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-rwxr-xr-xwqflask/base/data_set.py16
-rwxr-xr-xwqflask/base/trait.py9
-rw-r--r--wqflask/utility/tools.py18
-rwxr-xr-xwqflask/utility/webqtlUtil.py16
-rwxr-xr-xwqflask/wqflask/do_search.py4
-rwxr-xr-xwqflask/wqflask/docs.py4
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py6
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py28
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.coffee13
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.js137
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.coffee1031
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.js54
-rw-r--r--wqflask/wqflask/static/new/javascript/panelutil.coffee19
-rw-r--r--wqflask/wqflask/static/new/javascript/panelutil.js13
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee63
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js61
-rwxr-xr-xwqflask/wqflask/templates/base.html38
-rw-r--r--wqflask/wqflask/templates/base_macro.html28
-rwxr-xr-xwqflask/wqflask/templates/interval_mapping.html116
-rwxr-xr-xwqflask/wqflask/templates/marker_regression.html38
-rwxr-xr-xwqflask/wqflask/templates/old_index_page.html320
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html14
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_progress_bar.html15
-rwxr-xr-xwqflask/wqflask/views.py8
25 files changed, 807 insertions, 1264 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b17396e5..d46e4363 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -811,11 +811,11 @@ class PhenotypeDataSet(DataSet):
WHERE
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
- PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
+ PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (trait, self.id)
- results = g.db.execute(query).fetchall()
+ """
+ results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -898,15 +898,17 @@ class GenotypeDataSet(DataSet):
left join GenoSE on
(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
WHERE
- Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
+ Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- GenoFreeze.Name = '%s' AND
+ GenoFreeze.Name = %s AND
GenoXRef.DataId = GenoData.Id AND
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)
- results = g.db.execute(query).fetchall()
+ """
+ results = g.db.execute(query,
+ (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
+ trait, self.name)).fetchall()
return results
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2e0e86fb..4a088bc8 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -292,6 +292,7 @@ class GeneralTrait(object):
""" % (self.name, self.dataset.id)
print("query is:", query)
+ assert self.name.isdigit()
trait_info = g.db.execute(query).fetchone()
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
@@ -330,10 +331,10 @@ class GeneralTrait(object):
trait_info = g.db.execute(query).fetchone()
#print("trait_info is: ", pf(trait_info))
else: #Temp type
- query = """SELECT %s FROM %s WHERE Name = %s
- """ % (string.join(self.dataset.display_fields,','),
- self.dataset.type, self.name)
- trait_info = g.db.execute(query).fetchone()
+ query = """SELECT %s FROM %s WHERE Name = %s"""
+ trait_info = g.db.execute(query,
+ (string.join(self.dataset.display_fields,','),
+ self.dataset.type, self.name)).fetchone()
if trait_info:
self.haveinfo = True
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 1a5c19d9..6e35f00a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -49,3 +49,21 @@ def pylmm_command(default=None):
path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
return path,pylmm_command
+
+def plink_command(default=None):
+ """
+ Return the path to the repository and the python command to call
+ """
+ def get_valid_path(path):
+ """Test for a valid repository"""
+ if path:
+ sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
+ if path and os.path.isfile(path+'/plink'):
+ return path
+ else:
+ None
+
+ guess = os.environ.get('HOME')+'/plink'
+ path = get_setting('PLINK_PATH',default,guess,get_valid_path)
+ plink_command = path+'/plink'
+ return path,plink_command \ No newline at end of file
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index ab746228..f842dde0 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -881,22 +881,6 @@ def cmpGenoPos(A,B):
except:
return 0
-#XZhou: Must use "BINARY" to enable case sensitive comparison.
-def authUser(name,password,db, encrypt=None):
- try:
- if encrypt:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY \'%s\'' % (name,password)
- else:
- query = 'SELECT privilege, id,name,password, grpName FROM User WHERE name= BINARY \'%s\' and password= BINARY SHA(\'%s\')' % (name,password)
- db.execute(query)
- records = db.fetchone()
- if not records:
- raise ValueError
- return records#(privilege,id,name,password,grpName)
- except:
- return (None, None, None, None, None)
-
-
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
access_to_confidential_phenotype_trait = 0
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index a42503c1..cec71777 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -115,7 +115,7 @@ class MrnaAssaySearch(DoSearch):
DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
- base_query = """SELECT ProbeSet.Name as TNAME,
+ base_query = """SELECT distinct ProbeSet.Name as TNAME,
0 as thistable,
ProbeSetXRef.Mean as TMEAN,
ProbeSetXRef.LRS as TLRS,
@@ -394,7 +394,7 @@ class GenotypeSearch(DoSearch):
# This adds a clause to the query that matches the search term
# against each field in search_fields (above)
- fields_clause = []
+ where_clause = []
if "'" not in self.search_term[0]:
self.search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]"
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 07b0b81a..a8363a1f 100755
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -8,9 +8,9 @@ class Docs(object):
sql = """
SELECT Docs.title, Docs.content
FROM Docs
- WHERE Docs.entry LIKE '%s'
+ WHERE Docs.entry LIKE %s
"""
- result = g.db.execute(sql % (entry)).fetchone()
+ result = g.db.execute(sql, str(entry)).fetchone()
self.entry = entry
self.title = result[0]
self.content = result[1]
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 4b4b7f73..672a9401 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -74,6 +74,7 @@ class IntervalMapping(object):
json.dumps(self.json_data, webqtlConfig.TMPDIR + json_filename)
self.js_data = dict(
+ result_score_type = "LRS",
manhattan_plot = self.manhattan_plot,
additive = self.additive,
chromosomes = chromosome_mb_lengths,
@@ -85,7 +86,10 @@ class IntervalMapping(object):
def set_options(self, start_vars):
"""Sets various options (physical/genetic mapping, # permutations, which chromosome"""
- self.num_permutations = int(start_vars['num_perm'])
+ if start_vars['num_perm'] == "":
+ self.num_permutations = 0
+ else:
+ self.num_permutations = int(start_vars['num_perm'])
if start_vars['manhattan_plot'] == "true":
self.manhattan_plot = True
else:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 2b0e89b3..c003f5e8 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -39,9 +39,10 @@ from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
from utility.benchmark import Bench
-from utility.tools import pylmm_command
+from utility.tools import pylmm_command, plink_command
PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
+PLINK_PATH,PLINK_COMMAND = plink_command()
class MarkerRegression(object):
@@ -178,6 +179,7 @@ class MarkerRegression(object):
self.js_data = dict(
+ result_score_type = "LOD",
json_data = self.json_data,
this_trait = self.this_trait.name,
data_set = self.dataset.name,
@@ -458,29 +460,16 @@ class MarkerRegression(object):
def run_plink(self):
-
- os.chdir("/home/zas1024/plink")
-
plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)
- plink_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
-
+ plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
+ print("plink_command:", plink_command)
+
os.system(plink_command)
count, p_values = self.parse_plink_output(plink_output_filename)
- #gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
- # self.dataset.group.name,
- # self.dataset.group.name,
- # self.dataset.group.name)
- #print("gemma_command:" + gemma_command)
- #
- #os.system(gemma_command)
- #
- #included_markers, p_values = self.parse_gemma_output()
- #
- #self.dataset.group.get_specified_markers(markers = included_markers)
#for marker in self.dataset.group.markers.markers:
# if marker['name'] not in included_markers:
@@ -567,10 +556,7 @@ class MarkerRegression(object):
# get strain name from ped file in order
def get_samples_from_ped_file(self):
-
- os.chdir("/home/zas1024/plink")
-
- ped_file= open("{}.ped".format(self.dataset.group.name),"r")
+ ped_file= open("{}/{}.ped".format(PLINK_PATH, self.dataset.group.name),"r")
line = ped_file.readline()
sample_list=[]
