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authorzsloan2017-01-26 13:43:10 -0600
committerGitHub2017-01-26 13:43:10 -0600
commit298ca525114a570794d4326613be54ec223dce8b (patch)
tree1e0c445912af7ccb273a25b858889048eb96f756
parente63c4014e7bc34b440707be19af3779b72102fdb (diff)
parent7ea8ee22074c297925335cc048777f0ce8cb3912 (diff)
downloadgenenetwork2-298ca525114a570794d4326613be54ec223dce8b.tar.gz
Merge pull request #1 from genenetwork/testing
Various changes/fixes
-rw-r--r--doc/README.org48
-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py53
-rw-r--r--wqflask/wqflask/static/new/javascript/ctl_graph.js199
-rw-r--r--wqflask/wqflask/templates/ctl_results.html36
-rw-r--r--wqflask/wqflask/templates/ctl_setup.html8
6 files changed, 319 insertions, 29 deletions
diff --git a/doc/README.org b/doc/README.org
index 0f56914a..b38ea664 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -31,7 +31,7 @@ of GN2.
Large system deployments can get very [[http://biogems.info/contrib/genenetwork/gn2.svg ][complex]]. In this document we
explain the GeneNetwork version 2 (GN2) reproducible deployment system
-which is based on GNU Guix (see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix
+which is based on GNU Guix (see also [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix
system can be used to install GN with all its files and dependencies.
The official installation path is from a checked out version of the
@@ -52,15 +52,16 @@ Linux distribution (including CentOS). For more elaborate installation
instructions see [[#source-deployment][Source deployment]].
Note that GN2 consists of an approx. 5 GB installation including
-database.
+database. If you use a virtual machine we recommend to use at least
+double.
** Step 1: Install GNU Guix
Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow
-[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially you have to download and unpack the tar ball
-(which creates directories in /gnu and /var/guix), add build users and
-group (Guix builds software as unpriviliged users) and run the Guix
-daemon after fixing the paths (also known as the 'profile').
+[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially, download and unpack the tar ball (which
+creates directories in /gnu and /var/guix), add build users and group
+(Guix builds software as unpriviliged users) and run the Guix daemon
+after fixing the paths (also known as the 'profile').
Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission
to download binaries from the GNU server) and you should be able to
@@ -104,17 +105,23 @@ guix package -i git
export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt
#+end_src
-check out the git repsitories (gn-latest branch)
+check out the git repositories (gn-deploy branch)
#+begin_src bash
cd ~
mkdir genenetwork
cd genenetwork
-git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics
-git clone --branch gn-latest --recursive https://github.com/genenetwork/guix guix-gn-latest
-cd guix-gn-latest
+git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics
+git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy
+cd guix-gn-deploy
#+end_src bash
+To test whether this is working try:
+
+#+begin_src bash
+#+end_src bash
+
+
** Step 3: Authorize the GN Guix server
GN2 has its own GNU Guix binary distribution server. To trust it you have
@@ -146,7 +153,7 @@ GNU Guix package path by pointing the package path to our repository:
#+begin_src bash
rm /root/.config/guix/latest
-ln -s ~/genenetwork/guix-gn-latest/ /root/.config/guix/latest
+ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest
#+end_src
Now check whether you can find the GN2 package with
@@ -164,13 +171,16 @@ And install with
#+begin_src bash
env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \
guix package -i genenetwork2 \
- --substitute-urls="http://guix.genenetwork.org:8080 https://mirror.guixsd.org" \
- --fallback
+ --substitute-urls="http://guix.genenetwork.org"
#+end_src
Note: the order of the substitute url's may make a difference in speed
(put the one first that is fastest for your location and time of day).
+Note: if your system starts building or gives an error it may well be
+Step 3 did not succeed. The installation should actually be smooth at
+this point and only do binary installs (no compiling).
+
After installation you should be able to run genenetwork2 after updating
the Guix suggested environment vars. Check the output of
@@ -367,7 +377,7 @@ Create, install and run a recent version of the guix-daemon by
compiling the guix repository you have installed with git in
step 2. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully after
-: cd ~/genenetwork/guix-gn-latest
+: cd ~/genenetwork/guix-gn-deploy
Make sure to restart the guix daemon and run guix client from this
directory.
@@ -377,7 +387,7 @@ directory.
Reinstall genenetwork2 using the new tree
#+begin_src bash
-env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org:8080 https://mirror.guixsd.org"
+env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org"
#+end_src bash
Note the use of ./pre-inst-env here!
@@ -486,7 +496,7 @@ and a download of the test database.
<pjotrp> right?
