diff options
Diffstat (limited to 'wqflask')
20 files changed, 1234 insertions, 704 deletions
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 0433bf17..9b6b1b69 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -63,7 +63,14 @@ class Heatmap(object): self.all_sample_list = []
self.traits = []
+
+ chrnames = []
+ self.species = species.TheSpecies(dataset=self.trait_list[0][1])
+ for key in self.species.chromosomes.chromosomes.keys():
+ chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
+
for trait_db in self.trait_list:
+
this_trait = trait_db[0]
self.traits.append(this_trait.name)
this_sample_data = this_trait.data
@@ -91,7 +98,7 @@ class Heatmap(object): self.gen_reaper_results()
#self.gen_pylmm_results()
- chrnames = []
+ #chrnames = []
lodnames = []
chr_pos = []
pos = []
@@ -101,8 +108,9 @@ class Heatmap(object): lodnames.append(trait)
for marker in self.dataset.group.markers.markers:
- if marker['chr'] not in chrnames:
- chrnames.append(marker['chr'])
+ #if marker['chr'] not in chrnames:
+ # chr_ob = [marker['chr'], "filler"]
+ # chrnames.append(chr_ob)
chr_pos.append(marker['chr'])
pos.append(marker['Mb'])
markernames.append(marker['name'])
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py index 4ac7bde2..e70f11cb 100755 --- a/wqflask/wqflask/interval_mapping/interval_mapping.py +++ b/wqflask/wqflask/interval_mapping/interval_mapping.py @@ -169,7 +169,12 @@ class IntervalMapping(object): self.json_data['markernames'] = [] for qtl in reaper_results: reaper_locus = qtl.locus - self.json_data['chr'].append(reaper_locus.chr) + #if reaper_locus.chr == "20": + # print("changing to X") + # self.json_data['chr'].append("X") + #else: + # self.json_data['chr'].append(reaper_locus.chr) + ##self.json_data['chr'].append(reaper_locus.chr) self.json_data['pos'].append(reaper_locus.Mb) self.json_data['lod.hk'].append(qtl.lrs) self.json_data['markernames'].append(reaper_locus.name) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 648cb49b..59d87b36 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -12,6 +12,7 @@ import os import collections
import uuid
+import rpy2.robjects as robjects
import numpy as np
from scipy import linalg
@@ -60,13 +61,20 @@ class MarkerRegression(object): self.mapping_method = start_vars['method']
self.maf = start_vars['maf'] # Minor allele frequency
- print("self.maf:", self.maf)
+ #print("self.maf:", self.maf)
self.dataset.group.get_markers()
if self.mapping_method == "gemma":
qtl_results = self.run_gemma()
- elif self.mapping_method == "rqtl":
- qtl_results = self.run_rqtl()
+ elif self.mapping_method == "rqtl_plink":
+ qtl_results = self.run_rqtl_plink()
+ elif self.mapping_method == "rqtl_geno":
+ self.num_perm = start_vars['num_perm']
+ self.control = start_vars['control_marker']
+ self.control_db = start_vars['control_marker_db']
+ print("doing rqtl_geno")
+ qtl_results = self.run_rqtl_geno()
+ print("qtl_results:", qtl_results)
elif self.mapping_method == "plink":
qtl_results = self.run_plink()
#print("qtl_results:", pf(qtl_results))
@@ -79,12 +87,14 @@ class MarkerRegression(object): self.lod_cutoff = 2
self.filtered_markers = []
+ highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
for marker in qtl_results:
if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ highest_chr = marker['chr']
if 'lod_score' in marker:
self.filtered_markers.append(marker)
-
self.json_data['chr'] = []
self.json_data['pos'] = []
self.json_data['lod.hk'] = []
@@ -94,7 +104,11 @@ class MarkerRegression(object): self.qtl_results = []
for qtl in self.filtered_markers:
print("lod score is:", qtl['lod_score'])
- self.json_data['chr'].append(str(qtl['chr']))
+ if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+ print("changing to X")
+ self.json_data['chr'].append("X")
+ else:
+ self.json_data['chr'].append(str(qtl['chr']))
self.json_data['pos'].append(qtl['Mb'])
self.json_data['lod.hk'].append(str(qtl['lod_score']))
self.json_data['markernames'].append(qtl['name'])
@@ -104,9 +118,10 @@ class MarkerRegression(object): self.json_data['chrnames'] = []
for key in self.species.chromosomes.chromosomes.keys():
self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
-
chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+ print("json_data:", self.json_data)
+
self.js_data = dict(
json_data = self.json_data,
this_trait = self.this_trait.name,
@@ -186,7 +201,7 @@ class MarkerRegression(object): #
#
- def run_rqtl(self):
+ def run_rqtl_plink(self):
os.chdir("/home/zas1024/plink")
output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
@@ -199,6 +214,103 @@ class MarkerRegression(object): count, p_values = self.parse_rqtl_output(plink_output_filename)
+ def run_rqtl_geno(self):
+ robjects.packages.importr("qtl")
+ robjects.r('the_cross <- read.cross(format="csvr", dir="/home/zas1024/PLINK2RQTL/test", file="BXD.csvr")')
+ robjects.r('the_cross <- calc.genoprob(the_cross)')
+ pheno_as_string = "c("
+ #for i, val in enumerate(self.vals):
+ # if val == "x":
+ # new_val == "NULL"
+ # else:
+ # new_val = val
+ # if i < (len(self.vals) - 1):
+ # pheno_as_string += str(new_val) + ","
+ # else: pheno_as_string += str(new_val)
+ null_pos = []
+ for i, val in enumerate(self.vals):
+ if val == "x":
+ null_pos.append(i)
+ if i < (len(self.vals) - 1):
+ pheno_as_string += "NA,"
+ else:
+ pheno_as_string += "NA"
+ else:
+ if i < (len(self.vals) - 1):
+ pheno_as_string += str(val) + ","
+ else:
+ pheno_as_string += str(val)
+
+ pheno_as_string += ")"
+
+ print("self.control:", self.control)
+ if self.control != "":
+ print("self.control_db:", self.control_db)
+ control_trait = GeneralTrait(name=str(self.control), dataset_name=str(self.control_db))
+ control_vals = []
+ for sample in self.dataset.group.samplelist:
+ if sample in control_trait.data:
+ control_vals.append(control_trait.data[sample].value)
+ else:
+ control_vals.append("x")
+ print("control_vals:", control_vals)
+ control_as_string = "c("
+ for j, val2 in enumerate(control_vals):
+ if val2 == "x":
+ if j < (len(control_vals) - 1):
+ control_as_string += "NA,"
+ else:
+ control_as_string += "NA"
+ else:
+ if j < (len(control_vals) - 1):
+ control_as_string += str(val2) + ","
+ else:
+ control_as_string += str(val2)
+ #if i < (len(control_vals) - 1):
+ # control_as_string += str(new_val2) + ","
+ #else:
+ # control_as_string += str(new_val2)
+ control_as_string += ")"
+ print("control_as_string:", control_as_string)
+
+ r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+', addcovar='+control_as_string+')'
+
+ if self.num_perm > 0:
+ thresholds = robjects.r(r_string)
+ print("thresholds:", thresholds)
+
+ #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', addcovar='+control_as_string+')'
+ print("r_string:", r_string)
+ else:
+ #r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+', n.perm='+self.num_perm+')'
+ r_string = 'scanone(the_cross, pheno.col='+pheno_as_string+')'
+
+ print("r_string:", r_string)
+ result_data_frame = robjects.r(r_string)
+ #print("results:", result_data_frame)
+
+ qtl_results = self.process_rqtl_results(result_data_frame)
+
+ return qtl_results
+
+ def process_rqtl_results(self, result):
+ qtl_results = []
+
+ output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+ print("output", output)
+
+
+ for i, line in enumerate(result.iter_row()):
+ marker = {}
+ marker['name'] = result.rownames[i]