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
index 76be5490..df176f52 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
@@ -1,4 +1,4 @@
-create_manhattan_plot = ->
+create_lod_chart = ->
h = 500
w = 1200
margin = {left:60, top:40, right:40, bottom: 40, inner:5}
@@ -18,7 +18,7 @@ create_manhattan_plot = ->
.height(h)
.width(w)
.margin(margin)
- .ylab("LOD score")
+ .ylab(js_data.result_score_type + " score")
.manhattanPlot(js_data.manhattan_plot)
#.additive(additive)
@@ -44,8 +44,13 @@ create_manhattan_plot = ->
d3.select(this)
.transition().duration(500).attr("r", r*3)
.transition().duration(500).attr("r", r)
-
-create_manhattan_plot()
+
+$ ->
+ #window.setTimeout ( ->
+ # console.log(js_data)
+ #), 1000
+ #window.setTimeout(create_lod_chart(), 1000)
+ root.create_lod_chart = create_lod_chart
$("#export").click =>
#Get d3 SVG element
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js
index f61f05bd..a7cea8a5 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -1,73 +1,76 @@
// Generated by CoffeeScript 1.8.0
-var create_manhattan_plot;
+(function() {
+ var create_lod_chart;
-create_manhattan_plot = function() {
- var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
- h = 500;
- w = 1200;
- margin = {
- left: 60,
- top: 40,
- right: 40,
- bottom: 40,
- inner: 5
- };
- halfh = h + margin.top + margin.bottom;
- totalh = halfh * 2;
- totalw = w + margin.left + margin.right;
- if ('additive' in js_data) {
- additive = js_data.additive;
- } else {
- additive = false;
- }
- console.log("js_data:", js_data);
- mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot);
- data = js_data.json_data;
- d3.select("div#topchart").datum(data).call(mychart);
- chrrect = mychart.chrSelect();
- chrrect.on("mouseover", function() {
- return d3.select(this).attr("fill", "#E9CFEC");
- }).on("mouseout", function(d, i) {
- return d3.select(this).attr("fill", function() {
- if (i % 2) {
- return "#F1F1F9";
- }
- return "#FBFBFF";
+ create_lod_chart = function() {
+ var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+ h = 500;
+ w = 1200;
+ margin = {
+ left: 60,
+ top: 40,
+ right: 40,
+ bottom: 40,
+ inner: 5
+ };
+ halfh = h + margin.top + margin.bottom;
+ totalh = halfh * 2;
+ totalw = w + margin.left + margin.right;
+ if ('additive' in js_data) {
+ additive = js_data.additive;
+ } else {
+ additive = false;
+ }
+ console.log("js_data:", js_data);
+ mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot);
+ data = js_data.json_data;
+ d3.select("div#topchart").datum(data).call(mychart);
+ chrrect = mychart.chrSelect();
+ chrrect.on("mouseover", function() {
+ return d3.select(this).attr("fill", "#E9CFEC");
+ }).on("mouseout", function(d, i) {
+ return d3.select(this).attr("fill", function() {
+ if (i % 2) {
+ return "#F1F1F9";
+ }
+ return "#FBFBFF";
+ });
+ });
+ return mychart.markerSelect().on("click", function(d) {
+ var r;
+ r = d3.select(this).attr("r");
+ return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
});
- });
- return mychart.markerSelect().on("click", function(d) {
- var r;
- r = d3.select(this).attr("r");
- return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
- });
-};
+ };
-create_manhattan_plot();
+ root.create_lod_chart = create_lod_chart;
-$("#export").click((function(_this) {
- return function() {
- var filename, form, svg, svg_xml;
- svg = $("#topchart").find("svg")[0];
- svg_xml = (new XMLSerializer).serializeToString(svg);
- console.log("svg_xml:", svg_xml);
- filename = "manhattan_plot_" + js_data.this_trait;
- form = $("#exportform");
- form.find("#data").val(svg_xml);
- form.find("#filename").val(filename);
- return form.submit();
- };
-})(this));
+ $("#export").click((function(_this) {
+ return function() {
+ var filename, form, svg, svg_xml;
+ svg = $("#topchart").find("svg")[0];
+ svg_xml = (new XMLSerializer).serializeToString(svg);
+ console.log("svg_xml:", svg_xml);
+ filename = "manhattan_plot_" + js_data.this_trait;
+ form = $("#exportform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ };
+ })(this));
-$("#export_pdf").click((function(_this) {
- return function() {
- var filename, form, svg, svg_xml;
- svg = $("#topchart").find("svg")[0];
- svg_xml = (new XMLSerializer).serializeToString(svg);
- console.log("svg_xml:", svg_xml);
- filename = "manhattan_plot_" + js_data.this_trait;
- form = $("#exportpdfform");
- form.find("#data").val(svg_xml);
- form.find("#filename").val(filename);
- return form.submit();
- };
-})(this));
+ $("#export_pdf").click((function(_this) {
+ return function() {
+ var filename, form, svg, svg_xml;
+ svg = $("#topchart").find("svg")[0];
+ svg_xml = (new XMLSerializer).serializeToString(svg);
+ console.log("svg_xml:", svg_xml);
+ filename = "manhattan_plot_" + js_data.this_trait;
+ form = $("#exportpdfform");
+ form.find("#data").val(svg_xml);
+ form.find("#filename").val(filename);
+ return form.submit();
+ };
+ })(this));
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index b0f4b2f5..55ffdce0 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -1,514 +1,517 @@
-lodchart = () ->
- width = 800
- height = 500
- margin = {left:60, top:40, right:40, bottom: 40, inner:5}
- axispos = {xtitle:25, ytitle:30, xlabel:5, ylabel:5}
- titlepos = 20
- manhattanPlot = false
- additive = false
- ylim = null
- additive_ylim = null
- nyticks = 5
- yticks = null
- additive_yticks = null
- chrGap = 8
- darkrect = "#F1F1F9"
- lightrect = "#FBFBFF"
- lodlinecolor = "darkslateblue"
- additivelinecolor = "red"
- linewidth = 2
- suggestivecolor = "gainsboro"
- significantcolor = "#EBC7C7"
- pointcolor = "#E9CFEC" # pink
- pointsize = 0 # default = no visible points at markers
- pointstroke = "black"
- title = ""
- xlab = "Chromosome"
- ylab = "LRS score"
- additive_ylab = "Additive Effect"
- rotate_ylab = null
- yscale = d3.scale.linear()
- additive_yscale = d3.scale.linear()
- xscale = null
- pad4heatmap = false
- lodcurve = null
- lodvarname = null
- markerSelect = null
- chrSelect = null
- pointsAtMarkers = true
-
-
- ## the main function
- chart = (selection) ->
- selection.each (data) ->
-
- #console.log("data:", data)
-
- if manhattanPlot == true
- pointcolor = "darkslateblue"
- pointsize = 2
-
- lodvarname = lodvarname ? data.lodnames[0]
- data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values
- ylim = ylim ? [0, d3.max(data[lodvarname])]
- if additive
- data['additive'] = (Math.abs(x) for x in data['additive'])
- additive_ylim = additive_ylim ? [0, d3.max(data['additive'])]
-
- lodvarnum = data.lodnames.indexOf(lodvarname)
-
- # Select the svg element, if it exists.
- svg = d3.select(this).selectAll("svg").data([data])
-
- # Otherwise, create the skeletal chart.
- gEnter = svg.enter().append("svg").append("g")
-
- # Update the outer dimensions.
- svg.attr("width", width+margin.left+margin.right)
- .attr("height", height+margin.top+margin.bottom)
-
- # Update the inner dimensions.
- g = svg.select("g")
-
- # box
- g.append("rect")
- .attr("x", margin.left)
- .attr("y", margin.top)
- .attr("height", height)
- .attr("width", width)
- .attr("fill", darkrect)
- .attr("stroke", "none")
-
- yscale.domain(ylim)
- .range([height+margin.top, margin.top+margin.inner])
-
- # if yticks not provided, use nyticks to choose pretty ones
- yticks = yticks ? yscale.ticks(nyticks)
-
- #if data['additive'].length > 0
- if additive
- additive_yscale.domain(additive_ylim)
- .range([height+margin.top, margin.top+margin.inner + height/2])
-
- additive_yticks = additive_yticks ? additive_yscale.ticks(nyticks)
-
- # reorganize lod,pos by chromosomes
- reorgLodData(data, lodvarname)
-
- # add chromosome scales (for x-axis)
- data = chrscales(data, width, chrGap, margin.left, pad4heatmap)
- xscale = data.xscale
-
- # chr rectangles
- chrSelect =
- g.append("g").attr("class", "chrRect")
- .selectAll("empty")
- .data(data.chrnames)
- .enter()
- .append("rect")
- .attr("id", (d) -> "chrrect#{d[0]}")
- .attr("x", (d,i) ->
- return data.chrStart[i] if i==0 and pad4heatmap
- data.chrStart[i]-chrGap/2)
- .attr("width", (d,i) ->
- return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap
- data.chrEnd[i] - data.chrStart[i]+chrGap)
- .attr("y", margin.top)
- .attr("height", height)
- .attr("fill", (d,i) ->
- return darkrect if i % 2
- lightrect)
- .attr("stroke", "none")
- .on("click", (d) ->
- console.log("d is:", d)
- redraw_plot(d)
- )
-
- # x-axis labels
- xaxis = g.append("g").attr("class", "x axis")
- xaxis.selectAll("empty")
- .data(data.chrnames)
- .enter()
- .append("text")
- .text((d) -> d[0])
- .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)
- .attr("y", margin.top+height+axispos.xlabel)
- .attr("dominant-baseline", "hanging")
- .attr("text-anchor", "middle")
- .attr("cursor", "pointer")
- .on("click", (d) ->
- redraw_plot(d)
- )
-
- xaxis.append("text").attr("class", "title")
