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-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py9
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py1
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py2
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py17
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html3
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html106
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html185
-rw-r--r--wqflask/wqflask/views.py2
8 files changed, 250 insertions, 75 deletions
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b34beb7b..077386a3 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -173,9 +173,12 @@ class CorrelationMatrix(object):
for sample in self.all_sample_list:
groups.append(1)
- pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
-
- self.loadings_array = self.process_loadings()
+ try:
+ self.pca_works = "True"
+ pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
+ self.loadings_array = self.process_loadings()
+ except:
+ self.pca_works = "False"
self.js_data = dict(traits = [trait.name for trait in self.traits],
groups = groups,
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 087b95b4..db4f8f46 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -228,6 +228,7 @@ class MarkerRegression(object):
results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
self.dataset,
self.samples,
+ self.vals,
self.json_data,
self.num_perm,
self.bootCheck,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 211cf187..66884b0c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1204,6 +1204,8 @@ class MarkerRegression(object):
else:
if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+ if self.covariates != "":
+ string3 = 'Using following traits as covariates: ' + self.covariates
elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
string2 = 'Using R/qtl mapping method with no control for other QTLs.'
elif self.mapping_method == "plink":
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 50228b5e..6b58190f 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -1,17 +1,20 @@
-def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
genotype = dataset.group.read_genotype_file()
if manhattan_plot != True:
genotype = genotype.addinterval()
- samples, values, variances, sample_aliases = this_trait.export_informative()
-
trimmed_samples = []
trimmed_values = []
- for i in range(0, len(samples)):
- if this_trait.data[samples[i]].name in samples_before:
- trimmed_samples.append(samples[i])
- trimmed_values.append(values[i])
+ for i in range(0, len(samples_before)):
+ try:
+ trimmed_values.append(float(trait_vals[i]))
+ trimmed_samples.append(samples_before[i])
+ except:
+ pass
perm_output = []
bootstrap_results = []
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index ab793d58..d27788a8 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -61,6 +61,7 @@
<br>
<button class="btn btn-default" id="short_labels">Short Labels</button>
<button class="btn btn-default" id="long_labels">Long Labels</button>
+{% if pca_works == "True" %}
<br>
<br>
<h2>Factor Loadings Plot</h2>
@@ -93,7 +94,7 @@
</tbody>
</table>
</div>
-
+{% endif %}
{% endblock %}
{% block js %}
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index c5f815ce..ef233333 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,9 +1,10 @@
<div>
+ <div class="col-xs-7">
<div style="padding: 20px" class="form-horizontal">
<div class="form-group">
- <label for="corr_type" class="col-xs-1 control-label">Method</label>
- <div class="col-xs-2 controls">
+ <label for="corr_type" class="col-xs-2 control-label">Method</label>
+ <div class="col-xs-3 controls">
<select name="corr_type" class="form-control">
<option value="sample">Sample r</option>
<option value="lit">Literature r</option>
@@ -13,8 +14,8 @@
</div>
<div class="form-group">
- <label for="corr_dataset" class="col-xs-1 control-label">Database</label>
- <div class="col-xs-6 controls">
+ <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+ <div class="col-xs-10 controls">
<select name="corr_dataset" class="form-control">
{% for tissue in corr_tools.dataset_menu %}
{% if tissue.tissue %}
@@ -37,8 +38,8 @@
</div>
<div class="form-group">
- <label for="corr_return_results" class="col-xs-1 control-label">Return</label>
- <div class="col-xs-2 controls">
+ <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+ <div class="col-xs-3 controls">
<select name="corr_return_results" class="form-control">
{% for return_result in corr_tools.return_results_menu %}
<option value="{{ return_result }}"
@@ -53,8 +54,8 @@
</div>
<div class="form-group">
- <label for="corr_samples_group" class="col-xs-1 control-label">Samples</label>
- <div class="col-xs-2 controls">
+ <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+ <div class="col-xs-3 controls">
<select name="corr_samples_group" class="form-control">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
@@ -64,8 +65,8 @@
</div>
<div id="corr_sample_method" class="form-group">
- <label for="corr_sample_method" class="col-xs-1 control-label">Type</label>
- <div class="col-xs-2 controls">
+ <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
+ <div class="col-xs-3 controls">
<select name="corr_sample_method" class="form-control">
<option value="pearson">Pearson</option>
<option value="spearman">Spearman Rank</option>
@@ -73,14 +74,14 @@
</div>
</div>
<div class="form-group">
- <label class="col-xs-1 control-label">Min Expr</label>
- <div class="col-xs-2 controls">
+ <label class="col-xs-2 control-label">Min Expr</label>
+ <div class="col-xs-3 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">Location</label>
- <div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label">Location</label>
