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-rw-r--r--wqflask/wqflask/collect.py7
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py74
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py9
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py22
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py1
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py2
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py17
-rw-r--r--wqflask/wqflask/static/dbdoc/TODO.md1
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js130
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js137
-rw-r--r--wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js5
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js3
-rw-r--r--wqflask/wqflask/templates/collections/list.html12
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html176
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html3
-rw-r--r--wqflask/wqflask/templates/correlation_page.html28
-rw-r--r--wqflask/wqflask/templates/empty_collection.html15
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html106
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html232
-rw-r--r--wqflask/wqflask/views.py4
20 files changed, 474 insertions, 510 deletions
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 2f6c3a96..0f72b29d 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -349,8 +349,11 @@ def delete_collection():
db_session.delete(uc)
db_session.commit()
else:
- collection_name = params['collection_name']
- user_manager.AnonUser().delete_collection(collection_name)
+ if "collection_name" in params:
+ collection_name = params['collection_name']
+ else:
+ for this_collection in params['uc_id'].split(":"):
+ user_manager.AnonUser().delete_collection(this_collection)
flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 3d1c0d17..9b048346 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -32,6 +32,7 @@ import pp
import math
import collections
import resource
+import json
import scipy
@@ -51,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only.
from wqflask.correlation import correlation_functions
from utility.benchmark import Bench
import utility.webqtlUtil
+from wqflask import user_manager
from MySQLdb import escape_string as escape
@@ -248,7 +250,7 @@ class CorrelationResults(object):
else:
self.this_trait_vals.append("None")
num_overlap = len(self.this_trait_vals)
-
+ logger.debug("DOING PARALLEL")
self.do_parallel_correlation(db_filename, num_overlap)
else:
for trait, values in self.target_dataset.trait_data.iteritems():
@@ -335,6 +337,7 @@ class CorrelationResults(object):
#print("self.correlation_results: ", pf(self.correlation_results))
+ self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
#XZ, 09/18/2008: get all information about the user selected database.
#target_db_name = fd.corr_dataset
@@ -1195,6 +1198,17 @@ class CorrelationResults(object):
import math
import reaper
+ def cmpOrder2(A,B):
+ try:
+ if A[-1] < B[-1]:
+ return -1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return 1
+ except:
+ return 0
+
def calCorrelation(dbdata,userdata,N):
X = []
Y = []
@@ -1420,3 +1434,61 @@ class CorrelationResults(object):
# for one_result in results:
# for one_traitinfo in one_result:
# allcorrelations.append( one_traitinfo )
+
+def generate_corr_json(corr_results, this_trait, dataset, target_dataset):
+ results_list = []
+ for i, trait in enumerate(corr_results):
+ results_dict = {}
+ results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + user_manager.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + "'>"
+ results_dict['index'] = i + 1
+ results_dict['trait_id'] = "<a href='/show_trait?trait_id="+str(trait.name)+"&dataset="+str(dataset.name)+"'>"+str(trait.name)+"</a>"
+ if target_dataset.type == "ProbeSet":
+ results_dict['symbol'] = trait.symbol
+ results_dict['description'] = trait.description_display
+ results_dict['location'] = trait.location_repr
+ results_dict['mean'] = float(trait.mean)
+ if trait.LRS_score_repr != "N/A":
+ results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr)
+ else:
+ results_dict['lrs_score'] = "N/A"
+ results_dict['lrs_location'] = trait.LRS_location_repr
+ if trait.additive != "":
+ results_dict['additive'] = "%0.3f" % float(trait.additive)
+ else:
+ results_dict['additive'] = "N/A"
+ results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+ if trait.lit_corr == "" or trait.lit_corr == 0:
+ results_dict['lit_corr'] = "--"
+ else:
+ results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr)