- .attr("y", margin.top+height+axispos.xtitle)
- .attr("x", margin.left+width/2)
- .attr("fill", "slateblue")
- .text(xlab)
-
-
- redraw_plot = (chr_ob) ->
- #console.log("chr_name is:", chr_ob[0])
- #console.log("chr_length is:", chr_ob[1])
- $('#topchart').remove()
- $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
- chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot)
-
- # y-axis
- rotate_ylab = rotate_ylab ? (ylab.length > 1)
- yaxis = g.append("g").attr("class", "y axis")
- yaxis.selectAll("empty")
- .data(yticks)
- .enter()
- .append("line")
- .attr("y1", (d) -> yscale(d))
- .attr("y2", (d) -> yscale(d))
- .attr("x1", margin.left)
- .attr("x2", margin.left+7)
- .attr("fill", "none")
- .attr("stroke", "white")
- .attr("stroke-width", 1)
- .style("pointer-events", "none")
-
- yaxis.selectAll("empty")
- .data(yticks)
- .enter()
- .append("text")
- .attr("y", (d) -> yscale(d))
- .attr("x", margin.left-axispos.ylabel)
- .attr("fill", "blue")
- .attr("dominant-baseline", "middle")
- .attr("text-anchor", "end")
- .text((d) -> formatAxis(yticks)(d))
-
- yaxis.append("text").attr("class", "title")
- .attr("y", margin.top+height/2)
- .attr("x", margin.left-axispos.ytitle)
- .text(ylab)
- .attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
- .attr("text-anchor", "middle")
- .attr("fill", "slateblue")
-
- #if data['additive'].length > 0
- if additive
- rotate_additive_ylab = rotate_additive_ylab ? (additive_ylab.length > 1)
- additive_yaxis = g.append("g").attr("class", "y axis")
- additive_yaxis.selectAll("empty")
- .data(additive_yticks)
- .enter()
- .append("line")
- .attr("y1", (d) -> additive_yscale(d))
- .attr("y2", (d) -> additive_yscale(d))
- .attr("x1", margin.left + width)
- .attr("x2", margin.left + width - 7)
- .attr("fill", "none")
- .attr("stroke", "white")
- .attr("stroke-width", 1)
- .style("pointer-events", "none")
-
- additive_yaxis.selectAll("empty")
- .data(additive_yticks)
- .enter()
- .append("text")
- .attr("y", (d) -> additive_yscale(d))
- .attr("x", (d) -> margin.left + width + axispos.ylabel + 20)
- .attr("fill", "green")
- .attr("dominant-baseline", "middle")
- .attr("text-anchor", "end")
- .text((d) -> formatAxis(additive_yticks)(d))
-
- additive_yaxis.append("text").attr("class", "title")
- .attr("y", margin.top+1.5*height)
- .attr("x", margin.left + width + axispos.ytitle)
- .text(additive_ylab)
- .attr("transform", if rotate_additive_ylab then "rotate(270,#{margin.left + width + axispos.ytitle}, #{margin.top+height*1.5})" else "")
- .attr("text-anchor", "middle")
- .attr("fill", "green")
-
- if 'suggestive' of data
- suggestive_bar = g.append("g").attr("class", "suggestive")
- suggestive_bar.selectAll("empty")
- .data([data.suggestive])
- .enter()
- .append("line")
- .attr("y1", (d) -> yscale(d))
- .attr("y2", (d) -> yscale(d))
- .attr("x1", margin.left)
- .attr("x2", margin.left+width)
- .attr("fill", "none")
- .attr("stroke", suggestivecolor)
- .attr("stroke-width", 5)
- .style("pointer-events", "none")
-
- suggestive_bar = g.append("g").attr("class", "significant")
- suggestive_bar.selectAll("empty")
- .data([data.significant])
- .enter()
- .append("line")
- .attr("y1", (d) -> yscale(d))
- .attr("y2", (d) -> yscale(d))
- .attr("x1", margin.left)
- .attr("x2", margin.left+width)
- .attr("fill", "none")
- .attr("stroke", significantcolor)
- .attr("stroke-width", 5)
- .style("pointer-events", "none")
-
- if manhattanPlot == false
- # lod curves by chr
- lodcurve = (chr, lodcolumn) ->
- d3.svg.line()
- .x((d) -> xscale[chr](d))
- .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))
-
- if additive
- additivecurve = (chr, lodcolumn) ->
- d3.svg.line()
- .x((d) -> xscale[chr](d))
- .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn]))
-
- curves = g.append("g").attr("id", "curves")
-
- for chr in data.chrnames
- curves.append("path")
- .datum(data.posByChr[chr[0]])
- .attr("d", lodcurve(chr[0], lodvarnum))
- .attr("stroke", lodlinecolor)
- .attr("fill", "none")
- .attr("stroke-width", linewidth)
- .style("pointer-events", "none")
-
- if additive
- for chr in data.chrnames
- curves.append("path")
- .datum(data.posByChr[chr[0]])
- .attr("d", additivecurve(chr[0], lodvarnum))
- .attr("stroke", additivelinecolor)
- .attr("fill", "none")
- .attr("stroke-width", 1)
- .style("pointer-events", "none")
-
- # points at markers
- console.log("before pointsize")
- if pointsize > 0
- console.log("pointsize > 0 !!!")
- markerpoints = g.append("g").attr("id", "markerpoints_visible")
- markerpoints.selectAll("empty")
- .data(data.markers)
- .enter()
- .append("circle")
- .attr("cx", (d) -> xscale[d.chr](d.pos))
- .attr("cy", (d) -> yscale(d.lod))
- .attr("r", pointsize)
- .attr("fill", pointcolor)
- .attr("stroke", pointstroke)
- .attr("pointer-events", "hidden")
-
- # title
- titlegrp = g.append("g").attr("class", "title")
- .append("text")
- .attr("x", margin.left+width/2)
- .attr("y", margin.top-titlepos)
- .text(title)
-
- # another box around edge
- g.append("rect")
- .attr("x", margin.left)
- .attr("y", margin.top)
- .attr("height", height)
- .attr("width", () ->
- return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap
- data.chrEnd[-1..][0]-margin.left+chrGap/2)
- .attr("fill", "none")
- .attr("stroke", "black")
- .attr("stroke-width", "none")
-
- if pointsAtMarkers
- # these hidden points are what gets selected...a bit larger
- hiddenpoints = g.append("g").attr("id", "markerpoints_hidden")
-
- markertip = d3.tip()
- .attr('class', 'd3-tip')
- .html((d) ->
- [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])
- .direction("e")
- .offset([0,10])
- svg.call(markertip)
-
- markerSelect =
- hiddenpoints.selectAll("empty")
- .data(data.markers)
- .enter()
- .append("circle")
- .attr("cx", (d) -> xscale[d.chr](d.pos))
- .attr("cy", (d) -> yscale(d.lod))
- .attr("id", (d) -> d.name)
- .attr("r", d3.max([pointsize*2, 3]))
- .attr("opacity", 0)
- .attr("fill", pointcolor)
- .attr("stroke", pointstroke)
- .attr("stroke-width", "1")
- .on "mouseover.paneltip", (d) ->
- d3.select(this).attr("opacity", 1)
- markertip.show(d)
- .on "mouseout.paneltip", ->
- d3.select(this).attr("opacity", 0)
- .call(markertip.hide)
-
- ## configuration parameters
- chart.width = (value) ->
- return width unless arguments.length
- width = value
- chart
-
- chart.height = (value) ->
- return height unless arguments.length
- height = value
- chart
-
- chart.margin = (value) ->
- return margin unless arguments.length
- margin = value
- chart
-
- chart.titlepos = (value) ->
- return titlepos unless arguments.length
- titlepos
- chart
-
- chart.axispos = (value) ->
- return axispos unless arguments.length
- axispos = value
- chart
-
- chart.manhattanPlot = (value) ->
- return manhattanPlot unless arguments.length
- manhattanPlot = value
- chart
-
- chart.ylim = (value) ->
- return ylim unless arguments.length
- ylim = value
- chart
-
- #if data['additive'].length > 0
- chart.additive_ylim = (value) ->
- return additive_ylim unless arguments.length
- additive_ylim = value
- chart
-
- chart.nyticks = (value) ->
- return nyticks unless arguments.length
- nyticks = value
- chart
-
- chart.yticks = (value) ->
- return yticks unless arguments.length
- yticks = value
- chart
-
- chart.chrGap = (value) ->
- return chrGap unless arguments.length
- chrGap = value
- chart
-
- chart.darkrect = (value) ->
- return darkrect unless arguments.length
- darkrect = value
- chart
-
- chart.lightrect = (value) ->
- return lightrect unless arguments.length
- lightrect = value
- chart
-
- chart.linecolor = (value) ->
- return linecolor unless arguments.length
- linecolor = value
- chart
-
- chart.linewidth = (value) ->
- return linewidth unless arguments.length
- linewidth = value
- chart
-
- chart.pointcolor = (value) ->
- return pointcolor unless arguments.length
- pointcolor = value
- chart
-
- chart.pointsize = (value) ->
- return pointsize unless arguments.length
- pointsize = value
- chart
-
- chart.pointstroke = (value) ->
- return pointstroke unless arguments.length
- pointstroke = value
- chart
-
- chart.title = (value) ->
- return title unless arguments.length
- title = value
- chart
-
- chart.xlab = (value) ->
- return xlab unless arguments.length
- xlab = value
- chart
-
- chart.ylab = (value) ->
- return ylab unless arguments.length
- ylab = value
- chart
-
- chart.rotate_ylab = (value) ->
- return rotate_ylab if !arguments.length
- rotate_ylab = value
- chart
-
- chart.lodvarname = (value) ->
- return lodvarname unless arguments.length
- lodvarname = value
- chart
-
- chart.pad4heatmap = (value) ->
- return pad4heatmap unless arguments.length
- pad4heatmap = value
- chart
-
- chart.pointsAtMarkers = (value) ->
- return pointsAtMarkers unless arguments.length
- pointsAtMarkers = value
- chart
-
- chart.yscale = () ->
- return yscale
-
- chart.additive = () ->