<user01> yep
<user01> set to the ones in ~/.guix-profile/
-<pjotrp> good, and you are in gn-latest-guix repo [07:06]
+<pjotrp> good, and you are in gn-deploy-guix repo [07:06]
<user01> yep [07:07]
<pjotrp> git log shows
@@ -645,7 +655,7 @@ The following derivations would be built:
<pjotrp> and see what this lists [08:31]
<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix
package -i genenetwork2
- --substitute-urls=http://guix.genenetwork.org:8080 --dry-run
+ --substitute-urls=http://guix.genenetwork.org --dry-run
<pjotrp> should be all binary installs
<user01> it's not.. [08:32]
<user01> if I remove --substitute-urls, the list changes, does that mean I
@@ -716,7 +726,7 @@ The following derivations would be built:
<pjotrp> should not [09:24]
<pjotrp> what does env GUIX_PACKAGE_PATH=../guix-bioinformatics/
./pre-inst-env guix package -i genenetwork2
- --substitute-urls="http://guix.genenetwork.org:8080" --dry-run
+ --substitute-urls="http://guix.genenetwork.org" --dry-run
[09:25]
<pjotrp> say for r-prepocesscore
<pjotrp> download or build?
@@ -869,7 +879,7 @@ The following derivations would be built:
<pjotrp> I wrote an elixir package for guix :)
<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix
package -A elixir
- --substitute-urls="http://guix.genenetwork.org:8080" [10:08]
+ --substitute-urls="http://guix.genenetwork.org" [10:08]
<pjotrp> elixir 1.2.3 out
../guix-bioinformatics/gn/packages/elixir.scm:31:2
<pjotrp>
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 94b38e13..41c5d8ba 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -749,8 +749,8 @@ class PhenotypeDataSet(DataSet):
if this_trait.lrs:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = %s and
- Geno.Name = %s and
+ where Species.Name = '%s' and
+ Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
logger.sql(query)
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 1b1d7155..9515d23a 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -6,6 +6,8 @@ import scipy as sp # SciPy
import rpy2.robjects as ro # R Objects
import rpy2.rinterface as ri
+import simplejson as json
+
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility import webqtlUtil # Random number for the image
from utility import genofile_parser # genofile_parser
@@ -73,8 +75,30 @@ class CTL(object):
self.r_CTLnetwork = ro.r["CTLnetwork"] # Map the CTLnetwork function
self.r_CTLprofiles = ro.r["CTLprofiles"] # Map the CTLprofiles function
self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function
+ self.nodes_list = []
+ self.edges_list = []
print("Obtained pointers to CTL functions")
+ def addNode(self, gt):
+ node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name),
+ 'sid' : str(gt.name),
+ 'dataset' : str(gt.dataset.name),
+ 'label' : gt.name,
+ 'symbol' : gt.symbol,
+ 'geneid' : gt.geneid,
+ 'omim' : gt.omim } }
+ self.nodes_list.append(node_dict)
+
+ def addEdge(self, gtS, gtT, significant, x):
+ edge_data = {'id' : str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol),
+ 'source' : str(gtS.name) + ":" + str(gtS.dataset.name),
+ 'target' : str(gtT.name) + ":" + str(gtT.dataset.name),
+ 'lod' : significant[3][x],
+ 'color' : "#ff0000",
+ 'width' : significant[3][x] }
+ edge_dict = { 'data' : edge_data }
+ self.edges_list.append(edge_dict)
+
def run_analysis(self, requestform):
print("Starting CTL analysis on dataset")
self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
@@ -99,7 +123,7 @@ class CTL(object):
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
parser = genofile_parser.ConvertGenoFile(genofilelocation)
parser.process_csv()
-
+ print(dataset.group)
# Create a genotype matrix
individuals = parser.individuals
markers = []
@@ -129,9 +153,11 @@ class CTL(object):
rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True))
+ print(rPheno)
+
# Use a data frame to store the objects
- rPheno = r_data_frame(rPheno)
- rGeno = r_data_frame(rGeno)
+ rPheno = r_data_frame(rPheno, check_names = False)
+ rGeno = r_data_frame(rGeno, check_names = False)
# Debug: Print the genotype and phenotype files to disk
#r_write_table(rGeno, "~/outputGN/geno.csv")
@@ -156,7 +182,7 @@ class CTL(object):
self.r_lineplot(res, significance = significance)
r_dev_off()
- n = 2
+ n = 2 # We start from 2, since R starts from 1 :)
for trait in self.trait_db_list:
# Create the QTL like CTL plots
self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
@@ -169,6 +195,24 @@ class CTL(object):
# Flush any output from R
sys.stdout.flush()
+ # Create the interactive graph for cytoscape visualization (Nodes and Edges)
+ print(type(significant))
+ if not type(significant) == ri.RNULLType:
+ for x in range(len(significant[0])):
