fix pablo.js doesn't support names with dash unless in quotes

conekt/templates/admin/add/expression_profiles.html

@@ -57,25 +57,25 @@ <h1>Add Expression Profile</h1>
                 as it occurs in the matrix (omit the suffix '.htseq'), the second column indicates the condition sampled.
                 <br /><br />
                 <div class="well">
-                    SampleID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ConditionDescription
-                    SRR068956&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068957&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068958&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068959&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068971&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068975&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068976&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068977&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
-                    SRR068987&nbsp;&nbsp;&nbsp;&nbsp;Endosperm
+                    SampleID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ConditionDescription<br />
+                    SRR068956&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068957&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068958&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068959&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068971&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068975&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068976&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068977&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
+                    SRR068987&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                     ...
                 </div>
                 Furthermore a file to color code tissues can be provided. Here for each condition a color (that will be
                 used in profile plots needs to be specified. Note that the order in this fill will be the order in
                 profile plots! Colors need to be in rgba(0-255,0-255,0-255,0-1) format.
                 <br /><br />
                 <div class="well">
-                    Roots (apex), 7 DAG&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)
-                    Roots (differentation zone), 4 DAP&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)
+                    Roots (apex), 7 DAG&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)<br />
+                    Roots (differentation zone), 4 DAP&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)<br />
                     ...
                 </div>
             </div>

docs/building/003_expression_profiles.md

@@ -59,11 +59,31 @@ data and add everything to the database.
 
 ![Add expression profiles](../images/add_expression_profiles.png)
 
-## Adding summarized profiles
 
-In case the complete profile is to detailed and more general profiles need to be included 
-(useful for specificity searches), there is the option to combine multiple condition in one.
+## Calculating expression specificity and summerized profiles
 
-## Calculating expression specificity
+To enable Specificity searches, SPM values need to be pre-calculated. From the admin menu 
+select 'Add' -> 'Expression specificty'.
 
-*UNDER CONSTRUCTION*
+![Add expression specificity](../images/add_expression_specificty.png)
+
+Here you have two options available. The first one will calculate SPM values for all conditions
+in the profiles. Here you simply need to **select the species**, **enter a description** and click 
+**"Add Expression Specificities"**.
+
+In case different conditions need to be grouped, the second option should be used. Here you 
+**select the species** and **enter a description** similarly to the previous. Additionally a
+tab-delimited text file is required grouping conditions into broader categories. 
+
+```
+Roots (apex), 7 DAG Roots   rgba(153, 51, 0, 0.5)
+Roots (differentation zone), 4 DAP  Roots   rgba(153, 51, 0, 0.5)
+Roots (elongation zone), 4 DAP  Roots   rgba(153, 51, 0, 0.5)
+Roots (meristematic zone), 4 DAP    Roots   rgba(153, 51, 0, 0.5)
+Roots (QC cells), 6 DAS Roots   rgba(153, 51, 0, 0.5)
+...
+```
+
+Three columns are required, (i) the label in the full profile, (ii) the group it belongs to 
+and (iii) the color for that group. After adding that file click **"Add Expression Specificities"**
+in that section.