text track

lidaof · Nov 21, 2019 · 2a1daab · 2a1daab
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diff --git a/docs/_static/bedgraph_text_1.png b/docs/_static/bedgraph_text_1.png
diff --git a/docs/_static/bedgraph_text_2.png b/docs/_static/bedgraph_text_2.png
diff --git a/docs/_static/bedgraph_text_3.png b/docs/_static/bedgraph_text_3.png
diff --git a/docs/_static/bedtext_1.png b/docs/_static/bedtext_1.png
diff --git a/docs/_static/bedtext_2.png b/docs/_static/bedtext_2.png
diff --git a/docs/_static/bedtext_3.png b/docs/_static/bedtext_3.png
diff --git a/docs/_static/text_menu.png b/docs/_static/text_menu.png
diff --git a/docs/_static/worker_check.png b/docs/_static/worker_check.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -19,6 +19,7 @@ WashU Epigenome Browser
     datahub
     url
     local
+    text
     installation
     add
     faq

diff --git a/docs/text.rst b/docs/text.rst
@@ -0,0 +1,77 @@
+Text Tracks
+===========
+
+Tracks are usually prepared in binary format for efficient region access, like `bigWig`, `bigBed`, `HiC` and etc.
+Text file format is very flexible, thus caused some trouble for us to standardize the data input.
+While there are some circumstances that text track files could also be useful, it can be very convenient to just upload a text
+file and visualize the data on the browser without formatting the data to a binary format. Also we have received requests that
+adding text files as tracks from our users.
+
+bed
+---
+
+The most common text file would in `bed` format, like this one below::
+
+    chr1	13041	13106	reg1	1	+
+    chr1	753329	753698	reg2	2	+
+    chr1	753809	753866	reg3	3	+
+    chr1	754018	754252	reg4	4	+
+    chr1	754361	754414	reg5	5	+
+    chr1	754431	754492	reg6	6	+
+    chr1	755462	755550	reg7	7	+
+    chr1	761040	761094	reg8	8	+
+    chr1	787470	787560	reg9	9	+
+    chr1	791123	791197	reg10	10	+
+
+Say if we have a text file named ``bed-text.txt`` with the content above. Open the ``Text Tracks`` menu:
+
+.. image:: _static/text_menu.png
+
+This will bring the text track UI:
+
+.. image:: _static/bedtext_1.png
+
+Choose `bed` as the text file type, the choose our text file:
+
+.. image:: _static/bedtext_2.png
+
+After we submit this file, the track is added with the content of our text file:
+
+.. image:: _static/bedtext_3.png
+
+bedGraph
+--------
+
+``bedGraph`` is also very common, it's typically 4 columns bed file like below::
+
+    chr6	52155366	52155379	14
+    chr6	52155379	52155408	13
+    chr6	52155408	52155426	12
+    chr6	52155426	52155433	11
+    chr6	52155433	52155442	10
+    chr6	52155442	52155446	9
+    chr6	52155446	52155472	8
+    chr6	52155472	52155475	9
+    chr6	52155475	52155499	8
+    chr6	52155499	52155501	7
+
+Choose `bedGraph` from the track track UI:
+
+.. image:: _static/bedgraph_text_1.png
+
+The choose the bedGraph text file:
+
+.. image:: _static/bedgraph_text_2.png 
+
+The text track file is added:
+
+.. image:: _static/bedgraph_text_3.png 
+
+What if the text file is huge?
+------------------------------
+
+If your text track if huge in size, convert to binary format is recommended. However, you can still use the text file if you want.
+Make sure you check the `Use a Worker thread` checkbox, the browser will use a background thread for text file loading.
+
+.. image:: _static/worker_check.png
+