+ marker['chr'] = output[i][0]
+ marker['Mb'] = output[i][1]
+ marker['lod_score'] = output[i][2]
+
+ qtl_results.append(marker)
+
+ return qtl_results
+
def run_plink(self):
os.chdir("/home/zas1024/plink")
@@ -271,6 +383,41 @@ class MarkerRegression(object): output_file.write(new_line)
output_file.close()
+
+ def gen_pheno_txt_file_rqtl(self, pheno_filename = ''):
+ ped_sample_list = self.get_samples_from_ped_file()
+ output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")
+ header = 'FID\tIID\t%s\n' % self.this_trait.name
+ output_file.write(header)
+
+ new_value_list = []
+
+ #if valueDict does not include some strain, value will be set to -9999 as missing value
+ for i, sample in enumerate(ped_sample_list):
+ try:
+ value = self.vals[i]
+ value = str(value).replace('value=','')
+ value = value.strip()
+ except:
+ value = -9999
+
+ new_value_list.append(value)
+
+
+ new_line = ''
+ for i, sample in enumerate(ped_sample_list):
+ j = i+1
+ value = new_value_list[i]
+ new_line += '%s\t%s\t%s\n'%(sample, sample, value)
+
+ if j%1000 == 0:
+ output_file.write(newLine)
+ new_line = ''
+
+ if new_line:
+ output_file.write(new_line)
+
+ output_file.close()
# get strain name from ped file in order
def get_samples_from_ped_file(self):
@@ -292,42 +439,6 @@ class MarkerRegression(object): return sample_list
- ################################################################
- # Generate Chr list, Chr OrderId and Retrieve Length Information
- ################################################################
- #def getChrNameOrderIdLength(self,RISet=''):
- # try:
- # query = """
- # Select
- # Chr_Length.Name,Chr_Length.OrderId,Length from Chr_Length, InbredSet
- # where
- # Chr_Length.SpeciesId = InbredSet.SpeciesId AND
- # InbredSet.Name = '%s'
- # Order by OrderId
- # """ % (self.dataset.group.name)
- # results =g.db.execute(query).fetchall()
- # ChrList=[]
- # ChrLengthMbList=[]
- # ChrNameOrderIdDict={}
- # ChrOrderIdNameDict={}
- #
- # for item in results:
- # ChrList.append(item[0])
- # ChrNameOrderIdDict[item[0]]=item[1] # key is chr name, value is orderId
- # ChrOrderIdNameDict[item[1]]=item[0] # key is orderId, value is chr name
- # ChrLengthMbList.append(item[2])
- #
- # except:
- # ChrList=[]
- # ChrNameOrderIdDict={}
- # ChrLengthMbList=[]
- #
- # return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList
-
-
- def parse_rqtl_output(self, output_filename):
- return True
-
def parse_plink_output(self, output_filename):
plink_results={}
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 3034dec8..a4a24fd4 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -90,6 +90,10 @@ class ShowTrait(object): self.build_correlation_tools(self.this_trait) + #Get nearest marker for composite mapping + self.nearest_marker, self.nearest_marker_db = get_nearest_marker(self.this_trait) + + self.make_sample_lists(self.this_trait) if self.dataset.group.allsamples: @@ -101,6 +105,9 @@ class ShowTrait(object): hddn['method'] = "pylmm" hddn['mapping_display_all'] = True hddn['suggestive'] = 0 + hddn['num_perm'] = 0 + hddn['control_marker'] = self.nearest_marker + hddn['control_marker_db'] = self.nearest_marker_db hddn['maf'] = 0.01 hddn['compare_traits'] = [] @@ -1267,3 +1274,21 @@ def get_samplelist_from_trait_data(this_trait, all_samples_ordered): other_sample_names.append(sample) return other_sample_names, all_samples_ordered + +def get_nearest_marker(this_trait): + this_chr = this_trait.chr + this_mb = this_trait.mb + query = """SELECT ProbeSet.Name, ProbeSetFreeze.Name + FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze + WHERE ProbeSet.Chr = '{}' AND + ProbeSet.Id=ProbeSetXRef.ProbeSetId AND + ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id AND + ProbeSetFreeze.Name='{}' + ORDER BY ABS( Mb - {}) LIMIT 2""".format(this_trait.chr, this_trait.dataset.name, this_trait.mb) + print("query:", query) + + result = g.db.execute(query).fetchall() + + return result[1][0], result[1][1] + + diff --git a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee index 2b4b20c8..c8e1b318 100644 --- a/wqflask/wqflask/static/new/javascript/create_interval_map.coffee +++ b/wqflask/wqflask/static/new/javascript/create_interval_map.coffee @@ -78,38 +78,3 @@ $("#export_pdf").click => form.find("#data").val(svg_xml)
form.find("#filename").val(filename)
form.submit()
-
-# two LOD charts within one SVG
-#d3.json "data.json", (data) ->
-# mychart_em = lodchart().lodvarname("lod.em")
-# .height(h)
-# .width(w)
-# .margin(margin)
-# .ylab("LOD score (by EM)")
-# .pointsize(1)
-# .nyticks(9)
-# .title("Standard interval mapping")
-# mychart_hk = lodchart().lodvarname("lod.hk")
-# .height(h)
-# .width(w)
-# .margin(margin)
-# .ylab("LOD score (by H-K)")
-# .linecolor("Crimson")
-# .yticks([0, 1, 2, 4, 6, 8])
-# .title("Haley-Knott regression")
-#
-# svg = d3.select("div#bottomchart")
-# .append("svg")
-# .attr("height", totalh)
-# .attr("width", totalw)
-#
-# chart1 = svg.append("g").attr("id", "chart1")
-#
-# chart2 = svg.append("g").attr("id", "chart2")
-# .attr("transform", "translate(0, #{halfh})")
-#
-# chart1.datum(data)
-# .call(mychart_em)
-#
-# chart2.datum(data)
-# .call(mychart_hk)
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee index 6aa301a0..7831b2d4 100644 --- a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee +++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.coffee @@ -90,8 +90,8 @@ iplotMScanone_noeff = (lod_data, times, chartOpts) -> lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves")
for chr in lod_data.chrnames
lodchart_curves.append("path")
- .datum(lod_data.posByChr[chr])
- .attr("d", lodcurve(chr, lodcolumn))
+ .datum(lod_data.posByChr[chr[0]])
+ .attr("d", lodcurve(chr[0], lodcolumn))
.attr("stroke", linecolor)
.attr("fill", "none")
.attr("stroke-width", linewidth)
diff --git a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js index e539d353..8f6787c3 100644 --- a/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js +++ b/wqflask/wqflask/static/new/javascript/iplotMScanone_noeff.js @@ -68,7 +68,7 @@ iplotMScanone_noeff = function(lod_data, times, chartOpts) { _results = []; for (_i = 0, _len = _ref21.length; _i < _len; _i++) { chr = _ref21[_i]; - _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr]).attr("d", lodcurve(chr, lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none")); + _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none")); } return _results; }; diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee index c9b277cc..dd2ad31d 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee @@ -39,7 +39,7 @@ lodchart = () -> chart = (selection) ->
selection.each (data) ->
- console.log("data:", data)
+ #console.log("data:", data)
lodvarname = lodvarname ? data.lodnames[0]
data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values
@@ -142,8 +142,8 @@ lodchart = () -> redraw_plot = (chr_ob) ->
- console.log("chr_name is:", chr_ob[0])
- console.log("chr_length is:", chr_ob[1])
+ #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_Interval_Map(600, 1200, chr_ob)
@@ -254,35 +254,34 @@ lodchart = () -> .x((d) -> xscale[chr](d))
.y((d,i) -> yscale(data.lodByChr[chr][i][lodcolumn]))
- #if data['additive'].length > 0
- if 'additive' of data
- additivecurve = (chr, lodcolumn) ->
- d3.svg.line()
- .x((d) -> xscale[chr](d))