+ <div class="col-xs-5 controls">
<span>
Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">&nbsp;&nbsp;&nbsp;
Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
@@ -89,8 +90,8 @@
</div>
</div>
<div class="form-group">
- <label class="col-xs-1 control-label">Range</label>
- <div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label">Range</label>
+ <div class="col-xs-5 controls">
<input name="p_range_lower" value="" type="hidden">
<input name="p_range_upper" value="" type="hidden">
<span style="display: inline;">
@@ -103,48 +104,45 @@
</div>
<div class="form-group">
- <label for="corr_sample_method" class="col-xs-1 control-label"></label>
- <div class="col-xs-4 controls">
+ <label for="corr_sample_method" class="col-xs-2 control-label"></label>
+ <div class="col-xs-3 controls">
<button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
-
- <div class="form-group">
- <label for="descriptions" class="col-xs-1 control-label"></label>
- <div class="col-xs-6 controls">
- <span id="sample_r_desc" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
- is computed
- between trait data and any
- other traits in the sample database selected above. Use
- <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
- Rank</a>
- when the sample size is small (&lt;20) or when there are influential outliers.
- </span>
- <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
- (Lit r) between
- this gene and all other genes is computed<br>
- using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
- Semantic Gene Organizer</a>
- and human, rat, and mouse data from PubMed.
- Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
- <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
- </span>
- <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
- (Tissue r)
- estimates the similarity of expression of two genes
- or transcripts across different cells, tissues, or organs
- (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
- Tissue correlations
- are generated by analyzing expression in multiple samples usually taken from single cases.<br>
- <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
- computed for all pairs of genes using data from mouse samples.<br>
- </span>
- </div>
- </div>
</div>
+ </div>
+ <div class="col-xs-5">
+ <span id="sample_r_desc" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
+ is computed
+ between trait data and any
+ other traits in the sample database selected above. Use
+ <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
+ Rank</a>
+ when the sample size is small (&lt;20) or when there are influential outliers.
+ </span>
+ <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
+ (Lit r) between
+ this gene and all other genes is computed<br>
+ using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
+ Semantic Gene Organizer</a>
+ and human, rat, and mouse data from PubMed.
+ Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
+ <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
+ </span>
+ <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
+ (Tissue r)
+ estimates the similarity of expression of two genes
+ or transcripts across different cells, tissues, or organs
+ (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
+ Tissue correlations
+ are generated by analyzing expression in multiple samples usually taken from single cases.<br>
+ <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
+ computed for all pairs of genes using data from mouse samples.<br>
+ </span>
+ </div>
</div> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index dcec2b9e..60219cf5 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,6 +1,11 @@
<div>
+<<<<<<< HEAD
{% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
<div class="col-xs-4">
+=======
+ {% if dataset.group.mapping_names|length > 0 %}
+ <div class="col-xs-5">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<div class="tabbable"> <!-- Only required for left/right tabs -->
<ul class="nav nav-pills">
@@ -41,8 +46,13 @@
<div style="padding-top: 10px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
+=======
+ <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -52,32 +62,67 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
<div style="margin-left: 20px;" class="col-xs-3 controls">
+=======
+ <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label class="col-xs-4 control-label">Use LOCO</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
- <input type="radio" name="use_loco" value="True">
+ <input type="radio" name="use_loco" value="True" checked="">
Yes
</label>
<label class="radio-inline">
- <input type="radio" name="use_loco" value="False" checked="">
+ <input type="radio" name="use_loco" value="False">
No
</label>
</div>
</div>
</div>
<div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+<<<<<<< HEAD
<div class="mapping_method_fields form-group">
<button type="button" id="select_covariates" class="btn btn-default">
Select Covariates
</button>
<button type="button" id="remove_covariates" class="btn btn-default">
Remove Covariates
+=======
+ -->
+ <div class="mapping_method_fields form-group">
+ <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
+ <div style="margin-left:20px;" class="col-xs-7">
+ {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% elif g.cookie_session.display_num_collections() == "" %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+ <div style="margin-bottom: 10px;" class="btn-group" role="group">
+ <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+ <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+ </div>
+ <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+ {% endif %}
+ </div>
+ </div>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+ Compute
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</button>
