Merge branch 'master' of github.com:lidaof/eg-docs

lidaof · Sep 15, 2020 · c4d6fcf · c4d6fcf
2 parents 30ad9b5 + 0399d81
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,4 +1,4 @@
 {
     "restructuredtext.confPath": "${workspaceFolder}/docs",
-    "python.pythonPath": "/Users/dli/anaconda3/bin/python"
+    "python.pythonPath": "/Users/d/opt/anaconda3/bin/python"
 }
diff --git a/docs/_static/bed_label.png b/docs/_static/bed_label.png
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diff --git a/docs/_static/image_track_example.png b/docs/_static/image_track_example.png
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diff --git a/docs/datahub.rst b/docs/datahub.rst
@@ -268,14 +268,14 @@ Example genomealign track
         }
     }
 
-Example callingcard track
+Example qBED track
 -------------------------
 
 .. code-block:: json
 
     {
-        "type":"callingcard",
-        "url":"https://htcf.wustl.edu/files/RdNgrGeQ/HCT116-PBase.ccf.gz",
+        "type":"qbed",
+        "url":"https://htcf.wustl.edu/files/RdNgrGeQ/HCT116-PBase.qbed.gz",
         "name":"piggyBac insertions",
         "showOnHubLoad":"true",
         "options":{
@@ -289,9 +289,9 @@ Example callingcard track
           },
     }
 
-.. note:: Default callingcard track options are ``"logScale":"none"``, ``"show":"all"``, ``"markersize":3``, and ``"opacity":[100]``.
+.. note:: Default qBED track options are ``"logScale":"none"``, ``"show":"all"``, ``"markersize":3``, and ``"opacity":[100]``.
           Log-scaling can be set by specifying ``"logScale":"log10"``. To change opacity, pass a single value in brackets, as in the above example.
-          Calling card tracks will, by default, plot all entries in view. For information-dense regions, this can lead to excessive memory consumption.
+          qBED tracks will, by default, plot all entries in view. For information-dense regions, this can lead to excessive memory consumption.
           To plot a random subsample instead, specify ``"show":"sample"`` and pass the number of points to visualize to ``"sampleSize"``, e.g.
           ``"sampleSize":1000``
 
@@ -376,7 +376,7 @@ type
 * genomealign
 * longrange
 * bigInteract
-* callingcard
+* qBED
 * matplot
 * snp
 * ruler
@@ -561,17 +561,24 @@ displayMode
    * - geneAnnotation
      - *full*, *density*
    * - HiC
-     - *arc*, *heatmap*, *flatarc*
+     - *arc*, *heatmap*, *flatarc*, *square*
    * - genomealign
      - *rough*, *fine*
 
 flatarc mode
 """"""""""""
 
-``flatarc`` mode is like ``arc`` mode, sometimes the curve would be displayed flatter, in fact it's a cubic curve.
+For interaction track. ``flatarc`` mode is like ``arc`` mode, sometimes the curve would be displayed flatter, in fact it's a cubic curve.
 
 .. image:: _static/flatarc.png
 
+square mode
+"""""""""""
+
+For interaction track. ``square`` mode gives JuiceBox style like view for HiC maps.
+
+.. image:: _static/square.png
+
 aggregateMethod
 ^^^^^^^^^^^^^^^
 
@@ -617,3 +624,33 @@ maxMethyl
 ^^^^^^^^^
 
 For methylC tracks specify the y-axis max (for both strands) using ``maxMethyl``. Options range from (0-1].
+
+zoomLevel
+^^^^^^^^^
+
+For ``bigWig`` track only. ``bigWig`` files usually contain multiple resolutions, when viewing a large region,
+the Browser usually fetches a lower resolution for faster response, user can change this behaviour by changing this option.
+
+The example below first show viewing a bigWig track in a big region with ``AUTO`` zoom level, you can see the data is pretty flat,
+when we change zoom level to 0, 1, etc, we can see more details from the data, but takes more time to load.
+
+Automatical zoom level:
+
+.. image:: _static/bw_zoom1.png
+
+Right click, change zoom level to 0: (can also setup in data hub under ``options``)
+
+.. image:: _static/bw_zoom2.png
+
+View changed after change zoom level to 0:
+
+.. image:: _static/bw_zoom3.png
+
+alwaysDrawLabel
+^^^^^^^^^^^^^^^
+
+For ``bed`` and ``categorical`` tracks only. Usually for each ``bed`` and ``categorical` item in those tracks,
+the label are only drawn only when there are enough space inside the item block, by specificy this option to `true`,
+the label will always be drawn in the screen.
+
+.. image:: _static/bed_label.png