- .y((d,i) -> additive_yscale(data.additiveByChr[chr][i][lodcolumn]))
+ #if 'additive' of data
+ # 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")
+ 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 data['additive'].length > 0
- if 'additive' of data
- 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")
-
+ ##if data['additive'].length > 0
+ #if 'additive' of data
+ # 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
if pointsize > 0
markerpoints = g.append("g").attr("id", "markerpoints_visible")
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index 0f91fc71..49ca962f 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -51,8 +51,7 @@ 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, _len, _ref; - console.log("data:", data); + var additive_yaxis, chr, curves, g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis, _i, _len, _ref; lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; data[lodvarname] = (function() { var _i, _len, _ref, _results; @@ -128,8 +127,6 @@ lodchart = function() { 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 = function(chr_ob) { var chr_plot; - 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>'); return chr_plot = new Chr_Interval_Map(600, 1200, chr_ob); @@ -185,22 +182,11 @@ lodchart = function() { return yscale(data.lodByChr[chr][i][lodcolumn]); }); }; - if ('additive' in data) { - additivecurve = function(chr, lodcolumn) { - return d3.svg.line().x(function(d) { - return xscale[chr](d); - }).y(function(d, i) { - return additive_yscale(data.additiveByChr[chr][i][lodcolumn]); - }); - }; - } curves = g.append("g").attr("id", "curves"); - if ('additive' in data) { - _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", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); - } + _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"); } if (pointsize > 0) { markerpoints = g.append("g").attr("id", "markerpoints_visible"); diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee index 6ffaefeb..5f3716bc 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.coffee +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.coffee @@ -33,10 +33,14 @@ lodheatmap = () -> rectHeight = yscale(0)-yscale(1)
xLR = {}
- console.log("data.chrnames:", data.chrnames)
+ #console.log("data.posByChr:", data.posByChr["2"])
+ #console.log("data.chrnames:", data.chrnames)
for chr in data.chrnames
- console.log("chr is:", chr)
- xLR[chr] = getLeftRight(data.posByChr[chr])
+ #console.log("posByChr:", data.posByChr)
+ #console.log("chr is:", chr)
+ xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]])
+
+ #console.log("xLR:", xLR)
# z-axis (color) limits; if not provided, make symmetric about 0
zmin = 0
@@ -54,7 +58,9 @@ lodheatmap = () -> zthresh = zthresh ? zmin - 1
data.cells = []
- for chr in data.chrnames
+ for chr_ob in data.chrnames
+ chr = chr_ob[0]
+ #console.log("xLR[chr]:", xLR[chr])
for pos, i in data.posByChr[chr]
for lod,j in data.lodByChr[chr][i]
if lod >= zthresh or lod <= -zthresh
@@ -78,7 +84,7 @@ lodheatmap = () -> .data(data.chrnames)
.enter()
.append("rect")
- .attr("id", (d) -> "box#{d}")
+ .attr("id", (d) -> "box#{d[0]}")
.attr("x", (d,i) -> data.chrStart[i])
.attr("y", (d) -> margin.top)
.attr("height", height)
@@ -101,7 +107,7 @@ lodheatmap = () -> .append("text")
.attr("x", (d,i) -> (data.chrStart[i] + data.chrEnd[i])/2)
.attr("y", margin.top+height+axispos.xlabel)
- .text((d) -> d)
+ .text((d) -> d[0])
xaxis.append("text").attr("class", "title")
.attr("x", margin.left+width/2)
.attr("y", margin.top+height+axispos.xtitle)
diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js index b009b4cd..5ea16590 100644 --- a/wqflask/wqflask/static/new/javascript/lodheatmap.js +++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js @@ -33,7 +33,7 @@ lodheatmap = function() { cellSelect = null; chart = function(selection) { return selection.each(function(data) { - var cells, celltip, chr, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4; + var cells, celltip, chr, chr_ob, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4; data = reorgLodData(data); data = chrscales(data, width, chrGap, margin.left, true); xscale = data.xscale; @@ -41,12 +41,10 @@ lodheatmap = function() { yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]); rectHeight = yscale(0) - yscale(1); xLR = {}; - console.log("data.chrnames:", data.chrnames); _ref = data.chrnames; for (_i = 0, _len = _ref.length; _i < _len; _i++) { chr = _ref[_i]; - console.log("chr is:", chr); - xLR[chr] = getLeftRight(data.posByChr[chr]); + xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); } zmin = 0; zmax = 0; @@ -73,7 +71,8 @@ lodheatmap = function() { data.cells = []; _ref2 = data.chrnames; for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { - chr = _ref2[_k]; + chr_ob = _ref2[_k]; + chr = chr_ob[0]; _ref3 = data.posByChr[chr]; for (i = _l = 0, _len3 = _ref3.length; _l < _len3; i = ++_l) { pos = _ref3[i]; @@ -98,7 +97,7 @@ lodheatmap = function() { svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); g = svg.select("g"); g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { - return "box" + d; + return "box" + d[0]; }).attr("x", function(d, i) { return data.chrStart[i]; }).attr("y", function(d) { @@ -111,7 +110,7 @@ lodheatmap = function() { xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("x", function(d, i) { return (data.chrStart[i] + data.chrEnd[i]) / 2; }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { - return d; + return d[0]; }); xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee index 37226b8a..cc087493 100644 --- a/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee +++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.coffee @@ -32,8 +32,7 @@ lodchart = () -> ## the main function
chart = (selection) ->
selection.each (data) ->
-
- console.log("data:", data)
+
lodvarname = lodvarname ? data.lodnames[0]
data[lodvarname] = (Math.abs(x) for x in data[lodvarname]) # take absolute values
@@ -68,6 +67,8 @@ lodchart = () -> # if yticks not provided, use nyticks to choose pretty ones
yticks = yticks ? yscale.ticks(nyticks)
+ console.log("data:", data)
+
# reorganize lod,pos by chromosomes
data = reorgLodData(data, lodvarname)
@@ -206,7 +207,7 @@ lodchart = () -> markertip = d3.tip()
.attr('class', 'd3-tip')
.html((d) ->
- [d.name, " LRS = #{d3.format('.2f')(d.lod)}"])
+ [d.name, " LOD = #{d3.format('.2f')(d.lod)}"])
.direction("e")
.offset([0,10])
svg.call(markertip)
@@ -374,90 +375,90 @@ lodchart = () -> # reorganize lod/pos by chromosome
# lodvarname==null -> case for multiple LOD columns (lodheatmap)
# lodvarname provided -> case for one LOD column (lodchart)
-reorgLodData = (data, lodvarname=null) ->
- data.posByChr = {}
- data.lodByChr = {}
-
- for chr,i in data.chrnames
- data.posByChr[chr[0]] = []
- data.lodByChr[chr[0]] = []
- for pos, j in data.pos
- if data.chr[j] == 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 lodvarname?
- data.markers = []
- for marker,i in data.markernames
- if marker != ""
- data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
-
- data
+#reorgLodData = (data, lodvarname=null) ->
+# data.posByChr = {}
+# data.lodByChr = {}
+#
+# for chr,i in data.chrnames
+# data.posByChr[chr[0]] = []
+# data.lodByChr[chr[0]] = []
+# for pos, j in data.pos
+# if data.chr[j] == 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 lodvarname?
