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-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py48
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html26
-rwxr-xr-xwqflask/wqflask/templates/show_trait_calculate_correlations.html17
3 files changed, 72 insertions, 19 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 63631350..6a120325 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -104,6 +104,12 @@ class CorrelationResults(object):
self.sample_data = {}
self.corr_type = start_vars['corr_type']
self.corr_method = start_vars['corr_sample_method']
+ if start_vars['min_expr'] == "":
+ self.min_expr = 0
+ else:
+ self.min_expr = float(start_vars['min_expr'])
+ self.p_range_lower = float(start_vars['p_range_lower'])
+ self.p_range_upper = float(start_vars['p_range_upper'])
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -164,27 +170,30 @@ class CorrelationResults(object):
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
print("trait name:", trait)
trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
+ print("trait_object.mean:", trait_object.mean)
+ print("self.min_expr:", self.min_expr)
+ print("self.p_range_upper:", self.p_range_upper)
+ if (float(trait_object.mean) > self.min_expr and
+ float(self.correlation_data[trait][0]) > self.p_range_lower and
+ float(self.correlation_data[trait][0]) < self.p_range_upper):
+
+ (trait_object.sample_r,
+ trait_object.sample_p,
+ trait_object.num_overlap) = self.correlation_data[trait]
- (trait_object.sample_r,
- trait_object.sample_p,
- trait_object.num_overlap) = self.correlation_data[trait]
-
- #trait_object.sample_p = self.correlation_data[trait][1]
- #trait_object.num_overlap = self.correlation_data[trait][2]
-
- #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
- #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
+ #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
+ #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
- # Set some sane defaults
- trait_object.tissue_corr = 0
- trait_object.tissue_pvalue = 0
- trait_object.lit_corr = 0
- if self.corr_type == "tissue":
- trait_object.tissue_corr = tissue_corr_data[trait][1]
- trait_object.tissue_pvalue = tissue_corr_data[trait][2]
- elif self.corr_type == "lit":
- trait_object.lit_corr = lit_corr_data[trait][1]
- self.correlation_results.append(trait_object)
+ # Set some sane defaults
+ trait_object.tissue_corr = 0
+ trait_object.tissue_pvalue = 0
+ trait_object.lit_corr = 0
+ if self.corr_type == "tissue":
+ trait_object.tissue_corr = tissue_corr_data[trait][1]
+ trait_object.tissue_pvalue = tissue_corr_data[trait][2]
+ elif self.corr_type == "lit":
+ trait_object.lit_corr = lit_corr_data[trait][1]
+ self.correlation_results.append(trait_object)
self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species)
@@ -478,6 +487,7 @@ class CorrelationResults(object):
this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
this_trait_vals, target_vals)
+ #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
if self.corr_method == 'pearson':
sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
else:
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 55464635..c5921ccf 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -12,6 +12,8 @@
<link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
{% endblock %}
@@ -147,6 +149,7 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<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/noUiSlider/nouislider.js"></script>
<script type="text/javascript" charset="utf-8">
function getValue(x) {
@@ -251,6 +254,29 @@
"paging": false
} );
{% endif %}
+
+ var slider = document.getElementById('p_range_slider');
+ noUiSlider.create(slider, {
+ start: [-1.0, 1.0],
+ range: {
+ 'min': [-1.0],
+ 'max': [1.0]
+ }
+ });
+
+ var slider_display = [
+ document.getElementById('p_range_lower'),
+ document.getElementById('p_range_upper')
+ ];
+ var slider_values = [
+ $('input[name=p_range_lower]'),
+ $('input[name=p_range_upper]')
+ ];
+
+ slider.noUiSlider.on('update', function( values, handle ) {
+ slider_display[handle].innerHTML = values[handle];
+ slider_values[handle].val(values[handle]);
+ });
});
</script>
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index f02d1705..cefe9763 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -72,6 +72,23 @@
</select>
</div>
</div>
+
+ <div class="form-group">
+ <label class="col-xs-1 control-label">Min Expr</label>
+ <div class="col-xs-2 controls">
+ <input name="min_expr" value="" type="text" class="form-control" style="width: 50px;">
+ </div>
+ </div>
+ <div class="form-group">
+ <label class="col-xs-1 control-label">Range</label>
+ <div class="col-xs-3 controls">
+ <input name="p_range_lower" value="" type="hidden">
+ <input name="p_range_upper" value="" type="hidden">
+ <div id="p_range_slider" ></div>
+ <span style="font: 400 12px Arial; color: #888; display: block; margin: 15px 0;" id="p_range_lower"></span>
+ <span style="font: 400 12px Arial; color: #888; display: block; margin: 15px 0;" id="p_range_upper"></span>
+ </div>
+ </div>
<div class="form-group">
<label for="corr_sample_method" class="col-xs-1 control-label"></label>