diff --git a/conekt/templates/admin/add/expression_profiles.html b/conekt/templates/admin/add/expression_profiles.html index 7bb24d4..b8c6de9 100644 --- a/conekt/templates/admin/add/expression_profiles.html +++ b/conekt/templates/admin/add/expression_profiles.html @@ -57,16 +57,16 @@

Add Expression Profile

as it occurs in the matrix (omit the suffix '.htseq'), the second column indicates the condition sampled.

- SampleID     ConditionDescription - SRR068956    Endosperm - SRR068957    Endosperm - SRR068958    Endosperm - SRR068959    Endosperm - SRR068971    Endosperm - SRR068975    Endosperm - SRR068976    Endosperm - SRR068977    Endosperm - SRR068987    Endosperm + SampleID     ConditionDescription
+ SRR068956    Endosperm
+ SRR068957    Endosperm
+ SRR068958    Endosperm
+ SRR068959    Endosperm
+ SRR068971    Endosperm
+ SRR068975    Endosperm
+ SRR068976    Endosperm
+ SRR068977    Endosperm
+ SRR068987    Endosperm
...
Furthermore a file to color code tissues can be provided. Here for each condition a color (that will be @@ -74,8 +74,8 @@

Add Expression Profile

profile plots! Colors need to be in rgba(0-255,0-255,0-255,0-1) format.

- Roots (apex), 7 DAG    rgba(153, 51, 0, 0.5) - Roots (differentation zone), 4 DAP    rgba(153, 51, 0, 0.5) + Roots (apex), 7 DAG    rgba(153, 51, 0, 0.5)
+ Roots (differentation zone), 4 DAP    rgba(153, 51, 0, 0.5)
...
diff --git a/docs/building/003_expression_profiles.md b/docs/building/003_expression_profiles.md index b544081..b88079b 100644 --- a/docs/building/003_expression_profiles.md +++ b/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* \ No newline at end of file +![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. \ No newline at end of file