Merge pull request #4 from EvoAlias/master

Added to Usage Doc

docs/usage.rst

@@ -149,24 +149,27 @@ can easily show you the interaction between two genomic loci and methylation sta
 
 .. image:: _static/vr2.png
 
+Apps
+----
+
 Session
--------
+~~~~~~~
 
 Choosing ``Session`` from the ``Apps`` menu will bring you to the session interface
 shown below:
 
 .. image:: _static/session.png
 
 Save session
-~~~~~~~~~~~~
+^^^^^^^^^^^^
 
 Click the **Save session** button to save a session. A session
 bundle Id will be created which allows the user to retrieve their session at a later date.
 
 .. image:: _static/save_session.png
 
 Retrieve session
-~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^
 
 The **session bundle Id** can be used later to retrieve a session by pasting the session
 bundle id in the session interface and clicking the ``Retrieve session`` button.
@@ -182,7 +185,7 @@ Click the green *Restore* button and your session will be restored:
 .. image:: _static/session_restored.png
 
 Live browsing
--------------
+~~~~~~~~~~~~~
 
 From the ``Apps`` menu choose **Go Live**, the browser will navigate you to a new
 link which you can share with someone else, like your collaborator, your PI,
@@ -191,7 +194,7 @@ or your friends. Whatever operations are done by you are mirrored on the display
 .. image:: _static/live.png
 
 Screenshot
-----------
+~~~~~~~~~~
 
 Users can create publication quality images using the *Screenshot*  tool from the ``Apps`` menu.
 Click the *Screenshot* button and a new window will po pup that re-renders all your
@@ -259,3 +262,28 @@ The tracks within the custom hub can then be added from the generated facet tabl
 You can also load a local data hub file in JSON format from your computer using the *file upload* interface, right below the *URL submit* hub interface.
 
 Also see the :doc:`tracks` and :doc:`datahub` sections for how to prepare your tracks and datahub files.
+
+Track Customization
+-------------------
+
+Tracks can be customized in a multitude of manners. 
+
+Track Color
+~~~~~~~~~~~
+
+Right clicking on ``annotation`` and ``numerical`` tracks will display ``Primary Color``, ``Secondary Color``, and ``Background Color`` which can all be customized using the color picker. For ``methylC`` tracks and ``categorical`` tracks the ``Color`` and ``Background`` of each class of elements (e.g. CG, CHG, and CHH) can be personalized. Additionally, for ``methylC``tracks the ``Read depth line color`` can be customized. 
+
+Track Height
+~~~~~~~~~~~~
+
+For each track the height can be customized by right clicking on the track and typing in a number to the panel. At 20 pixels and below for ``numerical`` tracks the track will display as a heatmap. 
+
+Track Display Mode
+~~~~~~~~~~~~~~~~~~
+
+For each ``numerical``, ``annotation``, or ``BAM`` track the display can be changed to ``DENSITY`` or ``FULL`` mode by right clicking on the track. 
+
+Track Y-axis Scale
+~~~~~~~~~~~~~~~~~~
+
+For each ``numerical`` track the y-axis can be displayed in ``AUTO`` or ``FIXED`` mode by right clicking on the track. The ``AUTO`` mode will scale the axis based on numerical values in the immediate area of the view range. The ``FIXED`` mode allows the user to select ``a Y-Axis min`` or ``Y-axis max``. For values above the set max the ``Primary color above max`` can be set for easy viewing. For values below the set minimum the ``Primary color below min`` can bet set.