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-rw-r--r--wqflask/utility/tools.py18
-rwxr-xr-xwqflask/wqflask/do_search.py2
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py3
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py28
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.coffee11
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.js10
-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.coffee44
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js413
-rwxr-xr-xwqflask/wqflask/templates/interval_mapping.html117
-rwxr-xr-xwqflask/wqflask/templates/old_index_page.html320
-rwxr-xr-xwqflask/wqflask/views.py6
15 files changed, 838 insertions, 1251 deletions
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/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 8c1b6730..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,
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 5f491652..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,
@@ -88,7 +89,7 @@ class IntervalMapping(object):
if start_vars['num_perm'] == "":
self.num_permutations = 0
else:
- self.num_permutations = start_vars['num_perm']
+ 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 f1da65d7..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)
@@ -45,7 +45,12 @@ create_manhattan_plot = ->
.transition().duration(500).attr("r", r*3)
.transition().duration(500).attr("r", r)
-root.create_manhattan_plot = 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 546d7c18..a7cea8a5 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.8.0
(function() {
- var create_manhattan_plot;
+ var create_lod_chart;
- create_manhattan_plot = function() {
+ create_lod_chart = function() {
var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
h = 500;
w = 1200;
@@ -22,7 +22,7 @@
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);
+ 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();
@@ -43,7 +43,7 @@
});
};
- root.create_manhattan_plot = create_manhattan_plot;
+ root.create_lod_chart = create_lod_chart;
$("#export").click((function(_this) {
return function() {
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 29a637ee..df58eb39 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -76,37 +76,22 @@ 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%"
- onComplete: => root.create_manhattan_plot()
+ 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").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)
-)
-
$('#suggestive').hide()
$('input[name=display_all]').change(() =>
@@ -178,6 +163,25 @@ $("#gemma_compute").on("click", =>
do_ajax_post(url, form_data)
)
+$("#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 03862cf8..259e4685 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,227 +1,224 @@
// Generated by CoffeeScript 1.9.2
-(function() {
- 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() {
- var url;
- console.log("In submit_special");
- console.log("this is:", this);
- console.log("$(this) is:", $(this));
- url = $(this).data("url");
- console.log("url is:", url);
- $("#trait_data_form").attr("action", url);
- return $("#trait_data_form").submit();
- };
-
- update_time_remaining = function(percent_complete) {
- var minutes_remaining, now, period, total_seconds_remaining;
- now = new Date();
- period = now.getTime() - root.start_time;
- console.log("period is:", period);
- if (period > 8000) {
- total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
- minutes_remaining = Math.round(total_seconds_remaining / 60);
- if (minutes_remaining < 3) {
- return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
- } else {
- return $('#time_remaining').text(minutes_remaining + " minutes remaining");
- }
+var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+
+submit_special = function() {
+ var url;
+ console.log("In submit_special");
+ console.log("this is:", this);
+ console.log("$(this) is:", $(this));
+ url = $(this).data("url");
+ console.log("url is:", url);
+ $("#trait_data_form").attr("action", url);
+ return $("#trait_data_form").submit();
+};
+
+update_time_remaining = function(percent_complete) {
+ var minutes_remaining, now, period, total_seconds_remaining;
+ now = new Date();
+ period = now.getTime() - root.start_time;
+ console.log("period is:", period);
+ if (period > 8000) {
+ total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+ minutes_remaining = Math.round(total_seconds_remaining / 60);
+ if (minutes_remaining < 3) {
+ return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+ } else {
+ return $('#time_remaining').text(minutes_remaining + " minutes remaining");
}
+ }
+};
+
