Add citation info and others

lidaof · Jun 24, 2019 · f8bfe1a · f8bfe1a
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diff --git a/docs/_static/upload1.png b/docs/_static/upload1.png
diff --git a/docs/contact.rst b/docs/contact.rst
@@ -18,6 +18,15 @@ Get help on social media
 You can also get help from social media:
 
 #. Google group: https://groups.google.com/forum/#!forum/epgg
-#. Google plus forum: https://goo.gl/ruXs2Y (Google is shutting down it, use github issues or google group)
 #. Facebook page: https://www.facebook.com/WashUEpiGenomeBrowser/
 #. Twitter: https://twitter.com/wuepgg
+#. Youtube Channel: https://www.youtube.com/channel/UCnGVWbxJv-DPDCAFDQ1oFQA
+
+Cite the browser
+----------------
+
+If you used the browser in your research, please help us by citing the following paper:
+
+* Daofeng Li, Silas Hsu, Deepak Purushotham, Renee L Sears, Ting Wang, WashU Epigenome Browser update 2019, Nucleic Acids Research, gkz348, https://doi.org/10.1093/nar/gkz348 [PMID: 31165883_].
+
+.. _31165883: https://www.ncbi.nlm.nih.gov/pubmed/31165883
diff --git a/docs/datahub.rst b/docs/datahub.rst
@@ -269,7 +269,7 @@ Example genomealign track
     }
 
 Example matplot track
---------------------
+---------------------
 
 .. code-block:: json
 
@@ -393,13 +393,13 @@ to build a *hierarchical structure*. ::
         "url": "https://egg.wustl.edu/d/hg19/GSM997242_1.bigWig", 
         "metadata": {
             "Sample": [
-                "Adult Cells/Tissues", 
+                "Adult Cells/Tissues",
                 "Blood", 
                 "Other blood cells", 
                 "CD4+_CD25-_Th_Primary_Cells"
-            ],    
+            ],
             "Donor": [
-                "Donor Identifier", 
+                "Donor Identifier",
                 "Donor_332"
             ],    
             "Assay": [
@@ -541,4 +541,10 @@ Default value is 0 (no smooth applied).
 maxRows
 ^^^^^^^
 
-``maxRows`` options controls the number of rows for the annotation track, like a geneAnnotation track.
+``maxRows`` options controls the number of rows for the annotation track, like a geneAnnotation track.
+
+hiddenPixels
+^^^^^^^^^^^^
+
+For annotation tracks, when an element spans less than `hiddenPixels` in the screen,
+this item will not be displayed. Default value is 0.5 pixel. Set to 0 will display all elements.
diff --git a/docs/faq.rst b/docs/faq.rst
@@ -21,8 +21,8 @@ Data fetch failed
 Please check the URL to your file is correct. If yes, most case, your webserver doesn't enable CORS.
 Please see :doc:`tracks` page for how to enable CORS settings.
 
-Use HTTP or HTTPS?
-------------------
+Use HTTP or HTTPS
+-----------------
 
 Both our main site and AWS mirror support both HTTP and HTTPS protocol, since webpage
 hosted through HTTPS cannot access resource hosted by HTTP, you should use our HTTP site.
@@ -41,3 +41,12 @@ a Firebase fetal error like following:
 
 This means you need to setup a Firebase database for the Session/Live function to work properly,
 check :ref:`Firebase_setup` please
+
+Local track security
+--------------------
+
+Local track function is perfect for view protected or private data, since there is no data transfer on the web. 
+More discussions about this please check here_.
+
+.. _here: https://github.com/lidaof/eg-react/issues/114
+
diff --git a/docs/local.rst b/docs/local.rst
@@ -2,24 +2,24 @@ Local track files
 =================
 
 We realize that not every research group has the ability to set up a web server with CORS enabled. As of version 48.0.0,
-we added the ability to read local track files or an entire folder as a datahub. This means the user can *upload* track files
-from their hard drive to the browser. The format for these track files is the same as those that are hosted on a webserver.
+we added the ability to read local track files or an entire folder as a datahub. This means the user can **view** track files
+from their hard drive to the browser. The format for these track files is same as those that are hosted on a webserver.
 
-.. note:: The tracks *uploaded* through the file upload feature *cannot* be saved to the browser's local
+.. note:: The tracks *viewed* through the local track feature *cannot* be saved to the browser's local
           storage. Thus, when you refresh the browser your local tracks will be gone. Tracks need to be
-          re-upload to re-grant the browser permission to read  local files.
+          re-selected or re-grant the browser permission to read local files.
           This is a security setup of Javascript. To avoid uploading multiple files repeatedly, the user can create
           a ``hub.config.json`` file to specify files as a local datahub. In this manner, after a refresh event the user
-          can just upload their local datahub again instead of uploading individual tracks separately.
+          can just choose their local datahub again instead of choosing individual tracks separately.
 
 .. important:: Since the user needs to give permission for the web browser to access
                files on a local hard drive, tracks from a local hard drive **cannot** be saved
                into ``Session``. Please consider using HTTP(S) hosted tracks to work with the session function.
 
-Upload files as tracks
-----------------------
+View local files as tracks
+--------------------------
 
-To use your local files, make sure to format your files correctly. First, open the ``Upload Track``
+To use your local files, make sure to format your files correctly. First, open the ``View Local Tracks``
 menu from ``Tracks``:
 
 .. image:: _static/upload1.png
@@ -28,9 +28,9 @@ By default, you will be on the ``Add Local Track`` tab. Second, choose your trac
 
 .. image:: _static/upload2.png
 
-Third, choose your files. You can choose many files of same type if the track upload type only requires one
-file (``bigWig``, ``bigBed``, ``HiC``, and ``bigInteract``) or if the track upload type requires a data
-file and **index** file (``bedGraph``, ``methylC``, etc.) then you need to upload each pair individually.
+Third, choose your files. You can choose many files of same type if the track type only requires one
+file (``bigWig``, ``bigBed``, ``HiC``, and ``bigInteract``) or if the track type requires a data
+file and **index** file (``bedGraph``, ``methylC``, etc.) then you need to choose *each pair* individually.
 
 .. image:: _static/upload3.png
 
@@ -50,7 +50,7 @@ The bedGraph track is added to the browser view:
 
 .. image:: _static/upload7.png
 
-Upload files or a folder as a datahub
+View files or a folder as a datahub
 -------------------------------------
 
 If you want to upload many different types of track files to the browser, you can do that too!
@@ -87,7 +87,7 @@ Create a file called ``hub.config.json`` for the browser to configure your local
 
 .. note:: Please note the ``name`` and ``options`` attribute specified in this file. The syntax is the same as a remote datahub file.
 
-.. note:: Track files not specified in ``hub.config.json`` will be skipped.
+.. note:: Track files not specified in ``hub.config.json`` will be skipped. Orders of tracks will follow the order defined in ``hub.config.json`` file.
 
 You can either choose an entire folder by clicking the first button: