Matplot

docs/datahub.rst

@@ -220,7 +220,7 @@ Example refbed track
 
 .. note:: ``categoryColors`` designates colors for the gene type as indicated in the 9th column. The default scheme is shown above for
           the five classes created by the ``Converting_Gencode_or_Ensembl_GTF_to_refBed.bash`` script, but any number of categories can
-          be defined.  
+          be defined.
 
 Example HiC track
 -----------------
@@ -268,6 +268,45 @@ Example genomealign track
         }
     }
 
+Example matplot track
+--------------------
+
+.. code-block:: json
+
+    {
+        "type": "matplot",
+        "name": "matplot wrap",
+        "tracks": [
+            {
+            "type": "bigwig",
+            "url": "https://vizhub.wustl.edu/public/tmp/TW463_20-5-bonemarrow_MeDIP.bigWig",
+            "name": "MeDIP",
+            "options": {
+                "color": "red",
+                "backgroundColor":"#FFE7AB"
+                },
+            "metadata": {
+                "sample": "bone",
+                "assay": "MeDIP"
+                }
+            },
+            {
+            "type": "bigwig",
+            "url": "https://vizhub.wustl.edu/public/tmp/TW551_20-5-bonemarrow_MRE.CpG.bigWig",
+            "name": "MRE",
+            "options": {
+                "color": "blue",
+                "backgroundColor":"#C0E3CC"
+                },
+            "metadata": {
+                "sample": "bone",
+                "assay": "MRE"
+                }
+            }
+        ]
+    }
+
+
 Example Ruler track
 --------------------
 
@@ -299,6 +338,9 @@ type
 * genomealign
 * longrange
 * bigInteract
+* callingcard
+* matplot
+* snp
 * ruler
 
 .. note:: ``type`` is case insensitive.
@@ -445,7 +487,7 @@ yMin
 colorAboveMax
 ^^^^^^^^^^^^^
 
-``colorAboveMax`` defines the color displayed when a *fixed* yScale_ is used and a value exceeds the 
+``colorAboveMax`` defines the color displayed when a *fixed* yScale_ is used and a value exceeds the
 yMax_ defined.
 
 color2BelowMin
@@ -483,3 +525,10 @@ At high zoom-out level when 1 on-screen pixel spans >1bp, the underlying track d
 summarized into a single value for browser display.
 ``aggregateMethod`` is used to control how the data is summarized. Supported values include:
 ``MEAN``, ``SUM``, ``COUNT``, ``MAX``, ``MIN``. Default value is ``MEAN``.
+
+smooth
+^^^^^^
+
+``smooth`` option allows you to smooth the graph of a quantitative track using window mean values.
+The browser will use the mean values from region [current_position - smooth, current_position + smooth].
+Default value is 0 (no smooth applied).

docs/tracks.rst

@@ -428,3 +428,19 @@ Place your sorted text file in the public folder. Since genomic data is often la
     bgzip example_sorted.ccf
     tabix -p bed example_sorted.ccf.gz
 
+Matplot track
+-------------
+
+A matplot (also called a line plot) displays multiple numerical tracks on the same X and Y axes to easily compare datasets. Data is plotted as curves instead of bar plots.
+
+To use matplot, choose more than 1 numerical tracks:
+
+.. image:: _static/mat1.png
+
+Right click, and choose *Apply matplot* button, The new matplot track will be shown:
+
+.. image:: _static/mat2.png
+
+and it also supports many configurations:
+
+.. image:: _static/mat3.png

docs/usage.rst

@@ -182,9 +182,9 @@ Users can submit a list of regions or genes to the browser, by choose ``Apps`` -
 
 .. 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. 
+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