+get_progress = function() {
+ var params, params_str, temp_uuid, url;
+ console.log("temp_uuid:", $("#temp_uuid").val());
+ temp_uuid = $("#temp_uuid").val();
+ params = {
+ key: temp_uuid
};
-
- get_progress = function() {
- var params, params_str, temp_uuid, url;
- console.log("temp_uuid:", $("#temp_uuid").val());
- temp_uuid = $("#temp_uuid").val();
- params = {
- key: temp_uuid
- };
- params_str = $.param(params);
- url = "/get_temp_data?" + params_str;
- console.log("url:", url);
- $.ajax({
- type: "GET",
- url: url,
- success: (function(_this) {
- return function(progress_data) {
- var percent_complete;
- percent_complete = progress_data['percent_complete'];
- console.log("in get_progress data:", progress_data);
- $('#marker_regression_progress').css("width", percent_complete + "%");
- if (root.start_time) {
- if (!isNaN(percent_complete)) {
- return update_time_remaining(percent_complete);
- }
- } else {
- return root.start_time = new Date().getTime();
+ params_str = $.param(params);
+ url = "/get_temp_data?" + params_str;
+ console.log("url:", url);
+ $.ajax({
+ type: "GET",
+ url: url,
+ success: (function(_this) {
+ return function(progress_data) {
+ var percent_complete;
+ percent_complete = progress_data['percent_complete'];
+ console.log("in get_progress data:", progress_data);
+ $('#marker_regression_progress').css("width", percent_complete + "%");
+ if (root.start_time) {
+ if (!isNaN(percent_complete)) {
+ return update_time_remaining(percent_complete);
}
- };
- })(this)
- });
- return false;
- };
-
- block_outliers = function() {
- return $('.outlier').each((function(_this) {
- return function(_index, element) {
- return $(element).find('.trait_value_input').val('x');
+ } else {
+ return root.start_time = new Date().getTime();
+ }
};
- })(this));
- };
-
- do_ajax_post = function(url, form_data) {
- $.ajax({
- type: "POST",
- url: url,
- data: form_data,
- error: (function(_this) {
- return function(xhr, ajaxOptions, thrownError) {
- alert("Sorry, an error occurred");
- console.log(xhr);
- clearInterval(_this.my_timer);
- $('#progress_bar_container').modal('hide');
- return $("body").html("We got an error.");
- };
- })(this),
- success: (function(_this) {
- return function(data) {
- clearInterval(_this.my_timer);
- $('#progress_bar_container').modal('hide');
- return open_mapping_results(data);
- };
- })(this)
- });
- console.log("settingInterval");
- this.my_timer = setInterval(get_progress, 1000);
- return false;
- };
-
- open_mapping_results = function(data) {
- return $.colorbox({
- html: data,
- href: "#mapping_results_holder",
- height: "90%",
- width: "90%",
- onComplete: (function(_this) {
- return function() {
- return root.create_manhattan_plot();
- };
- })(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>');
- };
-
- $("#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));
-
- $('#suggestive').hide();
-
- $('input[name=display_all]').change((function(_this) {
- return function() {
- console.log("check");
- if ($('input[name=display_all]:checked').val() === "False") {
- return $('#suggestive').show();
- } else {
- return $('#suggestive').hide();
- }
- };
- })(this));
-
- $("#pylmm_compute").on("click", (function(_this) {
- return function() {
- var form_data, url;
- $("#progress_bar_container").modal();
- url = "/marker_regression";
- $('input[name=method]').val("pylmm");
- $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
- };
- })(this));
+ })(this)
+ });
+ return false;
+};
- $("#rqtl_geno_compute").on("click", (function(_this) {
- return function() {
- var form_data, url;
- $("#progress_bar_container").modal();
- url = "/marker_regression";
- $('input[name=method]').val("rqtl_geno");
- $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
- $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
+block_outliers = function() {
+ return $('.outlier').each((function(_this) {
+ return function(_index, element) {
+ return $(element).find('.trait_value_input').val('x');
};
})(this));
+};
+
+do_ajax_post = function(url, form_data) {
+ $.ajax({
+ type: "POST",
+ url: url,
+ data: form_data,
+ error: (function(_this) {
+ return function(xhr, ajaxOptions, thrownError) {
+ alert("Sorry, an error occurred");
+ console.log(xhr);
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html("We got an error.");
+ };
+ })(this),
+ success: (function(_this) {
+ return function(data) {
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return open_mapping_results(data);
+ };
+ })(this)
+ });
+ console.log("settingInterval");
+ this.my_timer = setInterval(get_progress, 1000);
+ return false;
+};
+
