diff options
| -rw-r--r-- | wqflask/utility/tools.py | 18 | ||||
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/interval_mapping/interval_mapping.py | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.coffee | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.js | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.coffee | 1031 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.js | 54 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.coffee | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.js | 13 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee | 44 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 413 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/interval_mapping.html | 117 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/old_index_page.html | 320 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 6 |
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"> Databases marked with <b>**</b> - suffix are not public yet.<br> - 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"> Enter terms, genes, ID numbers in the - <b>Search</b> field.<br> - Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, - synap*).<br> - 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"> <input type= - "button" class="btn" value="Make Default" onclick= - "setDefault(this.form);"> <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> ______________________________________________________</p> - - <p style="font-size:13px;font-family:verdana;color:black"><b> Quick HELP - Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank" - class="fs14"><b>User's Guide</b></a></p> You can also use advanced - commands. Copy these simple examples<br> - 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> - </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 |