New funcs geneplot, fetch seq etc.

lidaof · Feb 28, 2019 · 5d2d73a · 5d2d73a
1 parent 109f425
commit 5d2d73a
Show file tree

Hide file tree

Showing 16 changed files with 116 additions and 6 deletions.
diff --git a/docs/_static/fetch_seq.png b/docs/_static/fetch_seq.png
diff --git a/docs/_static/fetch_seq1.png b/docs/_static/fetch_seq1.png
diff --git a/docs/_static/fetch_seq2.png b/docs/_static/fetch_seq2.png
diff --git a/docs/_static/geneplot_1.png b/docs/_static/geneplot_1.png
diff --git a/docs/_static/geneplot_2.png b/docs/_static/geneplot_2.png
diff --git a/docs/_static/geneplot_3.png b/docs/_static/geneplot_3.png
diff --git a/docs/_static/geneplot_4.png b/docs/_static/geneplot_4.png
diff --git a/docs/_static/geneplot_5.png b/docs/_static/geneplot_5.png
diff --git a/docs/_static/geneplot_6.png b/docs/_static/geneplot_6.png
diff --git a/docs/_static/geneplot_7.png b/docs/_static/geneplot_7.png
diff --git a/docs/_static/session_dn_up.png b/docs/_static/session_dn_up.png
diff --git a/docs/_static/snp_1.png b/docs/_static/snp_1.png
diff --git a/docs/_static/snp_2.png b/docs/_static/snp_2.png
diff --git a/docs/_static/snp_3.png b/docs/_static/snp_3.png
diff --git a/docs/tracks.rst b/docs/tracks.rst
@@ -388,3 +388,43 @@ cool
 Thanks to the higlass team who provides the data API, the browser is able to display cool tracks by using the data uuid
 from the higlass server, for example, you can use the uuid ``Hyc3TZevQVm3FcTAZShLQg`` to represent the track for *Aiden et al. (2009) GM06900 HINDIII 1kb*,
 for a full list of available cool tracks please check http://higlass.io/api/v1/tilesets/?dt=matrix
+
+Calling card track
+------------------
+
+Calling card data must be stored in a tab-delimited, plain text format. This format requires a minimum of four columns and can support up to six. The four required columns are CHROM, START, STOP, and COUNT, where COUNT refers to the number of reads for that insertion. The START and STOP columns can be either 0- or 1-indexed. The fifth and sixth columns are optional and represent STRAND and BARCODE, respectively. Here is an example of a four-column calling card file::
+
+    chr1    41954321        41954325        1
+    chr1    41954321        41954325        18
+    chr1    52655214        52655218        1
+    chr1    52655214        52655218        1
+    chr1    54690384        54690388        3
+    chr1    54713998        54714002        1
+    chr1    54713998        54714002        1
+    chr1    54713998        54714002        13
+    chr1    54747055        54747059        1
+    chr1    54747055        54747059        4
+    chr1    60748489        60748493        2
+
+Here is an example of a six-column calling card file::
+
+    chr1    51441754        51441758        1       -       CTAGAGACTGGC
+    chr1    51441754        51441758        21      -       CTTTCCTCCCCA
+    chr1    51982564        51982568        3       +       CGCGATCGCGAC
+    chr1    52196476        52196480        1       +       AGAATATCTTCA
+    chr1    52341019        52341023        1       +       TACGAAACACTA
+    chr1    59951043        59951047        1       +       ACAAGACCCCAA
+    chr1    59951043        59951047        1       +       ACAAGAGAGACT
+    chr1    61106283        61106287        1       -       ATGCACTACTTC
+    chr1    61106283        61106287        7       -       CGTTTTTCACCT
+    chr1    61542006        61542010        1       -       CTGAGAGACTGG
+
+our text file must be sorted by the first three columns. If your filename is example.ccf, you sort it with the following command: ``sort -k1V -k2n -k3n example.ccf > example_sorted.ccf``
+
+Note that you can have strand information without a barcode, but you cannot have barcode information without a strand column.
+
+Place your sorted text file in the public folder. Since genomic data is often large, we must compress and index it for fast retrieval. Use the following commands to do so::
+
+    bgzip example_sorted.ccf
+    tabix -p bed example_sorted.ccf.gz
+
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -13,17 +13,17 @@ Genomic Region Locator
 ----------------------
 .. image:: _static/region_jump.png
 
-The genomic region locator allows the user to navigate to a region or gene. 
+The genomic region locator allows the user to navigate to a region or gene.
 