+ if trait.tissue_corr == "" or trait.tissue_corr == 0:
+ results_dict['tissue_corr'] = "--"
+ else:
+ results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr)
+ elif target_dataset.type == "Publish":
+ results_dict['description'] = trait.description_display
+ results_dict['authors'] = trait.authors
+ if trait.pubmed_id:
+ results_dict['pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>"
+ else:
+ results_dict['pubmed'] = "N/A"
+ results_dict['lrs_score'] = trait.LRS_score_repr
+ results_dict['lrs_location'] = trait.LRS_location_repr
+ if trait.additive != "":
+ results_dict['additive'] = "%0.3f" % float(trait.additive)
+ else:
+ results_dict['additive'] = "N/A"
+ results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % trait.sample_r + "</a>"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+ else:
+ results_dict['lrs_location'] = trait.LRS_location_repr
+ results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+
+ results_list.append(results_dict)
+
+ return json.dumps(results_list)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b34beb7b..077386a3 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -173,9 +173,12 @@ class CorrelationMatrix(object):
for sample in self.all_sample_list:
groups.append(1)
- pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
-
- self.loadings_array = self.process_loadings()
+ try:
+ self.pca_works = "True"
+ pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
+ self.loadings_array = self.process_loadings()
+ except:
+ self.pca_works = "False"
self.js_data = dict(traits = [trait.name for trait in self.traits],
groups = groups,
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 68920130..7563eb2c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,7 +3,7 @@ import os, math, string, random, json
from base import webqtlConfig
from base.trait import GeneralTrait
from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ )
def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
"""Generates p-values for each marker using GEMMA"""
- assert_bin(GEMMA_COMMAND);
if this_dataset.group.genofile != None:
genofile_name = this_dataset.group.genofile[:-5]
else:
@@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name):
# if marker['chr'] != previous_chr:
# previous_chr = marker['chr']
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[10])
+ marker['p_value'] = float(line.split("\t")[11])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
@@ -203,20 +202,15 @@ def parse_gemma_output(genofile_name):
marker_obs.append(marker)
included_markers.append(line.split("\t")[1])
- p_values.append(float(line.split("\t")[10]))
+ p_values.append(float(line.split("\t")[11]))
return marker_obs
def parse_loco_output(this_dataset, gwa_output_filename):
output_filelist = []
- jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json"
- assert_file(jsonfn)
- try:
- with open(jsonfn) as data_file:
- data = json.load(data_file)
- except:
- logger.error("Can not parse "+jsonfn)
+ with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
+ data = json.load(data_file)
files = data['files']
for file in files:
@@ -241,7 +235,7 @@ def parse_loco_output(this_dataset, gwa_output_filename):
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[10])
+ marker['p_value'] = float(line.split("\t")[11])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
@@ -251,6 +245,6 @@ def parse_loco_output(this_dataset, gwa_output_filename):
marker_obs.append(marker)
included_markers.append(line.split("\t")[1])
- p_values.append(float(line.split("\t")[10]))
+ p_values.append(float(line.split("\t")[11]))
- return marker_obs
+ return marker_obs \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c189fb96..3ec61e55 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -228,6 +228,7 @@ class MarkerRegression(object):
results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
self.dataset,
self.samples,
+ self.vals,
self.json_data,
self.num_perm,
self.bootCheck,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 211cf187..66884b0c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1204,6 +1204,8 @@ class MarkerRegression(object):
else:
if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+ if self.covariates != "":
+ string3 = 'Using following traits as covariates: ' + self.covariates
elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
string2 = 'Using R/qtl mapping method with no control for other QTLs.'
elif self.mapping_method == "plink":
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 50228b5e..6b58190f 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -1,17 +1,20 @@