+# data.markers = []
+# for marker,i in data.markernames
+# if marker != ""
+# data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
+#
+# data
# calculate chromosome start/end + scales, for heat map
-chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
- # start and end of chromosome positions
- chrStart = []
- chrEnd = []
- chrLength = []
- totalChrLength = 0
- maxd = 0
- for chr in data.chrnames
- d = maxdiff(data.posByChr[chr[0]])
- maxd = d if d > maxd
-
- rng = d3.extent(data.posByChr[chr[0]])
- chrStart.push(rng[0])
- chrEnd.push(rng[1])
- L = rng[1] - rng[0]
- chrLength.push(L)
- totalChrLength += L
-
- # adjust lengths for heatmap
- if pad4heatmap
- data.recwidth = maxd
- chrStart = chrStart.map (x) -> x-maxd/2
- chrEnd = chrEnd.map (x) -> x+maxd/2
- chrLength = chrLength.map (x) -> x+maxd
- totalChrLength += (chrLength.length*maxd)
-
- # break up x axis into chromosomes by length, with gaps
- data.chrStart = []
- data.chrEnd = []
- cur = leftMargin
- cur += chrGap/2 unless pad4heatmap
- data.xscale = {}
- for chr,i in data.chrnames
- data.chrStart.push(cur)
- w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
- data.chrEnd.push(cur + w)
- cur = data.chrEnd[i] + chrGap
- # x-axis scales, by chromosome
- data.xscale[chr[0]] = d3.scale.linear()
- .domain([chrStart[i], chrEnd[i]])
- .range([data.chrStart[i], data.chrEnd[i]])
-
- # return data with new stuff added
- data
-
-# maximum difference between adjacent values in a vector
-maxdiff = (x) ->
- return null if x.length < 2
- result = x[1] - x[0]
- return result if x.length < 3
- for i in [2...x.length]
- d = x[i] - x[i-1]
- result = d if d > result
- result
-
-# determine rounding of axis labels
-formatAxis = (d) ->
- d = d[1] - d[0]
- ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
- ndig = 0 if ndig > 0
- ndig = Math.abs(ndig)
- d3.format(".#{ndig}f")
+#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
+# # start and end of chromosome positions
+# chrStart = []
+# chrEnd = []
+# chrLength = []
+# totalChrLength = 0
+# maxd = 0
+# for chr in data.chrnames
+# d = maxdiff(data.posByChr[chr[0]])
+# maxd = d if d > maxd
+#
+# rng = d3.extent(data.posByChr[chr[0]])
+# chrStart.push(rng[0])
+# chrEnd.push(rng[1])
+# L = rng[1] - rng[0]
+# chrLength.push(L)
+# totalChrLength += L
+#
+# # adjust lengths for heatmap
+# if pad4heatmap
+# data.recwidth = maxd
+# chrStart = chrStart.map (x) -> x-maxd/2
+# chrEnd = chrEnd.map (x) -> x+maxd/2
+# chrLength = chrLength.map (x) -> x+maxd
+# totalChrLength += (chrLength.length*maxd)
+#
+# # break up x axis into chromosomes by length, with gaps
+# data.chrStart = []
+# data.chrEnd = []
+# cur = leftMargin
+# cur += chrGap/2 unless pad4heatmap
+# data.xscale = {}
+# for chr,i in data.chrnames
+# data.chrStart.push(cur)
+# w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
+# data.chrEnd.push(cur + w)
+# cur = data.chrEnd[i] + chrGap
+# # x-axis scales, by chromosome
+# data.xscale[chr[0]] = d3.scale.linear()
+# .domain([chrStart[i], chrEnd[i]])
+# .range([data.chrStart[i], data.chrEnd[i]])
+#
+# # return data with new stuff added
+# data
+#
+## maximum difference between adjacent values in a vector
+#maxdiff = (x) ->
+# return null if x.length < 2
+# result = x[1] - x[0]
+# return result if x.length < 3
+# for i in [2...x.length]
+# d = x[i] - x[i-1]
+# result = d if d > result
+# result
+#
+## determine rounding of axis labels
+#formatAxis = (d) ->
+# d = d[1] - d[0]
+# ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
+# ndig = 0 if ndig > 0
+# ndig = Math.abs(ndig)
+# d3.format(".#{ndig}f")
diff --git a/wqflask/wqflask/static/new/javascript/manhattan_plot.js b/wqflask/wqflask/static/new/javascript/manhattan_plot.js index 203f3a1b..9618acb2 100644 --- a/wqflask/wqflask/static/new/javascript/manhattan_plot.js +++ b/wqflask/wqflask/static/new/javascript/manhattan_plot.js @@ -1,5 +1,5 @@ // Generated by CoffeeScript 1.7.1 -var chrscales, formatAxis, lodchart, maxdiff, reorgLodData; +var lodchart; lodchart = function() { var axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointhover, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; @@ -46,7 +46,6 @@ lodchart = function() { chart = function(selection) { return selection.each(function(data) { var g, gEnter, hiddenpoints, lodvarnum, markerpoints, markertip, redraw_plot, svg, titlegrp, x, xaxis, yaxis; - console.log("data:", data); lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; data[lodvarname] = (function() { var _i, _len, _ref, _results; @@ -67,6 +66,7 @@ lodchart = function() { 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]); yticks = yticks != null ? yticks : yscale.ticks(nyticks); + console.log("data:", data); data = reorgLodData(data, lodvarname); data = chrscales(data, width, chrGap, margin.left, pad4heatmap); xscale = data.xscale; @@ -138,7 +138,7 @@ lodchart = function() { if (pointsAtMarkers) { hiddenpoints = g.append("g").attr("id", "markerpoints_hidden"); markertip = d3.tip().attr('class', 'd3-tip').html(function(d) { - return [d.name, " LRS = " + (d3.format('.2f')(d.lod))]; + return [d.name, " LOD = " + (d3.format('.2f')(d.lod))]; }).direction("e").offset([0, 10]); svg.call(markertip); return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) { @@ -339,137 +339,3 @@ lodchart = function() { }; return chart; }; - -reorgLodData = function(data, lodvarname) { - var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2; - if (lodvarname == null) { - lodvarname = null; - } - data.posByChr = {}; - data.lodByChr = {}; - _ref = data.chrnames; - for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { - chr = _ref[i]; - data.posByChr[chr[0]] = []; - data.lodByChr[chr[0]] = []; - _ref1 = data.pos; - for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) { - pos = _ref1[j]; - if (data.chr[j] === chr[0]) { - data.posByChr[chr[0]].push(pos); - if (!Array.isArray(data.lodnames)) { - data.lodnames = [data.lodnames]; - } - lodval = (function() { - var _k, _len2, _ref2, _results; - _ref2 = data.lodnames; - _results = []; - for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { - lodcolumn = _ref2[_k]; - _results.push(data[lodcolumn][j]); - } - return _results; - })(); - data.lodByChr[chr[0]].push(lodval); - } - } - } - if (lodvarname != null) { - data.markers = []; - _ref2 = data.markernames; - for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) { - marker = _ref2[i]; - if (marker !== "") { - data.markers.push({ - name: marker, - chr: data.chr[i], - pos: data.pos[i], - lod: data[lodvarname][i] - }); - } - } - } - return data; -}; - -chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { - var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; - chrStart = []; - chrEnd = []; - chrLength = []; - totalChrLength = 0; - maxd = 0; - _ref = data.chrnames; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - chr = _ref[_i]; - d = maxdiff(data.posByChr[chr[0]]); - 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]; - chrLength.push(L); - totalChrLength += L; - } - if (pad4heatmap) { - data.recwidth = maxd; - chrStart = chrStart.map(function(x) { - return x - maxd / 2; - }); - chrEnd = chrEnd.map(function(x) { - return x + maxd / 2; - }); - chrLength = chrLength.map(function(x) { - return x + maxd; - }); - totalChrLength += chrLength.length * maxd; - } - data.chrStart = []; - data.chrEnd = []; - cur = leftMargin; - if (!pad4heatmap) { - cur += chrGap / 2; - } - data.xscale = {}; - _ref1 = data.chrnames; - for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) { - chr = _ref1[i]; - data.chrStart.push(cur); - w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]); - data.chrEnd.push(cur + w); - cur = data.chrEnd[i] + chrGap; - data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); - } - return data; -}; - -maxdiff = function(x) { - var d, i, result, _i, _ref; - if (x.length < 2) { - return null; - } - result = x[1] - x[0]; - if (x.length < 3) { - return result; - } - for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) { - d = x[i] - x[i - 1]; - if (d > result) { - result = d; - } - } - return result; -}; - -formatAxis = function(d) { - var ndig; - d = d[1] - d[0]; - ndig = Math.floor(Math.log(d % 10) / Math.log(10)); - if (ndig > 0) { - ndig = 0; - } - ndig = Math.abs(ndig); - return d3.format("." + ndig + "f"); -}; diff --git a/wqflask/wqflask/static/new/javascript/panelutil.coffee b/wqflask/wqflask/static/new/javascript/panelutil.coffee new file mode 100644 index 00000000..d1eb83e5 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/panelutil.coffee @@ -0,0 +1,357 @@ +# A variety of utility functions used by the different panel functions
+
+# determine rounding of axis labels
+formatAxis = (d, extra_digits=0) ->
+ d = d[1] - d[0]
+ ndig = Math.floor( Math.log(d % 10) / Math.log(10) )
+ ndig = 0 if ndig > 0
+ ndig = Math.abs(ndig) + extra_digits
+ d3.format(".#{ndig}f")
+
+# unique values of array (ignore nulls)
+unique = (x) ->
+ output = {}
+ output[v] = v for v in x when v
+ output[v] for v of output
+
+# Pull out a variable (column) from a two-dimensional array
+pullVarAsArray = (data, variable) ->
+ v = []
+ for i of data
+ v = v.concat data[i][variable]
+ v
+
+
+# reorganize lod/pos by chromosome
+# lodvarname==null -> case for multiple LOD columns (lodheatmap)
+# lodvarname provided -> case for one LOD column (lodchart)
+reorgLodData = (data, lodvarname=null) ->
+ data.posByChr = {}
+ 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)
+
+ #console.log("data.posByChr:", data.posByChr)
+
+ if lodvarname?