- return additive
-
- #if data['additive'].length > 0
- chart.additive_yscale = () ->
- return additive_yscale
-
- chart.xscale = () ->
- return xscale
-
- if manhattanPlot == false
- chart.lodcurve = () ->
- return lodcurve
-
- #if data['additive'].length > 0
- chart.additivecurve = () ->
- return additivecurve
-
- chart.markerSelect = () ->
- return markerSelect
-
- chart.chrSelect = () ->
- return chrSelect
-
- # return the chart function
- chart
-
+lodchart = () ->
+ width = 800
+ height = 500
+ margin = {left:60, top:40, right:40, bottom: 40, inner:5}
+ axispos = {xtitle:25, ytitle:30, xlabel:5, ylabel:5}
+ titlepos = 20
+ manhattanPlot = false
+ additive = false
+ ylim = null
+ additive_ylim = null
+ nyticks = 5
+ yticks = null
+ additive_yticks = null
+ chrGap = 8
+ darkrect = "#F1F1F9"
+ lightrect = "#FBFBFF"
+ lodlinecolor = "darkslateblue"
+ additivelinecolor = "red"
+ linewidth = 2
+ suggestivecolor = "gainsboro"
+ significantcolor = "#EBC7C7"
+ pointcolor = "#E9CFEC" # pink
+ pointsize = 0 # default = no visible points at markers
+ pointstroke = "black"
+ title = ""
+ xlab = "Chromosome"
+ ylab = "LRS score"
+ additive_ylab = "Additive Effect"
+ rotate_ylab = null
+ yscale = d3.scale.linear()
+ additive_yscale = d3.scale.linear()
+ xscale = null
+ pad4heatmap = false
+ lodcurve = null
+ lodvarname = null
+ markerSelect = null
+ chrSelect = null
+ pointsAtMarkers = true
+
+
+ ## the main function
+ chart = (selection) ->
+ selection.each (data) ->
+
+ #console.log("data:", data)
+
+ if manhattanPlot == true
+ pointcolor = "darkslateblue"
+ pointsize = 2
+
+ lodvarname = lodvarname ? data.lodnames[0]
+ data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values
+ ylim = ylim ? [0, d3.max(data[lodvarname])]
+ if additive
+ data['additive'] = (Math.abs(x) for x in data['additive'])
+ additive_ylim = additive_ylim ? [0, d3.max(data['additive'])]
+
+ lodvarnum = data.lodnames.indexOf(lodvarname)
+
+ # Select the svg element, if it exists.
+ svg = d3.select(this).selectAll("svg").data([data])
+
+ # Otherwise, create the skeletal chart.
+ gEnter = svg.enter().append("svg").append("g")
+
+ # Update the outer dimensions.
+ svg.attr("width", width+margin.left+margin.right)
+ .attr("height", height+margin.top+margin.bottom)
+
+ # Update the inner dimensions.
+ g = svg.select("g")
+
+ # box
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top)
+ .attr("height", height)
+ .attr("width", width)
+ .attr("fill", darkrect)
+ .attr("stroke", "none")
+
+ yscale.domain(ylim)
+ .range([height+margin.top, margin.top+margin.inner])
+
+ # if yticks not provided, use nyticks to choose pretty ones
+ yticks = yticks ? yscale.ticks(nyticks)
+
+ #if data['additive'].length > 0
+ if additive
+ additive_yscale.domain(additive_ylim)
+ .range([height+margin.top, margin.top+margin.inner + height/2])
+
+ additive_yticks = additive_yticks ? additive_yscale.ticks(nyticks)
+
+ # reorganize lod,pos by chromosomes
+ reorgLodData(data, lodvarname)
+
+ # add chromosome scales (for x-axis)
+ data = chrscales(data, width, chrGap, margin.left, pad4heatmap)
+ xscale = data.xscale
+
+ # chr rectangles
+ chrSelect =
+ g.append("g").attr("class", "chrRect")
+ .selectAll("empty")
+ .data(data.chrnames)
+ .enter()
+ .append("rect")
+ .attr("id", (d) -> "chrrect#{d[0]}")
+ .attr("x", (d,i) ->
+ return data.chrStart[i] if i==0 and pad4heatmap
+ data.chrStart[i]-chrGap/2)
+ .attr("width", (d,i) ->
+ return data.chrEnd[i] - data.chrStart[i]+chrGap/2 if (i==0 or i+1 == data.chrnames.length) and pad4heatmap
+ data.chrEnd[i] - data.chrStart[i]+chrGap)
+ .attr("y", margin.top)
+ .attr("height", height)
+ .attr("fill", (d,i) ->
+ return darkrect if i % 2
+
+ lightrect)
+ .attr("stroke", "none")
+ .on("click", (d) ->
+ console.log("d is:", d)
+ redraw_plot(d)
+ )
+
+ # x-axis labels
+ xaxis = g.append("g").attr("class", "x axis")
+ xaxis.selectAll("empty")
+ .data(data.chrnames)
+ .enter()
+ .append("text")
+ .text((d) -> d[0])
+ .attr("x", (d,i) -> (data.chrStart[i]+data.chrEnd[i])/2)
+ .attr("y", margin.top+height+axispos.xlabel)
+ .attr("dominant-baseline", "hanging")
+ .attr("text-anchor", "middle")
+ .attr("cursor", "pointer")
+ .on("click", (d) ->
+ redraw_plot(d)
+ )
+
+ xaxis.append("text").attr("class", "title")
+ .attr("y", margin.top+height+axispos.xtitle)
+ .attr("x", margin.left+width/2)
+ .attr("fill", "slateblue")
+ .text(xlab)
+
+
+ redraw_plot = (chr_ob) ->
+ #console.log("chr_name is:", chr_ob[0])
+ #console.log("chr_length is:", chr_ob[1])
+ $('#topchart').remove()
+ $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
+ chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot)
+
+ # y-axis
+ rotate_ylab = rotate_ylab ? (ylab.length > 1)
+ yaxis = g.append("g").attr("class", "y axis")
+ yaxis.selectAll("empty")
+ .data(yticks)
+ .enter()
+ .append("line")
+ .attr("y1", (d) -> yscale(d))
+ .attr("y2", (d) -> yscale(d))
+ .attr("x1", margin.left)
+ .attr("x2", margin.left+7)
+ .attr("fill", "none")
+ .attr("stroke", "white")
+ .attr("stroke-width", 1)
+ .style("pointer-events", "none")
+
+ yaxis.selectAll("empty")
+ .data(yticks)
+ .enter()
+ .append("text")
+ .attr("y", (d) -> yscale(d))
+ .attr("x", margin.left-axispos.ylabel)
+ .attr("fill", "blue")
+ .attr("dominant-baseline", "middle")
+ .attr("text-anchor", "end")
+ .text((d) -> formatAxis(yticks)(d))
+
+ yaxis.append("text").attr("class", "title")
+ .attr("y", margin.top+height/2)
+ .attr("x", margin.left-axispos.ytitle)
+ .text(ylab)
+ .attr("transform", if rotate_ylab then "rotate(270,#{margin.left-axispos.ytitle},#{margin.top+height/2})" else "")
+ .attr("text-anchor", "middle")
+ .attr("fill", "slateblue")
+
+ #if data['additive'].length > 0
+ if additive
+ rotate_additive_ylab = rotate_additive_ylab ? (additive_ylab.length > 1)
+ additive_yaxis = g.append("g").attr("class", "y axis")
+ additive_yaxis.selectAll("empty")
+ .data(additive_yticks)
+ .enter()
+ .append("line")
+ .attr("y1", (d) -> additive_yscale(d))
+ .attr("y2", (d) -> additive_yscale(d))
+ .attr("x1", margin.left + width)
+ .attr("x2", margin.left + width - 7)
+ .attr("fill", "none")
+ .attr("stroke", "white")
+ .attr("stroke-width", 1)
+ .style("pointer-events", "none")
+
+ additive_yaxis.selectAll("empty")
+ .data(additive_yticks)
+ .enter()
+ .append("text")
+ .attr("y", (d) -> additive_yscale(d))
+ .attr("x", (d) -> margin.left + width + axispos.ylabel + 20)
+ .attr("fill", "green")
+ .attr("dominant-baseline", "middle")
+ .attr("text-anchor", "end")
+ .text((d) -> formatAxis(additive_yticks)(d))
+
+ additive_yaxis.append("text").attr("class", "title")
+ .attr("y", margin.top+1.5*height)
+ .attr("x", margin.left + width + axispos.ytitle)
+ .text(additive_ylab)
+ .attr("transform", if rotate_additive_ylab then "rotate(270,#{margin.left + width + axispos.ytitle}, #{margin.top+height*1.5})" else "")
+ .attr("text-anchor", "middle")
+ .attr("fill", "green")
+
+ if 'suggestive' of data
+ suggestive_bar = g.append("g").attr("class", "suggestive")
+ suggestive_bar.selectAll("empty")
+ .data([data.suggestive])
+ .enter()
+ .append("line")
+ .attr("y1", (d) -> yscale(d))
+ .attr("y2", (d) -> yscale(d))
+ .attr("x1", margin.left)
+ .attr("x2", margin.left+width)
+ .attr("fill", "none")
+ .attr("stroke", suggestivecolor)
+ .attr("stroke-width", 5)
+ .style("pointer-events", "none")
+
+ suggestive_bar = g.append("g").attr("class", "significant")
+ suggestive_bar.selectAll("empty")
+ .data([data.significant])
+ .enter()
+ .append("line")
+ .attr("y1", (d) -> yscale(d))
+ .attr("y2", (d) -> yscale(d))
+ .attr("x1", margin.left)
+ .attr("x2", margin.left+width)
+ .attr("fill", "none")
+ .attr("stroke", significantcolor)
+ .attr("stroke-width", 5)
+ .style("pointer-events", "none")
+
+ if manhattanPlot == false
+ # lod curves by chr
+ lodcurve = (chr, lodcolumn) ->
+ d3.svg.line()
+ .x((d) -> xscale[chr](d))
+ .y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))
+
+ if additive
+ additivecurve = (chr, lodcolumn) ->
+ d3.svg.line()
+ .x((d) -> xscale[chr](d))
+ .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn]))
+
+ curves = g.append("g").attr("id", "curves")
+
+ for chr in data.chrnames
+ if chr.indexOf(data['chr'])
+ curves.append("path")
+ .datum(data.posByChr[chr[0]])
+ .attr("d", lodcurve(chr[0], lodvarnum))
+ .attr("stroke", lodlinecolor)
+ .attr("fill", "none")
+ .attr("stroke-width", linewidth)
+ .style("pointer-events", "none")
+
+ if additive
+ for chr in data.chrnames
+ if chr.indexOf(data['chr'])
+ curves.append("path")
+ .datum(data.posByChr[chr[0]])
+ .attr("d", additivecurve(chr[0], lodvarnum))
+ .attr("stroke", additivelinecolor)
+ .attr("fill", "none")
+ .attr("stroke-width", 1)
+ .style("pointer-events", "none")
+
+ # points at markers
+ console.log("before pointsize")
+ if pointsize > 0
+ console.log("pointsize > 0 !!!")
