From 1053764068a50e2b95e0f0b07cb4111369ce8ff8 Mon Sep 17 00:00:00 2001
From: DannyArends
Date: Thu, 24 Mar 2016 22:08:44 +0100
Subject: Adding parameters, and passing them to the CTL algorithm

---
 wqflask/wqflask/ctl/ctl_analysis.py      | 26 +++++++++++++-----
 wqflask/wqflask/templates/ctl_setup.html | 46 ++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 7 deletions(-)

diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 44bade5c..77e34143 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -79,6 +79,18 @@ class CTL(object):
         self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
         self.trait_db_list = [x for x in self.trait_db_list if x]
 
+        print("strategy:", requestform.get("strategy"))
+        strategy = requestform.get("strategy")
+
+        print("nperm:", requestform.get("nperm"))
+        nperm = int(requestform.get("nperm"))
+
+        print("parametric:", requestform.get("parametric"))
+        parametric = bool(requestform.get("parametric"))
+
+        print("significance:", requestform.get("significance"))
+        significance = float(requestform.get("significance"))
+
         # Get the name of the .geno file belonging to the first phenotype
         datasetname = self.trait_db_list[0].split(":")[1]
         dataset = data_set.create_dataset(datasetname)
@@ -120,26 +132,26 @@ class CTL(object):
         rPheno = r_data_frame(rPheno)
         rGeno = r_data_frame(rGeno)
 
-        r_write_table(rGeno, "~/outputGN/geno.csv")
-        r_write_table(rPheno, "~/outputGN/pheno.csv")
+        # Debug: Print the genotype and phenotype files to disk
+        #r_write_table(rGeno, "~/outputGN/geno.csv")
+        #r_write_table(rPheno, "~/outputGN/pheno.csv")
 
         # Perform the CTL scan
-        res = self.r_CTLscan(rGeno, rPheno, ncores = 6)
+        res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, ncores = 6)
 
         # Get significant interactions
-        significant = self.r_CTLsignificant(res)
-
-        print(significant[0])
+        significant = self.r_CTLsignificant(res, significance = significance)
 
         # Create an image for output
         self.results = {}
         self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png"
         self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl']
         self.results['ctlresult'] = significant
+        self.results['requestform'] = requestform             # Store the user specified parameters for the output page
 
         # Create the lineplot
         r_png(self.results['imgloc'], width=1000, height=600)
-          self.r_lineplot(res)
+        self.r_lineplot(res, significance = significance)
         r_dev_off()
 
         # Flush any output from R
diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
index 0ba281c6..9c0d7bea 100644
--- a/wqflask/wqflask/templates/ctl_setup.html
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -8,11 +8,57 @@
 
 <form action="/ctl_results" method="post" class="form-horizontal">
 	<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+
+	<div class="dropdown">
+		<label for="Strategy">Strategy</label>
+		<div class="col-sm-10">
+		<select  name="strategy" id="strategy">
+			<option value="Exact">Exact</option>
+			<option value="Full">Full</option>
+			<option value="Pairwise">Pairwise</option>
+		</select>
+		</div>
+	</div>
+
+	<div class="dropdown">
+		<label for="Permutations">Number of permutation (Used when strategy is Full or Pairwise)</label>
+		<div class="col-sm-10">
+		<select  name="nperm" id="nperm">
+			<option value="100">100</option>
+			<option value="1000" selected="selected">1000</option>
+			<option value="10000">10000</option>
+		</select>
+		</div>
+	</div>
+
+	<div class="dropdown">
+		<label for="Coefficient">Type of correlation coefficient</label>
+		<div class="col-sm-10">
+		<select  name="parametric" id="parametric">
+			<option value="False">Spearman</option>
+			<option value="True">Pearson</option>
+		</select>
+		</div>
+	</div>
+
+
+	<div class="dropdown">
+		<label for="Significance">Significance level</label>
+		<div class="col-sm-10">
+		<select  name="significance" id="significance">
+			<option value="0.1">0.1</option>
+			<option value="0.05" selected="selected">0.05</option>
+			<option value="0.001">0.001</option>
+		</select>
+		</div>
+	</div>
+  <br>
 	<div class="form-group">
 		<div class="col-sm-10">
 			<input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
 		</div>
 	</div>
+
 </form>
 
 </div>
-- 
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