 Gene Search
 ~~~~~~~~~~~
 
-You can type a gene name/symbol, like ``Hox``, and when the input content reaches 3 characters 
+You can type a gene name/symbol, like ``Hox``, and when the input content reaches 3 characters
 the browser will try to find gene symbols starting with what you typed:
 
 .. image:: _static/gene_search1.png
 
-After a gene is selected a dropdown menu will pop up with isoforms for the gene. After clicking an isoform the browser will navigate you to its genomic region. 
+After a gene is selected a dropdown menu will pop up with isoforms for the gene. After clicking an isoform the browser will navigate you to its genomic region.
 
 .. image:: _static/gene_search2.png
 
@@ -40,11 +40,28 @@ the red **stop** button, what you said "HOX" will populate the gene search box a
 .. note:: This feature is dependent on web browser support. A web browser without support for
           speech recognition won't see this UI.
 
-Region Search 
+SNP search
+~~~~~~~~~~
+
+SNP search is also avaiable from the genomic region locator button:
+
+.. image:: _static/snp_1.png
+
+say you input a SNP id: rs1259546924, click the Go button, you will get information about this SNP:
+
+.. image:: _static/snp_2.png
+
+Click the blue postion link can navigate you to this SNP's position:
+
+.. image:: _static/snp_3.png
+
+.. note:: SNP search uses the Ensembl API services: https://rest.ensembl.org
+
+Region Search
 ~~~~~~~~~~~~~
 
 Below the gene search box you can use the region search box to navigate to specific genomic coordinates. Formats such as
-``chr6:52258852-52260880`` or ``chr6 52258852 52260880`` are accepted (the browser is not sensitive to the number of spaces or tabs between the `chr`, `start`, and `stop`. 
+``chr6:52258852-52260880`` or ``chr6 52258852 52260880`` are accepted (the browser is not sensitive to the number of spaces or tabs between the `chr`, `start`, and `stop`.
 
 .. image:: _static/coord_search.png
 
@@ -97,7 +114,7 @@ Toggle display of the Genome Navigator
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 By using the genome navigator (below) users can jump to any genomic region
-or chromosome(s). 
+or chromosome(s).
 
 .. image:: _static/genome_navigator.png
 
@@ -190,6 +207,39 @@ Go back to the browser, you can your browser view is ordered by your region set:
 
 .. image:: _static/region_view.png
 
+Geneplot
+~~~~~~~~
+
+**Geneplot** function allows users to see overall signal of a numerical track over user selected
+gene/region sets. Choose ``Geneplot`` from the ``Apps`` menu, if there is no region sets added before,
+the browser will bring the region set adding interface:
+
+.. image:: _static/geneplot_1.png
+
+After adding a region set, you can choose the available set from the dropdown in first step:
+
+.. image:: _static/geneplot_2.png
+
+Now you need to choose a numerical track, you can use your custom track or publicly avaiable tracks:
+
+.. image:: _static/geneplot_3.png
+
+After choose a numerical track, click the **Plot** button, this will generate the boxplot by default:
+
+.. image:: _static/geneplot_4.png
+
+Choose line plot:
+
+.. image:: _static/geneplot_5.png
+
+Choose heatmap:
+
+.. image:: _static/geneplot_6.png
+
+When you mouse over the plot, there is a button for you to download the plot as SVG file:
+
+.. image:: _static/geneplot_7.png
+
 Session
 ~~~~~~~
 
@@ -222,6 +272,13 @@ Click the green *Restore* button and your session will be restored:
 
 .. image:: _static/session_restored.png
 
+Download and Upload session
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Sessions can be downloaded to a json file to your local disk, or can be uploaded from your local drive as well.
+
+.. image:: _static/session_dn_up.png
+
 Live browsing
 ~~~~~~~~~~~~~
 
@@ -241,6 +298,19 @@ current browser view as a SVG image file.
 
 .. image:: _static/screenshot.png
 
+Fetch Sequence
+~~~~~~~~~~~~~~
+
+From the ``Apps`` menu choose **Fetch Sequence**,, this function allows user to retrieve genomic sequence of current view region, or users can also specified a list of regions
+to fetch the sequences. Each region should no longer than 10KB.
+
+.. image:: _static/fetch_seq1.png
+
+Click the **Fetch** or **Batch fetch** button to fetch the sequence. Click the **Copy** button can copy the fetched sequence
+to your clipboard.
+
+.. image:: _static/fetch_seq2.png
+
 Track management
 ----------------