+ markerpoints = g.append("g").attr("id", "markerpoints_visible")
+ markerpoints.selectAll("empty")
+ .data(data.markers)
+ .enter()
+ .append("circle")
+ .attr("cx", (d) -> xscale[d.chr](d.pos))
+ .attr("cy", (d) -> yscale(d.lod))
+ .attr("r", pointsize)
+ .attr("fill", pointcolor)
+ .attr("stroke", pointstroke)
+ .attr("pointer-events", "hidden")
+
+ # title
+ titlegrp = g.append("g").attr("class", "title")
+ .append("text")
+ .attr("x", margin.left+width/2)
+ .attr("y", margin.top-titlepos)
+ .text(title)
+
+ # another box around edge
+ g.append("rect")
+ .attr("x", margin.left)
+ .attr("y", margin.top)
+ .attr("height", height)
+ .attr("width", () ->
+ return(data.chrEnd[-1..][0]-margin.left) if pad4heatmap
+ data.chrEnd[-1..][0]-margin.left+chrGap/2)
+ .attr("fill", "none")
+ .attr("stroke", "black")
+ .attr("stroke-width", "none")
+
+ if pointsAtMarkers
+ # these hidden points are what gets selected...a bit larger
+ hiddenpoints = g.append("g").attr("id", "markerpoints_hidden")
+
+ markertip = d3.tip()
+ .attr('class', 'd3-tip')
+ .html((d) ->
+ [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])
+ .direction("e")
+ .offset([0,10])
+ svg.call(markertip)
+
+ markerSelect =
+ hiddenpoints.selectAll("empty")
+ .data(data.markers)
+ .enter()
+ .append("circle")
+ .attr("cx", (d) -> xscale[d.chr](d.pos))
+ .attr("cy", (d) -> yscale(d.lod))
+ .attr("id", (d) -> d.name)
+ .attr("r", d3.max([pointsize*2, 3]))
+ .attr("opacity", 0)
+ .attr("fill", pointcolor)
+ .attr("stroke", pointstroke)
+ .attr("stroke-width", "1")
+ .on "mouseover.paneltip", (d) ->
+ d3.select(this).attr("opacity", 1)
+ markertip.show(d)
+ .on "mouseout.paneltip", ->
+ d3.select(this).attr("opacity", 0)
+ .call(markertip.hide)
+
+ ## configuration parameters
+ chart.width = (value) ->
+ return width unless arguments.length
+ width = value
+ chart
+
+ chart.height = (value) ->
+ return height unless arguments.length
+ height = value
+ chart
+
+ chart.margin = (value) ->
+ return margin unless arguments.length
+ margin = value
+ chart
+
+ chart.titlepos = (value) ->
+ return titlepos unless arguments.length
+ titlepos
+ chart
+
+ chart.axispos = (value) ->
+ return axispos unless arguments.length
+ axispos = value
+ chart
+
+ chart.manhattanPlot = (value) ->
+ return manhattanPlot unless arguments.length
+ manhattanPlot = value
+ chart
+
+ chart.ylim = (value) ->
+ return ylim unless arguments.length
+ ylim = value
+ chart
+
+ #if data['additive'].length > 0
+ chart.additive_ylim = (value) ->
+ return additive_ylim unless arguments.length
+ additive_ylim = value
+ chart
+
+ chart.nyticks = (value) ->
+ return nyticks unless arguments.length
+ nyticks = value
+ chart
+
+ chart.yticks = (value) ->
+ return yticks unless arguments.length
+ yticks = value
+ chart
+
+ chart.chrGap = (value) ->
+ return chrGap unless arguments.length
+ chrGap = value
+ chart
+
+ chart.darkrect = (value) ->
+ return darkrect unless arguments.length
+ darkrect = value
+ chart
+
+ chart.lightrect = (value) ->
+ return lightrect unless arguments.length
+ lightrect = value
+ chart
+
+ chart.linecolor = (value) ->
+ return linecolor unless arguments.length
+ linecolor = value
+ chart
+
+ chart.linewidth = (value) ->
+ return linewidth unless arguments.length
+ linewidth = value
+ chart
+
+ chart.pointcolor = (value) ->
+ return pointcolor unless arguments.length
+ pointcolor = value
+ chart
+
+ chart.pointsize = (value) ->
+ return pointsize unless arguments.length
+ pointsize = value
+ chart
+
+ chart.pointstroke = (value) ->
+ return pointstroke unless arguments.length
+ pointstroke = value
+ chart
+
+ chart.title = (value) ->
+ return title unless arguments.length
+ title = value
+ chart
+
+ chart.xlab = (value) ->
+ return xlab unless arguments.length
+ xlab = value
+ chart
+
+ chart.ylab = (value) ->
+ return ylab unless arguments.length
+ ylab = value
+ chart
+
+ chart.rotate_ylab = (value) ->
+ return rotate_ylab if !arguments.length
+ rotate_ylab = value
+ chart
+
+ chart.lodvarname = (value) ->
+ return lodvarname unless arguments.length
+ lodvarname = value
+ chart
+
+ chart.pad4heatmap = (value) ->
+ return pad4heatmap unless arguments.length
+ pad4heatmap = value
+ chart
+
+ chart.pointsAtMarkers = (value) ->
+ return pointsAtMarkers unless arguments.length
+ pointsAtMarkers = value
+ chart
+
+ chart.yscale = () ->
+ return yscale
+
+ chart.additive = () ->
+ return additive
+
+ #if data['additive'].length > 0
+ chart.additive_yscale = () ->
+ return additive_yscale
+
+ chart.xscale = () ->
+ return xscale
+
+ if manhattanPlot == false
+ chart.lodcurve = () ->
+ return lodcurve
+
+ #if data['additive'].length > 0
+ chart.additivecurve = () ->
+ return additivecurve
+
+ chart.markerSelect = () ->
+ return markerSelect
+
+ chart.chrSelect = () ->
+ return chrSelect
+
+ # return the chart function
+ chart
+
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 92289bfe..631d8632 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -1,4 +1,4 @@
-// Generated by CoffeeScript 1.8.0
+// Generated by CoffeeScript 1.9.2
var lodchart;
lodchart = function() {
@@ -53,33 +53,33 @@ lodchart = function() {
pointsAtMarkers = true;
chart = function(selection) {
return selection.each(function(data) {
- var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _j, _len, _len1, _ref, _ref1;
+ var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, j, k, len, len1, lodvarnum, markerpoints, markertip, redraw_plot, ref, ref1, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis;
if (manhattanPlot === true) {
pointcolor = "darkslateblue";
pointsize = 2;
}
lodvarname = lodvarname != null ? lodvarname : data.lodnames[0];
data[lodvarname] = (function() {
- var _i, _len, _ref, _results;
- _ref = data[lodvarname];
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- x = _ref[_i];
- _results.push(Math.abs(x));
+ var j, len, ref, results;
+ ref = data[lodvarname];
+ results = [];
+ for (j = 0, len = ref.length; j < len; j++) {
+ x = ref[j];
+ results.push(Math.abs(x));
}
- return _results;
+ return results;
})();
ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
if (additive) {
data['additive'] = (function() {
- var _i, _len, _ref, _results;
- _ref = data['additive'];
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- x = _ref[_i];
- _results.push(Math.abs(x));
+ var j, len, ref, results;
+ ref = data['additive'];
+ results = [];
+ for (j = 0, len = ref.length; j < len; j++) {
+ x = ref[j];
+ results.push(Math.abs(x));
}
- return _results;
+ return results;
})();
additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])];
}
@@ -196,16 +196,20 @@ lodchart = function() {
};
}
curves = g.append("g").attr("id", "curves");
- _ref = data.chrnames;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- chr = _ref[_i];
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
+ ref = data.chrnames;
+ for (j = 0, len = ref.length; j < len; j++) {
+ chr = ref[j];
+ if (chr.indexOf(data['chr'])) {
+ curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
+ }
}
if (additive) {
- _ref1 = data.chrnames;
- for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
- chr = _ref1[_j];
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
+ ref1 = data.chrnames;
+ for (k = 0, len1 = ref1.length; k < len1; k++) {
+ chr = ref1[k];
+ if (chr.indexOf(data['chr'])) {
+ curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
+ }
}
}
}
@@ -450,4 +454,4 @@ lodchart = function() {
return chrSelect;
};
return chart;
-};
+}; \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee
index a3bc0b44..f7b51457 100644
--- a/wqflask/wqflask/static/new/javascript/panelutil.coffee
+++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee
@@ -30,16 +30,15 @@ reorgLodData = (data, lodvarname=null) ->
data.lodByChr = {}
for chr,i in data.chrnames
- #console.log("chr:", chr)
- data.posByChr[chr[0]] = []
- data.lodByChr[chr[0]] = []
- for pos, j in data.pos
- if data.chr[j].toString() == chr[0]
- #console.log(data.chr[j] + " AND " + chr[0])
- data.posByChr[chr[0]].push(pos)
- data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
- lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
- data.lodByChr[chr[0]].push(lodval)
+ if data.chr.indexOf(chr[0])
+ data.posByChr[chr[0]] = []
+ data.lodByChr[chr[0]] = []
+ for pos, j in data.pos
+ if data.chr[j].toString() == chr[0]
+ data.posByChr[chr[0]].push(pos)
+ data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
+ lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
+ data.lodByChr[chr[0]].push(lodval)
#console.log("data.posByChr:", data.posByChr)
diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js
index 3a180e60..7c14f4de 100644
--- a/wqflask/wqflask/static/new/javascript/panelutil.js
+++ b/wqflask/wqflask/static/new/javascript/panelutil.js
@@ -106,10 +106,13 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
if (d > maxd) {
