add region set view

lidaof · Oct 17, 2018 · 6fa696c · 6fa696c
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diff --git a/docs/_static/eg.png b/docs/_static/eg.png
diff --git a/docs/_static/region_edit.png b/docs/_static/region_edit.png
diff --git a/docs/_static/region_enter.png b/docs/_static/region_enter.png
diff --git a/docs/_static/region_entered.png b/docs/_static/region_entered.png
diff --git a/docs/_static/region_set.png b/docs/_static/region_set.png
diff --git a/docs/_static/region_ui.png b/docs/_static/region_ui.png
diff --git a/docs/_static/region_view.png b/docs/_static/region_view.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,6 +6,10 @@
 WashU Epigenome Browser
 =======================
 
+.. figure:: _static/eg.png
+
+            The gateway to epigenomes. (Art by **Ting Wang**)
+
 .. toctree::
     :maxdepth: 2
     :caption: Contents:

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -150,6 +150,38 @@ can easily show you the interaction between two genomic loci and methylation sta
 Apps
 ----
 
+Region set view
+~~~~~~~~~~~~~~~
+
+Users can submit a list of regions or genes to the browser, by choose ``Apps`` -> ``Region set view``:
+
+.. image:: _static/region_set.png
+
+The brings up the region set user interface, here you can enter a list of gene names or coordinates 
+to make a gene set one item per line. 
+Gene names and coordinates can be mixed for input. 
+Coordinate string must be in the form of "chr1:345-678" fields can be joined by space/tab/comma/colon/hyphen.
+
+.. image:: _static/region_ui.png
+
+After Click the *Add* button, will bring you to the region set editting interface, you can either add region one
+by one, or delete regions from the table, and set the flanking region strategy:
+
+.. image:: _static/region_edit.png
+
+Once you done with edit the set, cick the button *Add set*.
+Now you have the option to enter regin set view, click the button *Enter region set view*:
+
+.. image:: _static/region_enter.png
+
+This indicates you are in *region set view* mode and which set you are viewing:
+
+.. image:: _static/region_entered.png
+
+Go back to the browser, you can your browser view is ordered by your region set:
+
+.. image:: _static/region_view.png
+
 Session
 ~~~~~~~