-def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
genotype = dataset.group.read_genotype_file()
if manhattan_plot != True:
genotype = genotype.addinterval()
- samples, values, variances, sample_aliases = this_trait.export_informative()
-
trimmed_samples = []
trimmed_values = []
- for i in range(0, len(samples)):
- if this_trait.data[samples[i]].name in samples_before:
- trimmed_samples.append(samples[i])
- trimmed_values.append(values[i])
+ for i in range(0, len(samples_before)):
+ try:
+ trimmed_values.append(float(trait_vals[i]))
+ trimmed_samples.append(samples_before[i])
+ except:
+ pass
perm_output = []
bootstrap_results = []
diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md
new file mode 100644
index 00000000..c0a8bab7
--- /dev/null
+++ b/wqflask/wqflask/static/dbdoc/TODO.md
@@ -0,0 +1 @@
+TODO: Add all database documentation into this folder
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
index 43ac6086..bf0a14e6 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
@@ -1,6 +1,7 @@
var chart;
+var srchart;
-function drawg () {
+function drawg() {
//
chart = nv.models.scatterChart();
//
@@ -27,11 +28,45 @@ function drawg () {
chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
//
chart.tooltip.contentGenerator(function (obj) {
- // return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>';
- return '<b style="font-size: 18px">' + obj.point.name + '</b>';
+ return tiptext(obj);
});
}
+function srdrawg() {
+ //
+ srchart = nv.models.scatterChart();
+ //
+ srchart.showLegend(false);
+ srchart.duration(300);
+ srchart.color(d3.scale.category10().range());
+ srchart.pointRange([0, 400]);
+ srchart.pointDomain([0, 10]);
+ //
+ srchart.xAxis.axisLabel(js_data.trait_1);
+ srchart.xAxis.axisLabelDistance(11);
+ srchart.yAxis.axisLabel(js_data.trait_2);
+ srchart.yAxis.axisLabelDistance(11);
+ //
+ xmin = d3.min(js_data.rdata[0]);
+ xmax = d3.max(js_data.rdata[0]);
+ xrange = xmax - xmin;
+ ymin = d3.min(js_data.rdata[1]);
+ ymax = d3.max(js_data.rdata[1]);
+ yrange = ymax - ymin;
+ srchart.xDomain([0, xmax + xrange/10]);
+ srchart.yDomain([0, ymax + yrange/10]);
+ srchart.xAxis.tickFormat(d3.format(checkformat(xrange)));
+ srchart.yAxis.tickFormat(d3.format(checkformat(yrange)));
+ //
+ srchart.tooltip.contentGenerator(function (obj) {
+ return tiptext(obj);
+ });
+}
+
+function tiptext(obj) {
+ return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>';
+}
+
function getdata(size, shape) {
var data = [];
data.push({
@@ -50,6 +85,25 @@ function getdata(size, shape) {
}
return data;
}
+
+function srgetdata(size, shape) {
+ var data = [];
+ data.push({
+ values: [],
+ slope: js_data.srslope,
+ intercept: js_data.srintercept
+ });
+ for (j = 0; j < js_data.rdata[0].length; j++) {
+ data[0].values.push({
+ x: js_data.rdata[0][j],
+ y: js_data.rdata[1][j],
+ name: js_data.indIDs[j],
+ size: size,
+ shape: shape
+ });
+ }
+ return data;
+}
function checkformat(range) {
cell = range / 10.0;
@@ -64,50 +118,47 @@ function checkformat(range) {
function chartupdate() {
//
- var axisxcolor = $("#axisxcolor").val();
- $(".nvd3 .nv-axis.nv-x text").css("fill", axisxcolor);
+ var labelcolor = $("#labelcolor").val();
+ $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor);
+ $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor);
//
- var axisycolor = $("#axisycolor").val();
- $(".nvd3 .nv-axis.nv-y text").css("fill", axisycolor);
+ var labelfont = $("#labelfont").val();
+ $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont);
+ $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont);
//
- var axisxfont = $("#axisxfont").val();
- $(".nvd3 .nv-axis.nv-x text").css("font-size", axisxfont);
+ var numbercolor = $("#numbercolor").val();
+ $("g.tick text").css("fill", numbercolor);
//
- var axisyfont = $("#axisyfont").val();
- $(".nvd3 .nv-axis.nv-y text").css("font-size", axisyfont);
+ var numberfont = $("#numberfont").val();
+ $("g.tick text").css("font-size", numberfont);
//
- var domainxcolor = $("#domainxcolor").val();
- $(".nv-x .nv-axis g path.domain").css("stroke", domainxcolor);
- //
- var domainycolor = $("#domainycolor").val();
- $(".nv-y .nv-axis g path.domain").css("stroke", domainycolor);
- //
- var domainxwidth = $("#domainxwidth").val();
- $(".nv-x .nv-axis g path.domain").css("stroke-width", domainxwidth);
+ var axiscolor = $("#axiscolor").val();
+ $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor);
+ $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor);
//
- var domainywidth = $("#domainywidth").val();