maxd = d;
}
- rng = d3.extent(data.posByChr[chr[0]]);
- chrStart.push(rng[0]);
- chrEnd.push(rng[1]);
- L = rng[1] - rng[0];
+ //rng = d3.extent(data.posByChr[chr[0]]);
+ //chrStart.push(rng[0]);
+ //chrEnd.push(rng[1]);
+ //L = rng[1] - rng[0];
+ chrStart.push(0);
+ chrEnd.push(chr[1]);
+ L = chr[1]
chrLength.push(L);
totalChrLength += L;
}
@@ -436,4 +439,4 @@ abs = function(x) {
return x;
}
return Math.abs(x);
-};
+}; \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 881ea74d..211fedae 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -63,10 +63,12 @@ do_ajax_post = (url, form_data) ->
console.log(xhr)
clearInterval(this.my_timer)
$('#progress_bar_container').modal('hide')
+ $('#static_progress_bar_container').modal('hide')
$("body").html("We got an error.")
success: (data) =>
clearInterval(this.my_timer)
$('#progress_bar_container').modal('hide')
+ $('#static_progress_bar_container').modal('hide')
open_mapping_results(data)
#$("body").html(data)
)
@@ -76,36 +78,22 @@ do_ajax_post = (url, form_data) ->
return false
open_mapping_results = (data) ->
+ #results_window = window.open("/mapping_results_container")
+ #results_window.onload = ->
+ # results_window.document.getElementById("mapping_results_container").innerHTML = data
+
$.colorbox(
- html: data
- href: "#mapping_results_holder"
- height: "90%"
- width: "90%"
+ html: data
+ href: "#mapping_results_holder"
+ height: "90%"
+ width: "90%"
+ onComplete: => root.create_lod_chart()
)
showalert = (message,alerttype) ->
$('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">×</a><span>'+message+'</span></div>')
-$("#interval_mapping_compute").click(() =>
- showalert("One or more outliers exist in this data set. Please review values before mapping. \
- Including outliers when mapping may lead to misleading results. \
- We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
- or simply deleting them.", "alert-success")
- console.log("In interval mapping")
- $("#progress_bar_container").modal()
- url = "/interval_mapping"
-
- $('input[name=method]').val("reaper")
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val())
- $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'))
- $('input[name=suggestive]').val($('input[name=suggestive_reaper]'))
- form_data = $('#trait_data_form').serialize()
- console.log("form_data is:", form_data)
-
- do_ajax_post(url, form_data)
-)
-
$('#suggestive').hide()
$('input[name=display_all]').change(() =>
@@ -116,8 +104,8 @@ $('input[name=display_all]').change(() =>
$('#suggestive').hide()
)
-$("#pylmm_compute").click(() =>
- $("#progress_bar_container").modal({show:true})
+$("#pylmm_compute").on("click", =>
+ $("#progress_bar_container").modal()
url = "/marker_regression"
$('input[name=method]').val("pylmm")
$('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val())
@@ -133,7 +121,7 @@ $("#pylmm_compute").click(() =>
-$("#rqtl_geno_compute").click(() =>
+$("#rqtl_geno_compute").on("click", =>
$("#progress_bar_container").modal()
url = "/marker_regression"
$('input[name=method]').val("rqtl_geno")
@@ -150,7 +138,7 @@ $("#rqtl_geno_compute").click(() =>
)
-$("#plink_compute").click(() =>
+$("#plink_compute").on("click", =>
$("#static_progress_bar_container").modal()
url = "/marker_regression"
$('input[name=method]').val("plink")
@@ -163,7 +151,7 @@ $("#plink_compute").click(() =>
do_ajax_post(url, form_data)
)
-$("#gemma_compute").click(() =>
+$("#gemma_compute").on("click", =>
console.log("RUNNING GEMMA")
$("#static_progress_bar_container").modal()
url = "/marker_regression"
@@ -177,6 +165,25 @@ $("#gemma_compute").click(() =>
do_ajax_post(url, form_data)
)
+$("#interval_mapping_compute").on("click", =>
+ showalert("One or more outliers exist in this data set. Please review values before mapping. \
+ Including outliers when mapping may lead to misleading results. \
+ We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
+ or simply deleting them.", "alert-success")
+ console.log("In interval mapping")
+ $("#progress_bar_container").modal()
+ url = "/interval_mapping"
+
+ $('input[name=method]').val("reaper")
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val())
+ $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'))
+ $('input[name=suggestive]').val($('input[name=suggestive_reaper]'))
+ form_data = $('#trait_data_form').serialize()
+ console.log("form_data is:", form_data)
+
+ do_ajax_post(url, form_data)
+)
+
#$(".submit_special").click(submit_special)
composite_mapping_fields = ->
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 1779df4b..259e4685 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,4 +1,4 @@
-// Generated by CoffeeScript 1.8.0
+// Generated by CoffeeScript 1.9.2
var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining;
submit_special = function() {
@@ -100,31 +100,19 @@ open_mapping_results = function(data) {
html: data,
href: "#mapping_results_holder",
height: "90%",
- width: "90%"
+ width: "90%",
+ onComplete: (function(_this) {
+ return function() {
+ return root.create_lod_chart();
+ };
+ })(this)
});
};
showalert = function(message, alerttype) {
- return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+ return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">×</a><span>' + message + '</span></div>');
};
-$("#interval_mapping_compute").click((function(_this) {
- return function() {
- var form_data, url;
- showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
- console.log("In interval mapping");
- $("#progress_bar_container").modal();
- url = "/interval_mapping";
- $('input[name=method]').val("reaper");
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
- $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
- $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
- };
-})(this));
-
$('#suggestive').hide();
$('input[name=display_all]').change((function(_this) {
@@ -138,12 +126,10 @@ $('input[name=display_all]').change((function(_this) {
};
})(this));
-$("#pylmm_compute").click((function(_this) {
+$("#pylmm_compute").on("click", (function(_this) {
return function() {
var form_data, url;
- $("#progress_bar_container").modal({
- show: true
- });
+ $("#progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("pylmm");
$('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
@@ -154,7 +140,7 @@ $("#pylmm_compute").click((function(_this) {
};
})(this));
-$("#rqtl_geno_compute").click((function(_this) {
+$("#rqtl_geno_compute").on("click", (function(_this) {
return function() {
var form_data, url;
$("#progress_bar_container").modal();
@@ -169,14 +155,12 @@ $("#rqtl_geno_compute").click((function(_this) {
};
})(this));
-$("#plink_compute").click((function(_this) {
+$("#plink_compute").on("click", (function(_this) {
return function() {
var form_data, url;
$("#static_progress_bar_container").modal();
url = "/marker_regression";
$('input[name=method]').val("plink");
- $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val());
- $('input[name=suggestive]').val($('input[name=suggestive_plink]').val());
$('input[name=maf]').val($('input[name=maf_plink]').val());
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
@@ -184,7 +168,7 @@ $("#plink_compute").click((function(_this) {
};
})(this));
-$("#gemma_compute").click((function(_this) {
+$("#gemma_compute").on("click", (function(_this) {
return function() {
var form_data, url;
console.log("RUNNING GEMMA");
@@ -198,6 +182,23 @@ $("#gemma_compute").click((function(_this) {
};
})(this));
+$("#interval_mapping_compute").on("click", (function(_this) {
+ return function() {
+ var form_data, url;
+ showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
+ console.log("In interval mapping");
+ $("#progress_bar_container").modal();
+ url = "/interval_mapping";
+ $('input[name=method]').val("reaper");
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+ $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+ $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return do_ajax_post(url, form_data);
+ };
+})(this));
+
composite_mapping_fields = function() {
return $(".composite_fields").toggle();
};
@@ -220,4 +221,4 @@ $("#choose_closet_control").change(function() {
$("#display_all_lrs").change(function() {
return toggle_enable_disable("#suggestive_lrs");
-});
+}); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 462a59a2..78682710 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -1,3 +1,4 @@
+{% from "base_macro.html" import header, flash_me, timeago %}
<!DOCTYPE HTML>
<html lang="en">
<html xmlns="http://www.w3.org/1999/xhtml">
@@ -10,12 +11,6 @@
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-
- <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
- <!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
- <![endif]-->
-
<link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css" />
@@ -25,37 +20,6 @@
</head>
-{% macro header(main, second) %}