+ data.markers = []
+ for marker,i in data.markernames
+ if marker != ""
+ data.markers.push({name:marker, chr:data.chr[i], pos:data.pos[i], lod:data[lodvarname][i]})
+
+ data
+
+# calculate chromosome start/end + scales, for heat map
+chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
+ # start and end of chromosome positions
+ chrStart = []
+ chrEnd = []
+ chrLength = []
+ totalChrLength = 0
+ maxd = 0
+ for chr in data.chrnames
+ d = maxdiff(data.posByChr[chr[0]])
+ maxd = d if d > maxd
+
+ rng = d3.extent(data.posByChr[chr[0]])
+ chrStart.push(rng[0])
+ chrEnd.push(rng[1])
+ L = rng[1] - rng[0]
+ chrLength.push(L)
+ totalChrLength += L
+
+ # adjust lengths for heatmap
+ if pad4heatmap
+ data.recwidth = maxd
+ chrStart = chrStart.map (x) -> x-maxd/2
+ chrEnd = chrEnd.map (x) -> x+maxd/2
+ chrLength = chrLength.map (x) -> x+maxd
+ totalChrLength += (chrLength.length*maxd)
+
+ # break up x axis into chromosomes by length, with gaps
+ data.chrStart = []
+ data.chrEnd = []
+ cur = leftMargin
+ cur += chrGap/2 unless pad4heatmap
+ data.xscale = {}
+ for chr,i in data.chrnames
+ data.chrStart.push(cur)
+ w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
+ data.chrEnd.push(cur + w)
+ cur = data.chrEnd[i] + chrGap
+ # x-axis scales, by chromosome
+ data.xscale[chr[0]] = d3.scale.linear()
+ .domain([chrStart[i], chrEnd[i]])
+ .range([data.chrStart[i], data.chrEnd[i]])
+
+ # return data with new stuff added
+ data
+
+
+# reorganize lod/pos by chromosome
+# lodvarname==null -> case for multiple LOD columns (lodheatmap)
+# lodvarname provided -> case for one LOD column (lodchart)
+#reorgLodData = (data, lodvarname=null) ->
+# data.posByChr = {}
+# data.lodByChr = {}
+#
+# #console.log("data.chr", data.chr)
+# #console.log("data.chrnames:", data.chrnames)
+# the_chr = "0"
+# for chr,i in data.chrnames
+# data.posByChr[chr] = []
+# data.lodByChr[chr] = []
+# for pos,j in data.pos
+# console.log("data.chr[j][0]:", data.chr[j][0])
+# if data.chr[j][0] == chr
+# console.log("IS EQUAL")
+# data.posByChr[chr].push(pos)
+# data.lodnames = [data.lodnames] unless Array.isArray(data.lodnames)
+# lodval = (data[lodcolumn][j] for lodcolumn in data.lodnames)
+# data.lodByChr[chr].push(lodval)
+#
+# if lodvarname?
+# data.markers = []
+# for marker,i in data.markernames
+# if marker != ""
+# data.markers.push({name:marker, chr:data.chr[i][0], pos:data.pos[i], lod:data[lodvarname][i]})
+#
+# data
+
+# calculate chromosome start/end + scales, for heat map
+#chrscales = (data, width, chrGap, leftMargin, pad4heatmap) ->
+# # start and end of chromosome positions
+# chrStart = []
+# chrEnd = []
+# chrLength = []
+# totalChrLength = 0
+# maxd = 0
+# for chr in data.chrnames
+# d = maxdiff(data.posByChr[chr])
+# maxd = d if d > maxd
+#
+# rng = d3.extent(data.posByChr[chr])
+# chrStart.push(rng[0])
+# chrEnd.push(rng[1])
+# L = rng[1] - rng[0]
+# chrLength.push(L)
+# totalChrLength += L
+#
+# # adjust lengths for heatmap
+# if pad4heatmap
+# data.recwidth = maxd
+# chrStart = chrStart.map (x) -> x-maxd/2
+# chrEnd = chrEnd.map (x) -> x+maxd/2
+# chrLength = chrLength.map (x) -> x+maxd
+# totalChrLength += (chrLength.length*maxd)
+#
+# # break up x axis into chromosomes by length, with gaps
+# data.chrStart = []
+# data.chrEnd = []
+# cur = leftMargin
+# cur += chrGap/2 unless pad4heatmap
+# data.xscale = {}
+# for chr,i in data.chrnames
+# data.chrStart.push(cur)
+# w = Math.round((width-chrGap*(data.chrnames.length-pad4heatmap))/totalChrLength*chrLength[i])
+# data.chrEnd.push(cur + w)
+# cur = data.chrEnd[i] + chrGap
+# # x-axis scales, by chromosome
+# data.xscale[chr] = d3.scale.linear()
+# .domain([chrStart[i], chrEnd[i]])
+# .range([data.chrStart[i], data.chrEnd[i]])
+#
+# # return data with new stuff added
+# data
+
+# Select a set of categorical colors
+# ngroup is positive integer
+# palette = "dark" or "pastel"
+selectGroupColors = (ngroup, palette) ->
+ return [] if ngroup == 0
+
+ if palette == "dark"
+ return ["slateblue"] if ngroup == 1
+ return ["MediumVioletRed", "slateblue"] if ngroup == 2
+ return colorbrewer.Set1[ngroup] if ngroup <= 9
+ return d3.scale.category20().range()[0...ngroup]
+ else
+ return ["#bebebe"] if ngroup == 1
+ return ["lightpink", "lightblue"] if ngroup == 2
+ return colorbrewer.Pastel1[ngroup] if ngroup <= 9
+ # below is rough attempt to make _big_ pastel palette
+ return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8",
+ "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6",
+ "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4",
+ "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7",
+ "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"][0...ngroup]
+
+# expand element/array (e.g., of colors) to a given length
+# single elment -> array, then repeated to length n
+expand2vector = (input, n) ->
+ return input unless input? # return null if null
+ return input if Array.isArray(input) and input.length >= n
+ input = [input] unless Array.isArray(input)
+ input = (input[0] for i of d3.range(n)) if input.length == 1 and n > 1
+ input
+
+# median of a vector
+median = (x) ->
+ return null if !x?