- $(".nv-y .nv-axis g path.domain").css("stroke-width", domainywidth);
+ var axiswidth = $("#axiswidth").val();
+ $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth);
+ $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth);
//
- var clinecolor = $("#clinecolor").val();
- $("line.nv-regLine").css("stroke", clinecolor);
+ var linecolor = $("#linecolor").val();
+ $("line.nv-regLine").css("stroke", linecolor);
//
- var clinewidth = $("#clinewidth").val();
- $("line.nv-regLine").css("stroke-width", clinewidth);
+ var linewidth = $("#linewidth").val();
+ $("line.nv-regLine").css("stroke-width", linewidth);
//
- var axiscolor = $("#axiscolor").val();
- $(".tick").css("stroke", axiscolor);
- //
- var axiswidth = $("#axiswidth").val();
- $("line.nv-regLine").css("stroke-width", axiswidth);
+ var markcolor = $("#markcolor").val();
+ $(".nvd3 g path").css("fill", markcolor);
}
function chartupdatewh() {
//
var width = $("#width").val();
$("#scatterplot2 svg").css("width", width);
+ $("#srscatterplot2 svg").css("width", width);
//
var height = $("#height").val();
$("#scatterplot2 svg").css("height", height);
+ $("#srscatterplot2 svg").css("height", height);
//
window.dispatchEvent(new Event('resize'));
}
@@ -118,7 +169,9 @@ function chartupdatedata() {
var shape = $("#markshape").val();
//
d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart);
+ d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
nv.utils.windowResize(chart.update);
+ nv.utils.windowResize(srchart.update);
}
function savesvg(svgEl, name) {
@@ -140,10 +193,14 @@ function saveassvg_pcs() {
savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg");
}
+function saveassvg_srcs() {
+ savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
+}
+
drawg();
-chartupdate();
-chartupdatewh();
-chartupdatedata();
+srdrawg();
+
+
$(".chartupdate").change(function () {
chartupdate();
@@ -156,3 +213,10 @@ $(".chartupdatewh").change(function () {
$(".chartupdatedata").change(function () {
chartupdatedata();
});
+
+$(document).ready(function(){
+ //chartupdate();
+//chartupdatewh();
+chartupdatedata();
+//chartupdate();
+}); \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js
deleted file mode 100644
index d0392dd7..00000000
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2_sr.js
+++ /dev/null
@@ -1,137 +0,0 @@
-var srchart;
-
-function srdrawg () {
- //
- srchart = nv.models.scatterChart();
- //
- srchart.showLegend(false);
- srchart.duration(300);
- srchart.color(d3.scale.category10().range());
- srchart.pointRange([0, 400]);
- srchart.pointDomain([0, 10]);
- //
- srchart.xAxis.axisLabel(js_data.trait_1);
- srchart.xAxis.axisLabelDistance(11);
- srchart.yAxis.axisLabel(js_data.trait_2);
- srchart.yAxis.axisLabelDistance(11);
- //
- xmin = d3.min(js_data.rdata[0]);
- xmax = d3.max(js_data.rdata[0]);
- xrange = xmax - xmin;
- ymin = d3.min(js_data.rdata[1]);
- ymax = d3.max(js_data.rdata[1]);
- yrange = ymax - ymin;
- srchart.xDomain([0, xmax + xrange/10]);
- srchart.yDomain([0, ymax + yrange/10]);
- srchart.xAxis.tickFormat(d3.format(srcheckformat(xrange)));
- srchart.yAxis.tickFormat(d3.format(srcheckformat(yrange)));
- //
- srchart.tooltip.contentGenerator(function (obj) {
- // return '<b style="font-size: 18px">(' + obj.point.x + ', ' + obj.point.y + ')</b>';
- return '<b style="font-size: 18px">' + obj.point.name + '</b>';
- });
-}
-
-function srgetdata(size, shape) {
- var data = [];
- data.push({
- values: [],
- slope: js_data.srslope,
- intercept: js_data.srintercept
- });
- for (j = 0; j < js_data.rdata[0].length; j++) {
- data[0].values.push({
- x: js_data.rdata[0][j],
- y: js_data.rdata[1][j],
- name: js_data.indIDs[j],
- size: size,
- shape: shape
- });
- }
- return data;
-}
-
-function srcheckformat(range) {
- cell = range / 10.0;
- if (cell >= 1) {
- return ",r";
- } else {
- cell = -Math.log(cell);
- n = cell.toString().split(".")[0].length;
- return ",.0" + n + "f";
- }
-}
-
-function srchartupdate() {
- //
- var axisxcolor = $("#axisxcolor").val();
- $(".nvd3 .nv-axis.nv-x text").css("fill", axisxcolor);
- //
- var axisycolor = $("#axisycolor").val();
- $(".nvd3 .nv-axis.nv-y text").css("fill", axisycolor);
- //
- var axisxfont = $("#axisxfont").val();
- $(".nvd3 .nv-axis.nv-x text").css("font-size", axisxfont);
- //
- var axisyfont = $("#axisyfont").val();
- $(".nvd3 .nv-axis.nv-y text").css("font-size", axisyfont);
- //
- var domainxcolor = $("#domainxcolor").val();
- $(".nv-x .nv-axis g path.domain").css("stroke", domainxcolor);
- //
- var domainycolor = $("#domainycolor").val();