+ print(significant[0][x], significant[1][x], significant[2][x]) # Debug to console
+ tsS = significant[0][x].split(':') # Source
+ tsT = significant[2][x].split(':') # Target
+ gtS = TRAIT.GeneralTrait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB
+ gtT = TRAIT.GeneralTrait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB
+ self.addNode(gtS)
+ self.addNode(gtT)
+ self.addEdge(gtS, gtT, significant, x)
+
+ significant[0][x] = gtS.symbol + " (" + gtS.name + ")" # Update the trait name for the displayed table
+ significant[2][x] = gtT.symbol + " (" + gtT.name + ")" # Update the trait name for the displayed table
+
+ self.elements = json.dumps(self.nodes_list + self.edges_list)
+
def loadImage(self, path, name):
print("pre-loading imgage results:", self.results[path])
imgfile = open(self.results[path], 'rb')
@@ -188,6 +232,7 @@ class CTL(object):
print("Processing CTL output")
template_vars = {}
template_vars["results"] = self.results
+ template_vars["elements"] = self.elements
self.render_image(self.results)
sys.stdout.flush()
return(dict(template_vars))
diff --git a/wqflask/wqflask/static/new/javascript/ctl_graph.js b/wqflask/wqflask/static/new/javascript/ctl_graph.js
new file mode 100644
index 00000000..94bd7e9d
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/ctl_graph.js
@@ -0,0 +1,199 @@
+window.onload=function() {
+ // id of Cytoscape Web container div
+ //var div_id = "cytoscapeweb";
+
+ var cy = cytoscape({
+ container: $('#cytoscapeweb'), // container to render in
+
+ elements: elements_list,
+
+ style: [ // the stylesheet for the graph
+ {
+ selector: 'node',
+ style: {
+ 'background-color': '#666',
+ 'label': 'data(symbol)',
+ 'font-size': 10
+ }
+ },
+
+ {
+ selector: 'edge',
+ style: {
+ 'width': 'data(width)',
+ 'line-color': 'data(color)',
+ 'target-arrow-color': '#ccc',
+ 'target-arrow-shape': 'none',
+ 'font-size': 8,
+ 'curve-style': 'bezier'
+ }
+ }
+ ],
+
+ zoom: 12,
+ layout: { name: 'circle',
+ fit: true, // whether to fit the viewport to the graph
+ padding: 30 // the padding on fit
+ //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; },
+ },
+
+
+ zoomingEnabled: true,
+ userZoomingEnabled: true,
+ panningEnabled: true,
+ userPanningEnabled: true,
+ boxSelectionEnabled: false,
+ selectionType: 'single',
+
+ // rendering options:
+ styleEnabled: true
+ });
+
+ var eles = cy.$() // var containing all elements, so elements can be restored after being removed
+
+ var defaults = {
+ zoomFactor: 0.05, // zoom factor per zoom tick
+ zoomDelay: 45, // how many ms between zoom ticks
+ minZoom: 0.1, // min zoom level
+ maxZoom: 10, // max zoom level
+ fitPadding: 30, // padding when fitting
+ panSpeed: 10, // how many ms in between pan ticks
+ panDistance: 10, // max pan distance per tick
+ panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction)
+ panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed)
+ panInactiveArea: 8, // radius of inactive area in pan drag box
+ panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0
+ zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution)
+ fitSelector: undefined, // selector of elements to fit
+ animateOnFit: function(){ // whether to animate on fit
+ return false;
+ },
+ fitAnimationDuration: 1000, // duration of animation on fit
+
+ // icon class names
+ sliderHandleIcon: 'fa fa-minus',
+ zoomInIcon: 'fa fa-plus',
+ zoomOutIcon: 'fa fa-minus',
+ resetIcon: 'fa fa-expand'
+ };
+
+ cy.panzoom( defaults );
+
+ function create_qtips(cy){
+ cy.nodes().qtip({
+ content: function(){
+ gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().sid + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
+ ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
+ omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>'
+ qtip_content = gn_link + ncbi_link + omim_link
+ return qtip_content
+ //return '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'<a>'+'</b>'
+ },
+ // content: {
+ // title: '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.target() + '&dataset=' + this.dataset() + '" >'+this.target() +'<a>'+'</b>',
+ // text: this.target,
+ // button: true
+ // },
+ position: {
+ my: 'top center',
+ at: 'bottom center'
+ },
+ style: {
+ classes: 'qtip-bootstrap',
+ tip: {
+ width: 16,
+ height: 8
+ }
+ }
+ });
+
+ cy.edges().qtip({
+ content: function(){
+ edge_ID = '<b>Edge: ' + this.data().id + '</b><br>'
+ lod_score = 'LOD: ' + this.data().lod + '<br>'
+ return edge_ID + lod_score
+ },
+ position: {
+ my: 'top center',
+ at: 'bottom center'
+ },
+ style: {
+ classes: 'qtip-bootstrap',
+ tip: {
+ width: 16,
+ height: 8
+ }
+ }
+ });
+ }
+
+ create_qtips(cy)
+