- <header class="jumbotron subhead" id="overview" >
- <div class="container">
- <h1>{{ main }}</h1>
- <p class="lead">
- {{ second }}
- </p>
- </div>
- </header>
-
- {{ flash_me() }}
-{% endmacro %}
-
-
-{% macro flash_me() -%}
- {% with messages = get_flashed_messages(with_categories=true) %}
- {% if messages %}
- <div class="container">
- {% for category, message in messages %}
- <div class="alert {{ category }}">{{ message }}</div>
- {% endfor %}
- </div>
- {% endif %}
- {% endwith %}
-{% endmacro %}
-
-{% macro timeago(timestamp) %}
-<time class="timeago" datetime="{{ timestamp }}">{{ timestamp }}</time>
-{% endmacro %}
-
-
<body style="width: 1500px !important;">
<!-- Navbar ================================================== -->
diff --git a/wqflask/wqflask/templates/base_macro.html b/wqflask/wqflask/templates/base_macro.html
new file mode 100644
index 00000000..c2905ebe
--- /dev/null
+++ b/wqflask/wqflask/templates/base_macro.html
@@ -0,0 +1,28 @@
+{% macro flash_me() -%}
+ {% with messages = get_flashed_messages(with_categories=true) %}
+ {% if messages %}
+ <div class="container">
+ {% for category, message in messages %}
+ <div class="alert {{ category }}">{{ message }}</div>
+ {% endfor %}
+ </div>
+ {% endif %}
+ {% endwith %}
+{% endmacro %}
+
+{% macro header(main, second) %}
+ <header class="jumbotron subhead" id="overview" >
+ <div class="container">
+ <h1>{{ main }}</h1>
+ <p class="lead">
+ {{ second }}
+ </p>
+ </div>
+ </header>
+
+ {{ flash_me() }}
+{% endmacro %}
+
+{% macro timeago(timestamp) %}
+<time class="timeago" datetime="{{ timestamp }}">{{ timestamp }}</time>
+{% endmacro %}
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
deleted file mode 100755
index 82a96ba1..00000000
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ /dev/null
@@ -1,116 +0,0 @@
-{% block css %}
-<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-{% endblock %}
-{% block content %} <!-- Start of body -->
-
-
- <div id="mapping_results" class="container">
- <div>
- <h2>
- Whole Genome Mapping
- </h2>
- <form style ='float: left; padding: 5px;' id="exportform" action="export" method="post">
- <input type="hidden" id="data" name="data" value="">
- <input type="hidden" id="filename" name="filename" value="">
- <input type="submit" id="export" value="Download SVG">
- </form>
- <form style ='float: left; padding: 5px;' id="exportpdfform" action="export_pdf" method="post">
- <input type="hidden" id="data" name="data" value="">
- <input type="hidden" id="filename" name="filename" value="">
- <input type="submit" id="export_pdf" value="Download PDF">
- </form>
- </div>
- <div id="chart_container">
- <div class="qtlcharts" id="topchart">
-
- </div>
- </div>
- <div>
- <h2>
- Results
- </h2>
- </div>
- <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
- <thead>
- <tr>
- <td>Index</td>
- <td>LRS Score</td>
- <td>Chr</td>
- <td>Mb</td>
- <td>Locus</td>
- <td>Additive Effect</td>
- </tr>
- </thead>
- <tbody>
- {% for marker in qtl_results %}
- <tr>
- <td>{{ loop.index }}</td>
- <td>{{ marker.lrs_value|float }}</td>
- <td>{{ marker.chr|int }}</td>
- <td>{{ marker.Mb|float }}</td>
- <td>{{ marker.name }}</td>
- <td>{{ marker.additive|float }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
-
- </div>
-
- <!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script>
- js_data = {{ js_data | safe }}
- </script>
-
- <!--[if lt IE 9]>
-<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
- <![endif]-->
- <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_interval_map.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
- <script type="text/javascript" charset="utf-8">
- $(document).ready( function () {
- console.time("Creating table");
- $('#qtl_results').dataTable( {
- //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
- "sDom": "lTftipr",
- "oTableTools": {
- "aButtons": [
- "copy",
- "print",
- {
- "sExtends": "collection",
- "sButtonText": 'Save <span class="caret" />',
- "aButtons": [ "csv", "xls", "pdf" ]
- }
- ],
- "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
- },
- "iDisplayLength": 50,
- "bLengthChange": true,
- "bDeferRender": true,
- "bSortClasses": false
- } );
- console.timeEnd("Creating table");
- });
- </script>
-{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 6aed69d5..0cd004cd 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -1,15 +1,5 @@
-{% extends "base.html" %}
-{% block title %}Interval Mapping{% endblock %}
-{% block css %}
-<!-- <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-{% endblock %}
-{% block content %} <!-- Start of body -->
-
+{% from "base_macro.html" import header %}
+{% block content %}
{{ header("Mapping",
'{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
@@ -75,28 +65,6 @@
js_data = {{ js_data | safe }}
</script>
- <!--[if lt IE 9]>
-<!-- <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
- <![endif]-->
- <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
-<!-- <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->
- <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
-<!-- <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.js"></script>-->
- <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
console.time("Creating table");
@@ -123,4 +91,4 @@
console.timeEnd("Creating table");
});
</script>
-{% endblock %} \ No newline at end of file
+{% endblock %}
diff --git a/wqflask/wqflask/templates/old_index_page.html b/wqflask/wqflask/templates/old_index_page.html
deleted file mode 100755
index db0b2d9e..00000000
--- a/wqflask/wqflask/templates/old_index_page.html
+++ /dev/null
@@ -1,320 +0,0 @@
-{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
-{% block content %}
- <!-- Start of body -->
- <tr>
- <td bgcolor="#EEEEEE" class="solidBorder">
- <table width="100%" cellspacing="0" cellpadding="5">
- <tr>
- <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE">
- <p style="font-size:18px;font-family:verdana;color:black"><b>Select and
- Search</b></p>
-
- <form method="get" action="/search" class="form-search" name="SEARCHFORM">
- <table width="100%">
- <!-- SPECIES SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black" width="16%">
- <b>Species:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu0">
- <select name="species" size="1" id="species" onchange=
- "fillOptions('species');">
- </select>
- </div>
- </td>
- </tr><!-- GROUP SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu1">
- <select name="cross" size="1" id="cross" onchange="fillOptions('cross');">
- </select> <input type="button" class="btn" value="Info" onclick=
- "javascript:crossinfo();">
- </div>
- </td>
- </tr><!-- TYPE SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu2">
- <select name="tissue" size="1" id="tissue" onchange=
- "fillOptions('tissue');">
- </select>
- </div>
- </td>
- </tr><!-- DATABASE SELECTION -->
-
- <tr>
- <td align="right" height="35" style=
- "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left">
- <div id="menu3">
- <select name="database" size="1" id="database">
- </select> <input type="submit" class="btn" value="Info" name=
- "info_database">
- </div>
- </td>
- </tr><!-- USER HELP -->
-
- <tr>
- <td align="right" height="20" width="10%"></td>
-
- <td width="3%"></td>
-
- <td align="left" width="85%">
- <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <b>**</b>
- suffix are not public yet.<br>
- &nbsp;&nbsp;&nbsp;&nbsp;Access requires <a href="/account.html" target=
- "_blank" class="fs14"><small>user login</small></a>.</p>
- </td>
- </tr><!-- GET ANY SEARCH -->
-
- <tr>
- <td align="right" height="35" nowrap="on" style=
- "font-size:14px;font-family:verdana;color:black" width="10%">
- <b>Search:</b></td>
-
- <td width="3%"></td>
-
- <td nowrap width="85%" align="left"><input class="input-medium search-query"
- id="tfor" name="search_terms" style=
- "width:420px; background-color:white; font-family:verdana; font-size:14px"
- type="text" maxlength="500"></td>
- </tr><!-- GET ANY HELP -->
-
- <tr>
- <td align="right" height="20" width="10%"></td>
-
- <td width="3%"></td>
-
- <td width="85%" align="left">
- <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Enter terms, genes, ID numbers in the
- <b>Search</b> field.<br>
- &nbsp;&nbsp;&nbsp;&nbsp;Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
- synap*).<br>
- &nbsp;&nbsp;&nbsp;&nbsp;Use <b>quotes</b> for terms such as <i>"tyrosine
- kinase"</i>.</p>
- </td>
- </tr><!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
- <tr align="center">
- <td width="3%"></td>
-
- <td width="3%"></td>
-
- <td align="left" height="40" colspan="3"><input id="btsearch" type="submit"
- class="btn btn-primary" value="Search">&nbsp;&nbsp;&nbsp;&nbsp; <input type=
- "button" class="btn" value="Make Default" onclick=
- "setDefault(this.form);">&nbsp;&nbsp;&nbsp;&nbsp; <input type="button" class=
- "btn" value="Advanced Search" onclick=