- $(".nv-y .nv-axis g path.domain").css("stroke", domainycolor);
- //
- var domainxwidth = $("#domainxwidth").val();
- $(".nv-x .nv-axis g path.domain").css("stroke-width", domainxwidth);
- //
- var domainywidth = $("#domainywidth").val();
- $(".nv-y .nv-axis g path.domain").css("stroke-width", domainywidth);
- //
- var clinecolor = $("#clinecolor").val();
- $("line.nv-regLine").css("stroke", clinecolor);
- //
- var clinewidth = $("#clinewidth").val();
- $("line.nv-regLine").css("stroke-width", clinewidth);
-}
-
-function srchartupdatewh() {
- //
- var width = $("#srwidth").val();
- $("#srscatterplot2 svg").css("width", width);
- //
- var height = $("#srheight").val();
- $("#srscatterplot2 svg").css("height", height);
- //
- window.dispatchEvent(new Event('resize'));
-}
-
-function srchartupdatedata() {
- //
- var size = $("#srmarksize").val();
- var shape = $("#srmarkshape").val();
- //
- d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
- nv.utils.windowResize(srchart.update);
-}
-
-function saveassvg_srcs() {
- savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
-}
-
-srdrawg();
-srchartupdate();
-srchartupdatewh();
-srchartupdatedata();
-
-$(".srchartupdate").change(function () {
- srchartupdate();
-});
-
-$(".srchartupdatewh").change(function () {
- srchartupdatewh();
-});
-
-$(".srchartupdatedata").change(function () {
- srchartupdatedata();
-});
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 92e2b13b..f2e694d8 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -24,6 +24,7 @@ collection_click = function() {
submit_click = function() {
var covariates_string = "";
+ var covariates_display_string = "";
$('#collections_holder').find('input[type=checkbox]:checked').each(function() {
var this_dataset, this_trait;
this_trait = $(this).parents('tr').find('.trait').text();
@@ -31,12 +32,15 @@ submit_click = function() {
this_dataset = $(this).parents('tr').find('.dataset').text();
console.log("this_dataset is:", this_dataset);
covariates_string += this_trait + ":" + this_dataset + ","
+ covariates_display_string += this_trait + "\n"
});
// Trim the last comma
covariates_string = covariates_string.substring(0, covariates_string.length - 1)
+ //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
console.log("COVARIATES:", covariates_string)
$("input[name=covariates]").val(covariates_string)
+ $(".selected_covariates").val(covariates_display_string)
return $.colorbox.close();
};
@@ -46,6 +50,7 @@ trait_click = function() {
trait = $(this).parent().find('.trait').text();
dataset = $(this).parent().find('.dataset').text();
$("input[name=covariates]").val(trait + ":" + dataset)
+ $(".selected_covariates").text(trait)
return $.colorbox.close();
};
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 099d8010..df10c060 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -88,7 +88,8 @@
};
})(this));
$("#remove_covariates").click(function () {
- $("input[name=covariates]").val("")
+ $("input[name=covariates]").val("")
+ $(".selected_covariates").val("")
});
d3.select("#clear_compare_trait").on("click", (function(_this) {
return function() {
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index ad72052e..e7f3229b 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -26,13 +26,13 @@
{% endif %}
</div>
<div>
- <form id="collections_form" action="/delete" method="post">
- <input type="hidden" name="uc_id" id="uc_id" value="" />
- </form>
+ <form id="collections_form" action="/delete" method="post">
+ <input type="hidden" name="uc_id" id="uc_id" value="" />
+ </form>
<button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
<button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
<button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
- <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button>
+ <button class="btn btn-danger" id="remove_collections" data-url="/collections/delete">Remove Collections</button>
</div>
<br>
<div id="collections_list" style="width:50%;">
@@ -51,7 +51,11 @@
<tbody>
{% for uc in collections %}
<tr class="collection_line">
+ {% if g.user_session.user_ob %}
<td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
+ {% else %}
+ <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td>
+ {% endif %}
<td align="right">{{ loop.index }}
{% if g.user_session.user_ob %}
<td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index fb2bd55c..bb509270 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -75,72 +75,16 @@
<table class="table">
<tr>
-
- <td>Axis X Color</td>