+ $('#slide').change(function() {
+ eles.restore()
+
+ console.log(eles)
+
+ // nodes_to_restore = eles.filter("node[max_corr >= " + $(this).val() + "], edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]")
+ // nodes_to_restore.restore()
+
+ // edges_to_restore = eles.filter("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]")
+ // edges_to_restore.restore()
+
+ //cy.$("node[max_corr >= " + $(this).val() + "]").restore();
+ //cy.$("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]").restore();
+
+ cy.$("node[max_corr < " + $(this).val() + "]").remove();
+ cy.$("edge[correlation < " + $(this).val() + "][correlation > -" + $(this).val() + "]").remove();
+
+ cy.layout({ name: $('select[name=layout_select]').val(),
+ fit: true, // whether to fit the viewport to the graph
+ padding: 25 // the padding on fit
+ });
+
+ });
+
+ $('#reset_graph').click(function() {
+ eles.restore()
+ $('#slide').val(0)
+ cy.layout({ name: $('select[name=layout_select]').val(),
+ fit: true, // whether to fit the viewport to the graph
+ padding: 25 // the padding on fit
+ });
+ });
+
+ $('select[name=focus_select]').change(function() {
+ focus_trait = $(this).val()
+
+ eles.restore()
+ cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove()
+
+ cy.layout({ name: $('select[name=layout_select]').val(),
+ fit: true, // whether to fit the viewport to the graph
+ padding: 25 // the padding on fit
+ });
+ });
+
+ $('select[name=layout_select]').change(function() {
+ layout_type = $(this).val()
+ console.log("LAYOUT:", layout_type)
+ cy.layout({ name: layout_type,
+ fit: true, // whether to fit the viewport to the graph
+ padding: 25 // the padding on fit
+ });
+ });
+
+ $("a#image_link").click(function(e) {
+ var pngData = cy.png();
+
+ $(this).attr('href', pngData);
+ $(this).attr('download', 'network_graph.png');
+
+ console.log("TESTING:", image_link)
+
+ });
+
+
+};
+
+
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 00ccecb6..969ca18a 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -1,17 +1,30 @@
{% extends "base.html" %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/cytoscape/css/cytoscape.js-panzoom.css" />
+ <link rel="stylesheet" type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.css">
+ <style>
+ /* The Cytoscape Web container must have its dimensions set. */
+ html, body { height: 100%; width: 100%; padding: 0; margin: 0; }
+ #cytoscapeweb { width: 70%; height: 70%; }
+ </style>
+{% endblock %}
+
{% block title %}CTL results{% endblock %}
{% block content %} <!-- Start of body -->
<div class="container">
<h1>CTL Results</h1>
{{(request.form['trait_list'].split(',')|length)}} phenotypes as input<br>
- <h3>Network Figure</h3>
+
+ <!--
<a href="/tmp/{{ results['imgurl1'] }}">
<img alt="Embedded Image" src="data:image/png;base64,
{% for elem in results['imgdata1'] -%}
{% print("%c"|format(elem)) %}
{%- endfor %}
- " /></a>
+ " /></a> -->
+
<h3>CTL/QTL Plots for individual traits</h3>
{% for r in range(2, (request.form['trait_list'].split(',')|length +1)) %}
<a href="/tmp/{{ results['imgurl' + r|string] }}">
@@ -39,9 +52,26 @@
</tr>
{% endfor %}
</table>
+ <h3>Network Figure</h3>
+ <div id="cytoscapeweb" class="col-xs-9" style="min-height:700px !important;"></div>
+</div>
+{% endblock %}
+{% block js %}
+ <script>
+ elements_list = {{ elements | safe }}
+ </script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="http://cdnjs.cloudflare.com/ajax/libs/qtip2/2.2.0/jquery.qtip.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/cytoscape.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/AC_OETags.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/min/json2.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-panzoom.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/cytoscape/js/src/cytoscape-qtip.js"></script>
-</div>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/ctl_graph.js"></script>
{% endblock %}
+
diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
index a05379a8..a7ad5759 100644
--- a/wqflask/wqflask/templates/ctl_setup.html
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -11,7 +11,13 @@
Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input.
</div>
{% else %}
- <h1>CTL analysis parameters</h1>
+ <h1>CTL analysis</h1>
+ CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br>
+ Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br>
+ Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br>
+ The Journal of Open Source Software (2016)<br>
+ Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a>
+ <br><br>
{{(request.form['trait_list'].split(',')|length)}} traits as input
<form action="/ctl_results" method="post" class="form-horizontal">