More on usage

lidaof · Sep 30, 2018 · 5c7c753 · 5c7c753
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,3 +1,3 @@
 {
-    "restructuredtext.confPath": "/Users/dli/eg-docs/docs"
+    "restructuredtext.confPath": "c:\\Users\\D\\web\\eg-docs\\docs"
 }
diff --git a/docs/_static/coord_search.png b/docs/_static/coord_search.png
diff --git a/docs/_static/gene_search1.png b/docs/_static/gene_search1.png
diff --git a/docs/_static/gene_search2.png b/docs/_static/gene_search2.png
diff --git a/docs/_static/history_tool.png b/docs/_static/history_tool.png
diff --git a/docs/_static/move_tool.png b/docs/_static/move_tool.png
diff --git a/docs/_static/region_jump.png b/docs/_static/region_jump.png
diff --git a/docs/_static/reorder_tool.png b/docs/_static/reorder_tool.png
diff --git a/docs/_static/say_gene.png b/docs/_static/say_gene.png
diff --git a/docs/_static/tools.png b/docs/_static/tools.png
diff --git a/docs/_static/topnav.png b/docs/_static/topnav.png
diff --git a/docs/_static/view_history.png b/docs/_static/view_history.png
diff --git a/docs/_static/zoom_tool.png b/docs/_static/zoom_tool.png
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,8 +20,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'WashU Epigenome Browser'
-copyright = '2018, Daofeng Li, Silas Hsu, Deepak Purushotham and Ting Wang'
-author = 'Daofeng Li, Silas Hsu, Deepak Purushotham and Ting Wang'
+copyright = '2018, Daofeng Li, Renee Sears and Ting Wang'
+author = 'Daofeng Li, Renee Sears and Ting Wang'
 
 # The short X.Y version
 version = ''
@@ -134,7 +134,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'WashUEpigenomeBrowser.tex', 'WashU Epigenome Browser Documentation',
-     'Daofeng Li, Silas Hsu, Deepak Purushotham and Ting Wang', 'manual'),
+     'Daofeng Li, Renee Sears and Ting Wang', 'manual'),
 ]
 
 

diff --git a/docs/tracks.rst b/docs/tracks.rst
@@ -21,7 +21,9 @@ we can use generic Linux ``sort`` command or the ``bedSort`` tool from UCSC. The
 do the same thing.
 
     sort -k1,1 -k2,2n track.bedgraph > track.bedgraph.sorted
+
 or
+
     bedSort track.bedgraph track.bedgraph.sorted
 
 then compressed and index using tabix:
@@ -35,7 +37,7 @@ The two files must be in the same directory. Obtain the URL to "track.bedgraph.s
 .. _`compressed by bgzip and indexed by tabix`: http://www.htslib.org/doc/tabix.html
 
 Configure your webserver to enable CORS
--------------------------------------
+---------------------------------------
 
 Quoted from MDN_:
 

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -1,32 +1,94 @@
 Use the Browser
 ===============
 
+The Top Menu
+------------
+
+The image below shows the top navigation menu of the browser, the top navigation menu
+controls most of the browser functionality. From left to right are the browser logo with
+version information, the species and assembly information, genomic region locator, a set of
+zoom in/out tools, Tracks munu, Apps menu, Settings munu and Documentaion link.
+
+.. image:: _static/topnav.png
+
 Navigator to genomic regions
 ----------------------------
 
+Click the genomic region locator from top navigation menu, which will popup a window for you
+to type a region:
+
+.. image:: _static/region_jump.png
+
 Jump to a Gene
 ~~~~~~~~~~~~~~
 
+You can type a gene name/symbol, like ``Hox``, when the input content reaches 3 characters, 
+the browser will try to find gene symbols start with what you typed:
+
+.. image:: _static/gene_search1.png
+
+if there are hits,
+a dropdown menu will popup with isoforms from where you can click, and the browser will then
+navigator you to the isoform you chosen.
+
+.. image:: _static/gene_search2.png
+
 Voice input gene symbol
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-.. note:: The feature is dependent on web browser support, web browser without support for
+From this set of buttons, |saygene| , click **Say a Gene** button, your web browser
+will ask you for permission to access your microphone devices, choose *Allow*, then the browser will
+start to listen when you are saying, you can start say letters one by one, like H, O, X, if you click
+the red **stop** button, what you said HOX will be put inside of the gene search box and suggested gene symbols
+should also be popup, you can then choose the symbols and isoforms you want.
+
+.. |saygene| image:: _static/say_gene.png
+
+.. note:: This feature is dependent on web browser support, web browser without support for
           speech recognition won't see this UI.
 
 Jump to a specific region
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
+Below the gene search box, you can also type in genomic coordinates, formats like
+``chr6:52258852-52260880`` or ``chr6 52258852 52260880`` can be accepted (it doesn't matter
+how many space you have or you are using tabs or not).
+
+.. image:: _static/coord_search.png
+
 Operations in tracks view container
 -----------------------------------
 
-Move/Zoom/Re-order tool
+Right above the tracks container, there are bunch of tools for operating the tracks, they are
+move, re-order, zoom, undo, redo and history tools.
+
+.. image:: _static/tools.png
+
+Move/Re-order/Zoom tool
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-Default tool is `Move`.
+|movetool| is the default tools selected by the browser. This tools make the browser in ``moving``
+mode, when user drag the mouse, the tracks will move along with the dragging. |reordertool| allow
+tracks to be re-ordered, user can drag one drag up and down to change the order of tracks. |zoomtool|
+allows use to zoom in a specific region use the mouse, when use drag a region and release the mouse,
+the browser will zoom into that specific region dragged.
+
+.. |movetool| image:: _static/move_tool.png
+.. |reordertool| image:: _static/reorder_tool.png
+.. |zoomtool| image:: _static/zoom_tool.png
 
 Undo/Redo/History tool
 ~~~~~~~~~~~~~~~~~~~~~~
 
+|historytool| contains ``Undo``, ``Redo`` and ``History`` tools, say if you accidently moved
+the region you are focusing, you can click ``Undo`` button to go back, and click ``Redo`` allows
+you go forward to the step after you clicked ``Undo``, the ``History`` button gives you recent 10
+operations and you can jump to, or clear the whole history.
+
+.. |historytool| image:: _static/history_tool.png
+
+.. image:: _static/view_history.png
+
 Settings
 --------