+ n = x.length
+ x.sort((a,b) -> a-b)
+ if n % 2 == 1
+ return x[(n-1)/2]
+ (x[n/2] + x[(n/2)-1])/2
+
+# given a vector of x's, return hash with values to left and right, and the differences
+getLeftRight = (x) ->
+ n = x.length
+ x.sort( (a,b) -> a-b )
+
+ xdif = []
+ result = {}
+ for v in x
+ result[v] = {}
+
+ for i in [1...n]
+ #console.log("result:", result)
+ xdif.push(x[i]-x[i-1])
+ result[x[i]].left = x[i-1]
+ for i in [0...(n-1)]
+ result[x[i]].right = x[i+1]
+
+ xdif = median(xdif)
+ result.mediandiff = xdif
+
+ result[x[0]].left = x[0]-xdif
+ result[x[n-1]].right = x[n-1]+xdif
+ result.extent = [x[0]-xdif/2, x[n-1]+xdif/2]
+
+ result
+
+# maximum difference between adjacent values in a vector
+maxdiff = (x) ->
+ return null if x.length < 2
+ result = x[1] - x[0]
+ return result if x.length < 3
+ for i in [2...x.length]
+ d = x[i] - x[i-1]
+ result = d if d > result
+ result
+
+# matrix extent, min max
+matrixMin = (mat) ->
+ result = mat[0][0]
+ for i of mat
+ for j of mat[i]
+ result = mat[i][j] if result > mat[i][j]
+ result
+
+matrixMax = (mat) ->
+ result = mat[0][0]
+ for i of mat
+ for j of mat[i]
+ result = mat[i][j] if result < mat[i][j]
+ result
+
+matrixMaxAbs = (mat) ->
+ result = Math.abs(mat[0][0])
+ for i of mat
+ for j of mat[i]
+ result = Math.abs(mat[i][j]) if result < mat[i][j]
+ result
+
+matrixExtent = (mat) -> [matrixMin(mat), matrixMax(mat)]
+
+d3.selection.prototype.moveToFront = () ->
+ this.each () -> this.parentNode.appendChild(this)
+
+d3.selection.prototype.moveToBack = () ->
+ this.each () ->
+ firstChild = this.parentNode.firstchild
+ this.parentNode.insertBefore(this, firstChild) if firstChild
+
+forceAsArray = (x) ->
+ return x unless x? # if null, return null
+ return x if Array.isArray(x)
+ [x]
+
+# any values in vec that appear in missing are made null
+missing2null = (vec, missingvalues=['NA', '']) ->
+ vec.map (value) -> if missingvalues.indexOf(value) > -1 then null else value
+
+# display error at top of page
+displayError = (message) ->
+ if d3.select("div.error").empty() # no errors yet
+ d3.select("body")
+ .insert("div", ":first-child")
+ .attr("class", "error")
+ d3.select("div.error")
+ .append("p")
+ .text(message)
+
+# sum values in an array
+sumArray = (vec) -> (vec.reduce (a,b) -> a+b)
+
+# calculate cross-tabulation
+calc_crosstab = (data) ->
+ nrow = data.ycat.length
+ ncol = data.xcat.length
+
+ result = ((0 for col in [0..ncol]) for row in [0..nrow]) # matrix of 0's
+
+ # count things up
+ for i of data.x
+ result[data.y[i]][data.x[i]] += 1
+
+ # row and column sums
+ rs = rowSums(result)
+ cs = colSums(result)
+
+ # fill in column sums
+ for i in [0...ncol]
+ result[nrow][i] = cs[i]
+
+ # fill in row sums
+ for i in [0...nrow]
+ result[i][ncol] = rs[i]
+
+ # fill in total
+ result[nrow][ncol] = sumArray(rs)
+
+ result
+
+# rowSums: the sums for each row
+rowSums = (mat) -> (sumArray(x) for x in mat)
+
+# transpose: matrix transpose
+transpose = (mat) -> ((mat[i][j] for i in [0...mat.length]) for j in [0...mat[0].length])
+
+# colSums = the sums for each column
+colSums = (mat) -> rowSums(transpose(mat))
+
+# log base 2
+log2 = (x) ->
+ return(x) unless x?
+ Math.log(x)/Math.log(2.0)
+
+# log base 10
+log10 = (x) ->
+ return(x) unless x?
+ Math.log(x)/Math.log(10.0)
+
+# absolute value, preserving nulls
+abs = (x) ->
+ return(x) unless x?
+ Math.abs(x)
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 07384f2b..2acc1651 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -1,319 +1,439 @@ -// Generated by CoffeeScript 1.7.1
-var chrscales, expand2vector, forceAsArray, formatAxis, getLeftRight, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, pullVarAsArray, reorgLodData, selectGroupColors, unique;
-
-formatAxis = function(d) {
- var ndig;
- d = d[1] - d[0];
- ndig = Math.floor(Math.log(d % 10) / Math.log(10));
- if (ndig > 0) {
- ndig = 0;
- }
- ndig = Math.abs(ndig);
- return d3.format("." + ndig + "f");
-};
-
-unique = function(x) {
- var output, v, _i, _len, _results;
- output = {};
- for (_i = 0, _len = x.length; _i < _len; _i++) {
- v = x[_i];
- if (v) {
- output[v] = v;
- }
- }
- _results = [];
- for (v in output) {
- _results.push(output[v]);
- }
- return _results;
-};
-
-pullVarAsArray = function(data, variable) {
- var i, v;
- v = [];
- for (i in data) {
- v = v.concat(data[i][variable]);
- }
- return v;
-};
-
-reorgLodData = function(data, lodvarname) {
- var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2;
- if (lodvarname == null) {
- lodvarname = null;
- }
- data.posByChr = {};
- data.lodByChr = {};
- _ref = data.chrnames;
- for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) {
- chr = _ref[i];
- data.posByChr[chr] = [];
- data.lodByChr[chr] = [];
- _ref1 = data.pos;
- for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) {
- pos = _ref1[j];
- if (data.chr[j] === chr) {
- data.posByChr[chr].push(pos);
- if (!Array.isArray(data.lodnames)) {
- data.lodnames = [data.lodnames];
- }
- lodval = (function() {
- var _k, _len2, _ref2, _results;
- _ref2 = data.lodnames;
- _results = [];
- for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) {
- lodcolumn = _ref2[_k];
- _results.push(data[lodcolumn][j]);
- }
- return _results;
- })();
- data.lodByChr[chr].push(lodval);
- }
- }
- }
- if (lodvarname != null) {
- data.markers = [];
- _ref2 = data.markernames;
- for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) {
- marker = _ref2[i];
- if (marker !== "") {
- data.markers.push({
- name: marker,
- chr: data.chr[i],
- pos: data.pos[i],
- lod: data[lodvarname][i]
- });
- }
- }
- }
- return data;
-};
-
-chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) {
- var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1;
- chrStart = [];
- chrEnd = [];
- chrLength = [];
- totalChrLength = 0;
- maxd = 0;
- _ref = data.chrnames;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- chr = _ref[_i];
- d = maxdiff(data.posByChr[chr]);
- if (d > maxd) {
- maxd = d;
- }
- rng = d3.extent(data.posByChr[chr]);
- chrStart.push(rng[0]);
- chrEnd.push(rng[1]);
- L = rng[1] - rng[0];
- chrLength.push(L);
- totalChrLength += L;
- }
- if (pad4heatmap) {
- data.recwidth = maxd;
- chrStart = chrStart.map(function(x) {
- return x - maxd / 2;
- });
- chrEnd = chrEnd.map(function(x) {
- return x + maxd / 2;
- });
- chrLength = chrLength.map(function(x) {
- return x + maxd;
- });
- totalChrLength += chrLength.length * maxd;
- }
- data.chrStart = [];
- data.chrEnd = [];
- cur = leftMargin;
- if (!pad4heatmap) {
- cur += chrGap / 2;
- }
- data.xscale = {};
- _ref1 = data.chrnames;
- for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) {
- chr = _ref1[i];
- data.chrStart.push(cur);
- w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]);
- data.chrEnd.push(cur + w);
- cur = data.chrEnd[i] + chrGap;
- data.xscale[chr] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]);
- }
- return data;
-};
-
-selectGroupColors = function(ngroup, palette) {
- if (ngroup === 0) {
- return [];
- }
- if (palette === "dark") {
- if (ngroup === 1) {
- return ["slateblue"];
- }
- if (ngroup === 2) {
- return ["MediumVioletRed", "slateblue"];
- }
- if (ngroup <= 9) {
- return colorbrewer.Set1[ngroup];
- }
- return d3.scale.category20().range().slice(0, ngroup);
- } else {
- if (ngroup === 1) {
- return [d3.rgb(190, 190, 190)];
- }
- if (ngroup === 2) {
- return ["lightpink", "lightblue"];
- }
- if (ngroup <= 9) {
- return colorbrewer.Pastel1[ngroup];
- }
- return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup);
- }
-};
-
-expand2vector = function(input, n) {
- var i;
- if (Array.isArray(input) && input.length >= n) {
- return input;
- }
- if (!Array.isArray(input)) {
- input = [input];
- }
- if (input.length === 1 && n > 1) {
- input = (function() {
- var _results;
- _results = [];
- for (i in d3.range(n)) {
- _results.push(input[0]);
- }
- return _results;
- })();
- }
- return input;
-};
-
-median = function(x) {
- var n;
- if (x == null) {
- return null;
- }
- n = x.length;
- x.sort(function(a, b) {
- return a - b;
- });
- if (n % 2 === 1) {
- return x[(n - 1) / 2];
- }
- return (x[n / 2] + x[(n / 2) - 1]) / 2;
-};
-
-getLeftRight = function(x) {
- var i, n, result, v, xdif, _i, _j, _k, _len, _ref;
- n = x.length;
- x.sort(function(a, b) {
- return a - b;
- });
- xdif = [];
- result = {};
