Adding small figures per trait, so that users can see CTL and QTL for each individual phenotype

2 files changed, 39 insertions, 11 deletions

diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 77e34143..45bc4c6e 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -69,9 +69,10 @@ class CTL(object):
         self.r_CTLscan            = ro.r["CTLscan"]                        # Map the CTLscan function
         self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
         self.r_lineplot           = ro.r["ctl.lineplot"]                   # Map the ctl.lineplot function
+        self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
         self.r_CTLnetwork         = ro.r["CTLnetwork"]                     # Map the CTLnetwork function
         self.r_CTLprofiles        = ro.r["CTLprofiles"]                    # Map the CTLprofiles function
-        self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
+        self.r_plotCTLobject      = ro.r["plot.CTLobject"]                 # Map the CTLsignificant function
         print("Obtained pointers to CTL functions")
 
     def run_analysis(self, requestform):
@@ -144,26 +145,44 @@ class CTL(object):
 
         # 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['imgurl1'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png"
+        self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1']
+
         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)
+        r_png(self.results['imgloc1'], width=1000, height=600)
         self.r_lineplot(res, significance = significance)
         r_dev_off()
 
+        n = 2
+        for trait in self.trait_db_list:
+          # Create the QTL like CTL plots
+          self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png"
+          self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)]
+          r_png(self.results['imgloc' + str(n)], width=1000, height=600)
+          self.r_plotCTLobject(res, (n-1), significance = significance, main='Phenotype ' + trait)
+          r_dev_off()
+          n = n + 1
+
         # Flush any output from R
         sys.stdout.flush()
 
-    def render_image(self, results):
-        print("pre-loading imgage results:", self.results['imgloc'])
-        imgfile = open(self.results['imgloc'], 'rb')
+    def loadImage(self, path, name):
+        print("pre-loading imgage results:", self.results[path])
+        imgfile = open(self.results[path], 'rb')
         imgdata = imgfile.read()
         imgB64 = imgdata.encode("base64")
         bytesarray = array.array('B', imgB64)
-        self.results['imgdata'] = bytesarray
+        self.results[name] = bytesarray
+
+    def render_image(self, results):
+        self.loadImage("imgloc1", "imgdata1")
+        n = 2
+        for trait in self.trait_db_list:
+          self.loadImage("imgloc" + str(n), "imgdata" + str(n))
+          n = n + 1
 
     def process_results(self, results):
         print("Processing CTL output")
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 914c1d43..a5cb1c08 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -5,13 +5,22 @@
 <div class="container">
   <h1>CTL Results</h1>
   {{(request.form['trait_list'].split(',')|length -1)}} phenotypes as input<br>
-  <h3>Figure</h3>
-  <a href="/tmp/{{ results['imgurl'] }}">
+  <h3>Network Figure</h3>
+  <a href="/tmp/{{ results['imgurl1'] }}">
       <img alt="Embedded Image" src="data:image/png;base64,
-      {% for elem in results['imgdata'] -%}
+      {% for elem in results['imgdata1'] -%}
       {% print("%c"|format(elem)) %}
       {%- endfor %}
       " /></a>
+  <h3>CTL/QTL Plots for individual traits</h3>
+  {% for r in range(2, (request.form['trait_list'].split(',')|length +1)) %}
+  <a href="/tmp/{{ results['imgurl' + r|string] }}">
+      <img width=100 height=100 alt="Embedded Image" src="data:image/png;base64,
+      {% for elem in results['imgdata' + r|string] -%}
+      {% print("%c"|format(elem)) %}
+      {%- endfor %}
+      " /></a>
+  {% endfor %}
   <h3>Tabular results</h3>
   <table width="80%">
   <tr><th>trait</th><th>marker</th><th>trait</th><th>LOD</th><th>dCor</th></tr>