- "javascript:window.open('/index3.html', '_self');"></td>
- </tr>
- </table><input type="hidden" name="FormID" value="searchResult"> <input type=
- "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js"
- type="text/javascript">
-</script>
- </form><!-- QUICK HELP -->
-
- <p>&nbsp;______________________________________________________</p>
-
- <p style="font-size:13px;font-family:verdana;color:black"><b>&nbsp; Quick HELP
- Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank"
- class="fs14"><b>User's Guide</b></a></p>&nbsp;&nbsp;You can also use advanced
- commands. Copy these simple examples<br>
- &nbsp;&nbsp;into the <b>Get Any</b> or <b>Combined</b> search fields:
-
- <ul style="font-size:12px;font-family:verdana;color:black">
- <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on
- chromosome 1 between 25 and 30 Mb.</li>
-
- <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds
- highly expressed genes (15 to 16 log2 units) AND with peak <a href=
- "http://www.genenetwork.org/glossary.html#L" target="_blank" class=
- "fs14"><small>LRS</small></a> linkage between 23 and 46.</li>
-
- <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href=
- "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"
- class="fs14"><small>GeneRIF</small></a> links.</li>
-
- <li><b><i>WIKI=nicotine</i></b> searches <a href=
- "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class=
- "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated
- with the word <i>nicotine</i>.</li>
-
- <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the
- <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class=
- "fs14"><small>Gene Ontology</small></a>.</li>
-
- <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br>
- in <b>Combined</b> finds synapse-associated genes with <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
- "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores
- between 9 and 999.</li>
-
- <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br>
- in <b>Combined</b> finds diabetes-associated transcripts with peak <a href=
- "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
- "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS
- scores between 9 and 999.</li>
- </ul>
- </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) -->
- <!-- START OF TOP RIGHT PANEL -->
-
- <td valign="top" width="40%" bgcolor="#FFFFFF">
- <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with
- GeneNetwork</b></p>
-
- <p style="font-size:12px;font-family:verdana;color:black"></p>
-
- <ul>
- <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
- Browser</a> at UTHSC</li>
-
- <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
- UTHSC</li>
-
- <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
- Cloud (EC2)</a></li>
-
- <li>GeneNetwork Source Codes at <a href=
- "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
-
- <li>GeneNetwork Source Codes at <a href=
- "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
- </ul>
-
- <p>____________________________</p>
-
- <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b>
- &nbsp;&nbsp;</p>
-
- <ol style="font-size:12px;font-family:verdana;color:black">
- <li>Select <b>Species</b> (or select All)</li>
-
- <li>Select <b>Group</b> (a specific sample)</li>
-
- <li>Select <b>Type</b> of data:
-
- <ul>
- <li>Phenotype (traits)</li>
-
- <li>Genotype (markers)</li>
-
- <li>Expression (mRNAs)</li>
- </ul>
- </li>
-
- <li>Select a <b>Database</b></li>
-
- <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words,
- genes, ID numbers, probes, advanced search commands</li>
-
- <li>Click on the <b>Search</b> button</li>
-
- <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
- </ol>
-
- <p>____________________________</p>
-
- <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use
- GeneNetwork</b></p>
-
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute
- GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
- "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and
- typical steps in the analysis.</p>
- </blockquote>
-
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">For information about
- resources and methods, select the <img src=
- "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign=
- "middle"> buttons.</p>
-
- <p style="font-size:12px;font-family:verdana;color:black">Try the <a href=
- "http://alexandria.uthsc.edu/" target="_blank" class=
- "fs14"><small>Workstation</small></a> site to explore data and features that are
- being implemented.</p>
-
- <p style="font-size:12px;font-family:verdana;color:black">Review the <a href=
- "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a>
- and <a href="/statusandContact.html" target="_blank" class=
- "fs14"><small>Contacts</small></a> pages for information on the status of data sets
- and advice on their use and citation.</p>
- </blockquote>
-
- <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development
- Sites</b></p>
-
- <ul>
- <li><a href="http://www.genenetwork.org/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main
- site)</li>
-
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
-
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
-
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
-
- <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a>
- (Development)</li>
-
- <li><a href="http://genenetwork.memphis.edu/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
-
- <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
-
- <li><a href="http://genenetwork.epfl.ch/" target="_blank" style=
- "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
- </ul>
-
- <p style="font-size:14px;font-family:verdana;color:black"><b>History and
- Archive</b></p>
-
- <blockquote>
- <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href=
- "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time
- Machine</small></a> links to earlier versions that correspond to specific
- publication dates.</p>
- </blockquote>
- </td>
- </tr>
- </table>
- </td>
- </tr>
- <!-- End of body -->
- <script src="/javascript/searchtip.js" type="text/javascript">
- </script>
- <script type="text/javascript">
- $(document).ready(function () {
- initialDatasetSelection();
- });
- </script>
-{% endblock %}
-
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 1f53e089..cdde5d9d 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -12,6 +12,8 @@
<link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+
{% endblock %}
{% block content %} <!-- Start of body -->
@@ -133,13 +135,19 @@
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
<script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
-
- <script language="javascript" type="text/javascript" src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
+
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
-"></script>
<script type="text/javascript" charset="utf-8">
function getValue(x) {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index bd1e6f1e..1550647a 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -66,7 +66,7 @@
</div>
<div class="form-group">
<div style="padding-left:15px;" class="controls">
- <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression">
<i class="icon-ok-circle icon-white"></i> Open Mapping Tool
</button>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html
index 99906338..f9a34070 100755
--- a/wqflask/wqflask/templates/show_trait_progress_bar.html
+++ b/wqflask/wqflask/templates/show_trait_progress_bar.html
@@ -32,17 +32,4 @@
</div>
</div>
</div>
-</div>
-
-<!--<div id="static_progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true">
- <div class="modal-header">
- <h3 id="progress_bar">Loading... (Estimated time ~10-15m)</h3>
- </div>
- <div class="modal-body">
- <div class="progress progress-striped active">
- <div id="marker_regression_progress" class="bar" style="width: 100%"></div>
- </div>
- <div id="time_remaining">
- </div>
- </div>
-</div>--> \ No newline at end of file
+</div> \ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 79c1c967..f9b27207 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -288,6 +288,10 @@ def heatmap_page():
return rendered_template
+@app.route("/mapping_results_container")
+def mapping_results_container_page():
+ return render_template("mapping_results_container.html")
+
@app.route("/marker_regression", methods=('POST',))
def marker_regression_page():
initial_start_vars = request.form
@@ -312,7 +316,7 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v4"
+ version = "v3"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
@@ -439,7 +443,7 @@ def interval_mapping_page():
Redis.expire(key, 60*60)
with Bench("Rendering template"):
- rendered_template = render_template("interval_mapping.html", **result)
+ rendered_template = render_template("marker_regression.html", **result)
return rendered_template