- for (_i = 0, _len = x.length; _i < _len; _i++) {
- v = x[_i];
- result[v] = {};
- }
- for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) {
- xdif.push(x[i] - x[i - 1]);
- result[x[i]].left = x[i - 1];
- }
- for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) {
- result[x[i]].right = x[i + 1];
- }
- xdif = median(xdif);
- result.mediandiff = xdif;
- result[x[0]].left = x[0] - xdif;
- result[x[n - 1]].right = x[n - 1] + xdif;
- result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2];
- return result;
-};
-
-maxdiff = function(x) {
- var d, i, result, _i, _ref;
- if (x.length < 2) {
- return null;
- }
- result = x[1] - x[0];
- if (x.length < 3) {
- return result;
- }
- for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) {
- d = x[i] - x[i - 1];
- if (d > result) {
- result = d;
- }
- }
- return result;
-};
-
-matrixMin = function(mat) {
- var i, j, result;
- result = mat[0][0];
- for (i in mat) {
- for (j in mat[i]) {
- if (result > mat[i][j]) {
- result = mat[i][j];
- }
- }
- }
- return result;
-};
-
-matrixMax = function(mat) {
- var i, j, result;
- result = mat[0][0];
- for (i in mat) {
- for (j in mat[i]) {
- if (result < mat[i][j]) {
- result = mat[i][j];
- }
- }
- }
- return result;
-};
-
-matrixMaxAbs = function(mat) {
- var i, j, result;
- result = Math.abs(mat[0][0]);
- for (i in mat) {
- for (j in mat[i]) {
- if (result < mat[i][j]) {
- result = Math.abs(mat[i][j]);
- }
- }
- }
- return result;
-};
-
-matrixExtent = function(mat) {
- return [matrixMin(mat), matrixMax(mat)];
-};
-
-d3.selection.prototype.moveToFront = function() {
- return this.each(function() {
- return this.parentNode.appendChild(this);
- });
-};
-
-d3.selection.prototype.moveToBack = function() {
- return this.each(function() {
- var firstChild;
- firstChild = this.parentNode.firstchild;
- if (firstChild) {
- return this.parentNode.insertBefore(this, firstChild);
- }
- });
-};
-
-forceAsArray = function(x) {
- if (Array.isArray(x)) {
- return x;
- }
- return [x];
-};
+// Generated by CoffeeScript 1.7.1 +var abs, calc_crosstab, chrscales, colSums, displayError, expand2vector, forceAsArray, formatAxis, getLeftRight, log10, log2, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, missing2null, pullVarAsArray, reorgLodData, rowSums, selectGroupColors, sumArray, transpose, unique; + +formatAxis = function(d, extra_digits) { + var ndig; + if (extra_digits == null) { + extra_digits = 0; + } + d = d[1] - d[0]; + ndig = Math.floor(Math.log(d % 10) / Math.log(10)); + if (ndig > 0) { + ndig = 0; + } + ndig = Math.abs(ndig) + extra_digits; + return d3.format("." + ndig + "f"); +}; + +unique = function(x) { + var output, v, _i, _len, _results; + output = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + if (v) { + output[v] = v; + } + } + _results = []; + for (v in output) { + _results.push(output[v]); + } + return _results; +}; + +pullVarAsArray = function(data, variable) { + var i, v; + v = []; + for (i in data) { + v = v.concat(data[i][variable]); + } + return v; +}; + +reorgLodData = function(data, lodvarname) { + var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2; + if (lodvarname == null) { + lodvarname = null; + } + data.posByChr = {}; + data.lodByChr = {}; + _ref = data.chrnames; + for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { + chr = _ref[i]; + data.posByChr[chr[0]] = []; + data.lodByChr[chr[0]] = []; + _ref1 = data.pos; + for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) { + pos = _ref1[j]; + if (data.chr[j].toString() === chr[0]) { + data.posByChr[chr[0]].push(pos); + if (!Array.isArray(data.lodnames)) { + data.lodnames = [data.lodnames]; + } + lodval = (function() { + var _k, _len2, _ref2, _results; + _ref2 = data.lodnames; + _results = []; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + lodcolumn = _ref2[_k]; + _results.push(data[lodcolumn][j]); + } + return _results; + })(); + data.lodByChr[chr[0]].push(lodval); + } + } + } + if (lodvarname != null) { + data.markers = []; + _ref2 = data.markernames; + for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) { + marker = _ref2[i]; + if (marker !== "") { + data.markers.push({ + name: marker, + chr: data.chr[i], + pos: data.pos[i], + lod: data[lodvarname][i] + }); + } + } + } + return data; +}; + +chrscales = function(data, width, chrGap, leftMargin, pad4heatmap) { + var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; + chrStart = []; + chrEnd = []; + chrLength = []; + totalChrLength = 0; + maxd = 0; + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; + d = maxdiff(data.posByChr[chr[0]]); + 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]; + chrLength.push(L); + totalChrLength += L; + } + if (pad4heatmap) { + data.recwidth = maxd; + chrStart = chrStart.map(function(x) { + return x - maxd / 2; + }); + chrEnd = chrEnd.map(function(x) { + return x + maxd / 2; + }); + chrLength = chrLength.map(function(x) { + return x + maxd; + }); + totalChrLength += chrLength.length * maxd; + } + data.chrStart = []; + data.chrEnd = []; + cur = leftMargin; + if (!pad4heatmap) { + cur += chrGap / 2; + } + data.xscale = {}; + _ref1 = data.chrnames; + for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) { + chr = _ref1[i]; + data.chrStart.push(cur); + w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]); + data.chrEnd.push(cur + w); + cur = data.chrEnd[i] + chrGap; + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); + } + return data; +}; + +selectGroupColors = function(ngroup, palette) { + if (ngroup === 0) { + return []; + } + if (palette === "dark") { + if (ngroup === 1) { + return ["slateblue"]; + } + if (ngroup === 2) { + return ["MediumVioletRed", "slateblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Set1[ngroup]; + } + return d3.scale.category20().range().slice(0, ngroup); + } else { + if (ngroup === 1) { + return ["#bebebe"]; + } + if (ngroup === 2) { + return ["lightpink", "lightblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Pastel1[ngroup]; + } + return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup); + } +}; + +expand2vector = function(input, n) { + var i; + if (input == null) { + return input; + } + if (Array.isArray(input) && input.length >= n) { + return input; + } + if (!Array.isArray(input)) { + input = [input]; + } + if (input.length === 1 && n > 1) { + input = (function() { + var _results; + _results = []; + for (i in d3.range(n)) { + _results.push(input[0]); + } + return _results; + })(); + } + return input; +}; + +median = function(x) { + var n; + if (x == null) { + return null; + } + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + if (n % 2 === 1) { + return x[(n - 1) / 2]; + } + return (x[n / 2] + x[(n / 2) - 1]) / 2; +}; + +getLeftRight = function(x) { + var i, n, result, v, xdif, _i, _j, _k, _len, _ref; + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + xdif = []; + result = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + result[v] = {}; + } + for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) { + xdif.push(x[i] - x[i - 1]); + result[x[i]].left = x[i - 1]; + } + for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) { + result[x[i]].right = x[i + 1]; + } + xdif = median(xdif); + result.mediandiff = xdif; + result[x[0]].left = x[0] - xdif; + result[x[n - 1]].right = x[n - 1] + xdif; + result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2]; + return result; +}; + +maxdiff = function(x) { + var d, i, result, _i, _ref; + if (x.length < 2) { + return null; + } + result = x[1] - x[0]; + if (x.length < 3) { + return result; + } + for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) { + d = x[i] - x[i - 1]; + if (d > result) { + result = d; + } + } + return result; +}; + +matrixMin = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result > mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMax = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMaxAbs = function(mat) { + var i, j, result; + result = Math.abs(mat[0][0]); + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = Math.abs(mat[i][j]); + } + } + } + return result; +}; + +matrixExtent = function(mat) { + return [matrixMin(mat), matrixMax(mat)]; +}; + +d3.selection.prototype.moveToFront = function() { + return this.each(function() { + return this.parentNode.appendChild(this); + }); +}; + +d3.selection.prototype.moveToBack = function() { + return this.each(function() { + var firstChild; + firstChild = this.parentNode.firstchild; + if (firstChild) { + return this.parentNode.insertBefore(this, firstChild); + } + }); +}; + +forceAsArray = function(x) { + if (x == null) { + return x; + } + if (Array.isArray(x)) { + return x; + } + return [x]; +}; + +missing2null = function(vec, missingvalues) { + if (missingvalues == null) { + missingvalues = ['NA', '']; + } + return vec.map(function(value) { + if (missingvalues.indexOf(value) > -1) { + return null; + } else { + return value; + } + }); +}; + +displayError = function(message) { + if (d3.select("div.error").empty()) { + d3.select("body").insert("div", ":first-child").attr("class", "error"); + } + return d3.select("div.error").append("p").text(message); +}; + +sumArray = function(vec) { + return vec.reduce(function(a, b) { + return a + b; + }); +}; + +calc_crosstab = function(data) { + var col, cs, i, ncol, nrow, result, row, rs, _i, _j; + nrow = data.ycat.length; + ncol = data.xcat.length; + result = (function() { + var _i, _results; + _results = []; + for (row = _i = 0; 0 <= nrow ? _i <= nrow : _i >= nrow; row = 0 <= nrow ? ++_i : --_i) { + _results.push((function() { + var _j, _results1; + _results1 = []; + for (col = _j = 0; 0 <= ncol ? _j <= ncol : _j >= ncol; col = 0 <= ncol ? ++_j : --_j) { + _results1.push(0); + } + return _results1; + })()); + } + return _results; + })(); + for (i in data.x) { + result[data.y[i]][data.x[i]] += 1; + } + rs = rowSums(result); + cs = colSums(result); + for (i = _i = 0; 0 <= ncol ? _i < ncol : _i > ncol; i = 0 <= ncol ? ++_i : --_i) { + result[nrow][i] = cs[i]; + } + for (i = _j = 0; 0 <= nrow ? _j < nrow : _j > nrow; i = 0 <= nrow ? ++_j : --_j) { + result[i][ncol] = rs[i]; + } + result[nrow][ncol] = sumArray(rs); + return result; +}; + +rowSums = function(mat) { + var x, _i, _len, _results; + _results = []; + for (_i = 0, _len = mat.length; _i < _len; _i++) { + x = mat[_i]; + _results.push(sumArray(x)); + } + return _results; +}; + +transpose = function(mat) { + var i, j, _i, _ref, _results; + _results = []; + for (j = _i = 0, _ref = mat[0].length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) { + _results.push((function() { + var _j, _ref1, _results1; + _results1 = []; + for (i = _j = 0, _ref1 = mat.length; 0 <= _ref1 ? _j < _ref1 : _j > _ref1; i = 0 <= _ref1 ? ++_j : --_j) { + _results1.push(mat[i][j]); + } + return _results1; + })()); + } + return _results; +}; + +colSums = function(mat) { + return rowSums(transpose(mat)); +}; + +log2 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(2.0); +}; + +log10 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(10.0); +}; + +abs = function(x) { + if (x == null) { + return x; + } + return Math.abs(x); +}; 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 27bf80d5..fc687c7a 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee @@ -170,6 +170,42 @@ $ -> #this.my_timer = setInterval(get_progress, 1000) #return false ) + + $("#rqtl_geno_compute").click(() => + $("#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()) + $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()) + form_data = $('#trait_data_form').serialize() + console.log("form_data is:", form_data) + + #remove_outliers = confirm("Remove outliers?") + #if use_outliers == true + # block_outliers() + do_ajax_post(url, form_data) + + #$.ajax( + # type: "POST" + # url: url + # data: form_data + # error: (xhr, ajaxOptions, thrownError) => + # alert("Sorry, an error occurred") + # console.log(xhr) + # clearInterval(this.my_timer) + # $('#progress_bar_container').modal('hide') + # $("body").html("We got an error.") + # success: (data) => + # clearInterval(this.my_timer) + # $('#progress_bar_container').modal('hide') + # $("body").html(data) + #) + #console.log("settingInterval") + # + #this.my_timer = setInterval(get_progress, 1000) + #return false + ) + $("#plink_compute").click(() => $("#static_progress_bar_container").modal() 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 d02bca4b..a8a42ffa 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -130,6 +130,19 @@ $(function() { return do_ajax_post(url, form_data); }; })(this)); + $("#rqtl_geno_compute").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()); + $('input[name=control_marker]').val($('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").click((function(_this) { return function() { var form_data, url; diff --git a/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js b/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js index 328733f2..cfe3e9d2 100755 --- a/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js +++ b/wqflask/wqflask/static/packages/DT_bootstrap/DT_bootstrap.js @@ -148,12 +148,12 @@ if ( $.fn.DataTable.TableTools ) { /* Table initialisation */ -$(document).ready(function() { - $('#example').dataTable( { - "sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>", - "sPaginationType": "bootstrap", - "oLanguage": { - "sLengthMenu": "_MENU_ records per page" - } - } ); -} );
\ No newline at end of file +//$(document).ready(function() { +// $('#example').dataTable( { +// "sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>", +// "sPaginationType": "bootstrap", +// "oLanguage": { +// "sLengthMenu": "_MENU_ records per page" +// } +// } ); +//} );
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 705eda88..c58b7729 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -9,6 +9,9 @@ <li> <a href="#pylmm" data-toggle="tab">pyLMM</a> </li> + <li> + <a href="#rqtl_geno" data-toggle="tab">rqtl</a> + </li> {% if dataset.group.species == 'human' %} <li> <a href="#plink" data-toggle="tab">PLINK</a> @@ -49,7 +52,7 @@ <div class="control-group mapping_method_fields"> <label for="mapping_permutations" class="control-label">Permutations (n)</label> <div class="controls"> - <input name="num_permutations" value="2000" type="text" /> + <input name="num_perm_reaper" value="2000" type="text" /> </div> </div> @@ -66,7 +69,7 @@ <div class="controls" id="display_additive_effect"> <label class="radio inline"> <input type="radio" name="display_additive" - id="display_dditive" value="yes" checked> + id="display_additive" value="yes" checked> Yes </label> <label class="radio inline"> @@ -171,6 +174,33 @@ </div> </div> + <div class="tab-pane" id="rqtl_geno"> + + <div class="control-group"> + <label for="num_perm_rqtl_geno" class="control-label">Permutations (n)</label> + <div class="controls"> + <input name="num_perm_rqtl_geno" value="0" type="text" /> + </div> + </div> + <div class="control-group"> + <label for="control_rqtl_geno" class="control-label">Control Marker</label> + <div class="controls"> + <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" /> + </div> + </div> + + <div class="control-group"> + <div class="controls"> + <button id="rqtl_geno_compute" + class="btn btn-inverse submit_special" + data-url="/marker_regression" + title="Compute Marker Regression"> + <i class="icon-ok-circle icon-white"></i> Compute + </button> + </div> + </div> + + </div> {% if dataset.group.species == 'human' %} <div class="tab-pane" id="plink"> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3c448988..26e690d4 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -209,7 +209,7 @@ def heatmap_page(): start_vars = request.form temp_uuid = uuid.uuid4() - version = "v4" + version = "v5" key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): @@ -252,7 +252,10 @@ def marker_regression_page(): 'dataset', 'method', 'suggestive', - 'maf' + 'num_perm', + 'maf', + 'control_marker', + 'control_marker_db' ) start_vars = {} @@ -260,7 +263,7 @@ def marker_regression_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - version = "v3" + version = "v4" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): @@ -296,7 +299,7 @@ def marker_regression_page(): pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) print("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) - Redis.expire(key, 60*60) + Redis.expire(key, 1*60) with Bench("Rendering template"): rendered_template = render_template("marker_regression.html", **result) @@ -346,7 +349,7 @@ def interval_mapping_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - version = "v11" + version = "v4" key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): |