+open_mapping_results = function(data) {
+ return $.colorbox({
+ html: data,
+ href: "#mapping_results_holder",
+ height: "90%",
+ width: "90%",
+ onComplete: (function(_this) {
+ return function() {
+ return root.create_lod_chart();
+ };
+ })(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");
- $('input[name=maf]').val($('input[name=maf_plink]').val());
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
- };
- })(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>');
+};
- $("#gemma_compute").on("click", (function(_this) {
- return function() {
- var form_data, url;
- console.log("RUNNING GEMMA");
- $("#static_progress_bar_container").modal();
- url = "/marker_regression";
- $('input[name=method]').val("gemma");
- $('input[name=maf]').val($('input[name=maf_gemma]').val());
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return do_ajax_post(url, form_data);
- };
- })(this));
+$('#suggestive').hide();
- composite_mapping_fields = function() {
- return $(".composite_fields").toggle();
+$('input[name=display_all]').change((function(_this) {
+ return function() {
+ console.log("check");
+ if ($('input[name=display_all]:checked').val() === "False") {
+ return $('#suggestive').show();
+ } else {
+ return $('#suggestive').hide();
+ }
};
-
- mapping_method_fields = function() {
- return $(".mapping_method_fields").toggle();
+})(this));
+
+$("#pylmm_compute").on("click", (function(_this) {
+ return function() {
+ var form_data, url;
+ $("#progress_bar_container").modal();
+ url = "/marker_regression";
+ $('input[name=method]').val("pylmm");
+ $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return do_ajax_post(url, form_data);
+ };
+})(this));
+
+$("#rqtl_geno_compute").on("click", (function(_this) {
+ return function() {
+ var form_data, url;
+ $("#progress_bar_container").modal();
+ url = "/marker_regression";
+ $('input[name=method]').val("rqtl_geno");
+ $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+ $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+ $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return do_ajax_post(url, form_data);
+ };
+})(this));
+
+$("#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");
+ $('input[name=maf]').val($('input[name=maf_plink]').val());
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return do_ajax_post(url, form_data);
+ };
+})(this));
+
+$("#gemma_compute").on("click", (function(_this) {
+ return function() {
+ var form_data, url;
+ console.log("RUNNING GEMMA");
+ $("#static_progress_bar_container").modal();
+ url = "/marker_regression";
+ $('input[name=method]').val("gemma");
+ $('input[name=maf]').val($('input[name=maf_gemma]').val());
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return do_ajax_post(url, form_data);
};
+})(this));
+
+$("#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));
- $("#use_composite_choice").change(composite_mapping_fields);
+composite_mapping_fields = function() {
+ return $(".composite_fields").toggle();
+};
- $("#mapping_method_choice").change(mapping_method_fields);
+mapping_method_fields = function() {
+ return $(".mapping_method_fields").toggle();
+};
- toggle_enable_disable = function(elem) {
- return $(elem).prop("disabled", !$(elem).prop("disabled"));
- };
+$("#use_composite_choice").change(composite_mapping_fields);
- $("#choose_closet_control").change(function() {
- return toggle_enable_disable("#control_locus");
- });
+$("#mapping_method_choice").change(mapping_method_fields);
- $("#display_all_lrs").change(function() {
- return toggle_enable_disable("#suggestive_lrs");
- });
+toggle_enable_disable = function(elem) {
+ return $(elem).prop("disabled", !$(elem).prop("disabled"));
+};
+
+$("#choose_closet_control").change(function() {
+ return toggle_enable_disable("#control_locus");
+});
-}).call(this);
+$("#display_all_lrs").change(function() {
+ return toggle_enable_disable("#suggestive_lrs");
+}); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
deleted file mode 100755
index b0866a35..00000000
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ /dev/null
@@ -1,117 +0,0 @@
-{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.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>
-
- <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/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/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.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/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/views.py b/wqflask/wqflask/views.py
index c16c22df..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
@@ -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