</div>
</div>
@@ -94,8 +139,13 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
+=======
+ <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_reaper" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -105,20 +155,35 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="num_bootstrap" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -162,8 +227,13 @@
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
<input type="radio" name="manhattan_plot_reaper" value="True">
Yes
@@ -174,11 +244,20 @@
</label>
</div>
</div>
+<<<<<<< HEAD
<div class="form-group">
<div style="padding-left:15px;" class="controls">
<button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
+=======
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
<!--<div id="alert_placeholder"></div>-->
@@ -189,8 +268,13 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
+=======
+ <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_rqtl_geno" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -200,17 +284,28 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="num_perm_rqtl_geno" value="" type="text" class="form-control">
+=======
+ <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+ <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
+=======
+ <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -228,8 +323,13 @@
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label>
<div class="col-xs-4 controls">
+=======
+ <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select name="mapmethod_rqtl_geno" class="form-control">
<option value="em">em</option>
<option value="imp">imp</option>
@@ -243,8 +343,13 @@
</div>
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label>
<div class="col-xs-4 controls">
+=======
+ <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select name="mapmodel_rqtl_geno" class="form-control">
<option value="normal">normal</option>
<!--<option value="binary">binary</option>
@@ -269,8 +374,13 @@
</div>
-->
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
<div class="col-xs-12 controls">
+=======
+ <label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
<input type="radio" name="manhattan_plot_rqtl" value="True">
Yes
@@ -282,11 +392,20 @@
</div>
</div>
+<<<<<<< HEAD
<div class="form-group">
<div style="padding-left:15px;" class="controls">
<button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
+=======
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
</div>
@@ -295,8 +414,13 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
+=======
+ <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_pylmm" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -307,6 +431,7 @@
{% endif %}
<!--
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
@@ -343,6 +468,13 @@
<button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
+=======
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
</div>
@@ -354,8 +486,13 @@
<div style="padding-top: 10px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
+=======
+ <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -365,8 +502,13 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
<div style="margin-left: 20px;" class="col-xs-3 controls">
+=======
+ <label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
@@ -374,6 +516,7 @@
<div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
<div class="mapping_method_fields form-group">
+<<<<<<< HEAD
<button type="button" id="select_covariates" class="btn btn-default">
Select Covariates
</button>
@@ -385,6 +528,26 @@
<div class="form-group">
<div class="col-xs-4 controls">
+=======
+ <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
+ <div style="margin-left:20px;" class="col-xs-7">
+ {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% elif g.cookie_session.display_num_collections() == "" %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+ <div style="margin-bottom: 10px;" class="btn-group" role="group">
+ <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+ <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+ </div>
+ <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+ {% endif %}
+ </div>
+ </div>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+>>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
@@ -395,16 +558,16 @@
<div class="tab-pane" id="plink">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="maf_plink" value="0.01" type="text" class="form-control">
</div>
</div>
</div>
<div class="form-group">
- <label for="plink_compute" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
<button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
@@ -419,22 +582,26 @@
<div class="col-xs-6">
{% if dataset.group.mapping_id == "1" %}
<dl>
+ <dt>GEMMA</dt>
+ <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd>
<dt>Interval Mapping</dt>
<dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
- <dt>pyLMM</dt>
- <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
<dt>R/qtl</dt>
<dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+ <dt>pyLMM</dt>
+ <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
</dl>
{% else %}
<dl>
+ {% if mapping_method == "GEMMA" %}
<dt>GEMMA</dt>
<dd>
GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br>
- Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you receive an error, please wait a few minutes and try again.
</dd>
+ {% elif mapping_method == "PLINK" %}
<dt>PLINK</dt>
<dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
+ {% endif %}
</dl>
{% endif %}
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 4e81c29c..1c17840c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -582,7 +582,7 @@ def marker_regression_page():
'control_marker',
'control_marker_db',
'do_control',
- 'genofile',
+ 'genofile_string',
'pair_scan',
'startMb',
'endMb',