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-rw-r--r--wqflask/wqflask/static/new/javascript/biodalliance.js1
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html68
-rw-r--r--wqflask/wqflask/views.py3
3 files changed, 64 insertions, 8 deletions
diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
index b6808d8a..3cfc26eb 100644
--- a/wqflask/wqflask/static/new/javascript/biodalliance.js
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -23,6 +23,7 @@ BD.createBrowser = function(chr, start, end, speciesName, sources) {
sources: sources,
+ maxHeight: 1000,
setDocumentTitle: false,
prefix: '/dalliance/',
workerPrefix: 'build/',
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 47e282cf..aba903c7 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -266,8 +266,9 @@
checking the headers */
list = [
"/static/new/javascript/biodalliance.js",
- "http://d3js.org/d3.v3.min.js",
+ "/dalliance/build/dalliance-all.js",
"/static/new/js_external/underscore-min.js",
+ "http://d3js.org/d3.v3.min.js",
"https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"
];
for (var i = 0; i < list.length; i++) {
@@ -280,8 +281,8 @@
},
error: function() {
// page does not exist
- console.log("Failed to load "+url);
- alert("Failed to load Javascript for "+url);
+ console.log("Failed to load "+this.url);
+ alert("Failed to load Javascript for "+this.url);
}
})};
</script>
@@ -369,6 +370,55 @@
tier_type: 'sequence',
provides_entrypoints: true
});
+ BD.putSource({name: 'Genotype',
+ controlURI: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/BXD.json",
+ URIBase: "http://test-gn2.genenetwork.org/api_pre1/genotype/mouse/",
+ tier_type: 'rqtl-genotype',
+ pinned: true,
+ transposed: true,
+ style: [
+ { type: "default",
+ method: "U",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "black",
+ BGCOLOR: "white",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "B",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "blue",
+ BGCOLOR: "blue",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "H",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "green",
+ BGCOLOR: "green",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "D",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "red",
+ BGCOLOR: "red",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ ]
+ });
BD.putSource({name: 'QTL',
tier_type: 'qtl',
uri: 'http://localhost:5003/generated_text/{{csv_filename}}',
@@ -377,16 +427,20 @@
style: {
glyph: "LINEPLOT",
MIN: 0,
- MAX: 2.5,
- HEIGHT: 120,
+ MAX: 3,
+ HEIGHT: 200,
STEPS: 500,
COLOR1: "blue",
}
- }]
+ }],
+ });
+ BD.putSource({name: 'SNP density',
+ jbURI: "http://test-gn2.genenetwork.org/api_pre1/snp",
+ jbQuery: "",
+ stylesheet_uri: "http://test-gn2.genenetwork.org/api_pre1/stylesheets/snp-stylesheet.xml",
});
</script>
-
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
BD.putData({species: "{{ dataset.group.species }}" });
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 5cc22cc4..14e019d2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -481,7 +481,8 @@ def marker_regression_page():
writer = csv.writer(csv_file)
writer.writerow(("Locus", "Chr", "Mb", "LOD"))
for (row) in qtl_results:
- writer.writerow((row["name"], row["chr"], row["Mb"], row["lod_score"]))
+ score = row["lod_score"] if "lod_score" in row else row["lrs_value"]
+ writer.writerow((row["name"], row["chr"], row["Mb"], score))
result = template_vars.__dict__