(results)
+ r_string = 'scanone(the_cross, pheno.col="the_pheno", addcovar=covariates, intcovar=covariates[,'+ str(len(control_markers)) +'])'
+
#r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', addcovar='+control_as_string+')'
else:
#r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+')'
r_string = 'scanone(the_cross, pheno.col="the_pheno", n.perm='+self.num_perm+')'
+ if int(self.num_perm) > 0:
+ results = robjects.r(r_string)
+ self.suggestive, self.significant = self.process_rqtl_perm_results(results)
+ r_string = 'scanone(the_cross, pheno.col="the_pheno")'
print("r_string:", r_string)
result_data_frame = robjects.r(r_string)
#print("results:", result_data_frame)
qtl_results = self.process_rqtl_results(result_data_frame)
-
+
return qtl_results
+ def process_rqtl_perm_results(self, results):
+
+ perm_vals = []
+ for line in str(results).split("\n")[1:(int(self.num_perm)+1)]:
+ print("line:", line.split())
+ perm_vals.append(float(line.split()[1]))
+
+ self.suggestive = np.percentile(np.array(perm_vals), 67)
+ self.significant = np.percentile(np.array(perm_vals), 95)
+
+ return self.suggestive, self.significant
+
+
def process_rqtl_results(self, result):
qtl_results = []
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 51cf337c..833c3b06 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -92,7 +92,7 @@ class ShowTrait(object):
#Get nearest marker for composite mapping
- if self.dataset.type != "Geno":
+ if self.dataset.type != "Geno" and self.dataset.type != "Publish":
self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
@@ -109,8 +109,10 @@ class ShowTrait(object):
hddn['suggestive'] = 0
hddn['num_perm'] = 0
hddn['manhattan_plot'] = False
- if self.dataset.type != "Geno":
+ if self.dataset.type != "Geno" and self.dataset.type != "Publish":
hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
+ else:
+ hddn['control_marker'] = ""
hddn['maf'] = 0.01
hddn['compare_traits'] = []
@@ -489,10 +491,14 @@ class ShowTrait(object):
#self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol)
#try:
- this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
- if this_chr and txst and txen and this_trait.refseq_transcriptid :
- txst = int(txst*1000000)
- txen = int(txen*1000000)
+ print("this_trait.symbol:", this_trait.symbol)
+ result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+ if result != None:
+ this_chr, txst, txen = result[0], result[1], result[2]
+ #this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+ if this_chr and txst and txen and this_trait.refseq_transcriptid :
+ txst = int(txst*1000000)
+ txen = int(txen*1000000)
#tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
# title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',
# this_trait.refseq_transcriptid,
diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
index c8e1b318..b01e2651 100644
--- a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee
@@ -12,7 +12,7 @@ create_interval_map = () ->
.height(h)
.width(w)
.margin(margin)
-
+
data = js_data.json_data
d3.select("div#topchart")
diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
index 0cd9e124..a4c41227 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.coffee
@@ -14,6 +14,7 @@ create_manhattan_plot = ->
.height(h)
.width(w)
.margin(margin)
+ .ylab("LOD score")
.manhattanPlot(js_data.manhattan_plot)
data = js_data.json_data
diff --git a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
index d30e8e6a..c577fb93 100644
--- a/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
+++ b/wqflask/wqflask/static/new/javascript/create_manhattan_plot.js
@@ -16,7 +16,7 @@ create_manhattan_plot = function() {
totalh = halfh * 2;
totalw = w + margin.left + margin.right;
console.log("js_data:", js_data);
- mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).manhattanPlot(js_data.manhattan_plot);
+ mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot);
data = js_data.json_data;
d3.select("div#topchart").datum(data).call(mychart);
chrrect = mychart.chrSelect();
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 959f2366..d522b667 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -16,6 +16,9 @@ class Lod_Chart
@this_trait = js_data.this_trait
@data_set = js_data.data_set
@maf = js_data.maf #Minor allele frequency
+
+ @suggestive = js_data.suggestive
+ @significant = js_data.significant
@total_length = 0
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 1bdc784f..a033cf0c 100755
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -24,6 +24,8 @@ Lod_Chart = (function() {
this.this_trait = js_data.this_trait;
this.data_set = js_data.data_set;
this.maf = js_data.maf;
+ this.suggestive = js_data.suggestive;
+ this.significant = js_data.significant;
this.total_length = 0;
this.max_chr = this.get_max_chr();
this.x_coords = [];
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 72d2bbe4..d25c1d3a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -213,7 +213,7 @@ $ ->
$("#plink_compute").click(() =>
$("#static_progress_bar_container").modal()
url = "/marker_regression"
- $('input[name=method]').val("plink")
+ $('input[nsssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssegbame=method]').val("plink")
$('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val())
$('input[name=suggestive]').val($('input[name=suggestive_plink]').val())
$('input[name=maf]').val($('input[name=maf_plink]').val())
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 4eaceffe..d178879c 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -149,7 +149,7 @@ $(function() {
var form_data, url;
$("#static_progress_bar_container").modal();
url = "/marker_regression";
- $('input[name=method]').val("plink");
+ $('input[nsssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssegbame=method]').val("plink");
$('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val());
$('input[name=suggestive]').val($('input[name=suggestive_plink]').val());
$('input[name=maf]').val($('input[name=maf_plink]').val());