- <td><input class="chartupdate" id="axisxcolor" type="color" value="#000000"></td>
-
- <td>Axis X Font</td>
- <td><input class="chartupdate" id="axisxfont" type="text" value="16" style="width: 44px;"> px</td>
-
- <td>Domain X Color</td>
- <td><input class="chartupdate" id="domainxcolor" type="color" value="#000000"></td>
-
- <td>Domain X Width</td>
- <td><input class="chartupdate" id="domainxwidth" type="text" value="2" style="width: 44px;"> px</td>
-
- <td>Correlation Line Color</td>
- <td><input class="chartupdate" id="clinecolor" type="color" value="#000000"></td>
-
- <td>Axis Line Color</td>
- <td><input class="chartupdate" id="axiscolor" type="color" value="#000000"></td>
-
- </tr>
- <tr>
-
- <td>Axis Y Color</td>
- <td><input class="chartupdate" id="axisycolor" type="color" value="#000000"></td>
-
- <td>Axis Y Font</td>
- <td><input class="chartupdate" id="axisyfont" type="text" value="16" style="width: 44px;"> px</td>
-
- <td>Domain Y Color</td>
- <td><input class="chartupdate" id="domainycolor" type="color" value="#000000"></td>
-
- <td>Domain Y Width</td>
- <td><input class="chartupdate" id="domainywidth" type="text" value="2" style="width: 44px;"> px</td>
-
- <td>Correlation Line Width</td>
- <td><input class="chartupdate" id="clinewidth" type="text" value="1" style="width: 44px;"> px</td>
-
- <td>Axis Line Width</td>
- <td><input class="chartupdate" id="axiswidth" type="text" value="1" style="width: 44px;"> px</td>
-
- </tr>
+ <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
+ <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+ </tr>
</table>
-<br>
-
-<ul class="nav nav-tabs">
- <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
- <li> <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
-</ul>
-
-<div class="tab-content">
- <div class="tab-pane active" id="tp1">
-
-<br>
<table class="table">
- <tr>
-
- <td>Width</td>
- <td><input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px;"> px</td>
-
- <td>Height</td>
- <td><input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px;"> px</td>
-
- <td>Size</td>
- <td>
- <select class="chartupdatedata" id="marksize" style="width: 100px;">
+ <tr>
+ <td style="vertical-align: middle;">Mark
+ <input class="chartupdate" id="markcolor" type="color" value="#8fbbda">
+ <select class="chartupdatedata" id="marksize" style="width: 44px; height: 22px;">
<option value="0">0</option>
<option value="1">1</option>
<option value="2">2</option>
@@ -152,12 +96,12 @@
<option value="8">8</option>
<option value="9">9</option>
<option value="10">10</option>
+ <option value="15">15</option>
+ <option value="20">20</option>
+ <option value="25">25</option>
+ <option value="30">30</option>
</select>
- </td>
-
- <td>Shape</td>
- <td>
- <select class="chartupdatedata" id="markshape" style="width: 100px;">
+ <select class="chartupdatedata" id="markshape" style="width: 100px; height: 22px;">
<option value="circle" selected>Circle</option>
<option value="cross">Cross</option>
<option value="triangle-up">Triangle-up</option>
@@ -166,23 +110,47 @@
<option value="square">Square</option>
</select>
</td>
-
- </tr>
+ </tr>
</table>
-<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
+<table class="table">
+ <tr>
+ <td style="vertical-align: middle;">Label
+ <input class="chartupdate" id="labelcolor" type="color" value="#000000">
+ <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Number
+ <input class="chartupdate" id="numbercolor" type="color" value="#000000">
+ <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Axis
+ <input class="chartupdate" id="axiscolor" type="color" value="#000000">
+ <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
+ </td>
+ <td style="vertical-align: middle;">Line
+ <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
+ <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
+ </td>
+ </tr>
+</table>
-<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
+<br>
-<div id="scatterplot2">
- <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-</div>
+<ul class="nav nav-tabs">
+ <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
+ <li> <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
+</ul>
+
+<div class="tab-content">
+ <div class="tab-pane active" id="tp1">
<br>
-<div class="alert alert-info" style="width: 200px; margin-left: 80px;">
- y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
-</div>
+<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
+
+<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
+
+<div id="scatterplot2"><svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
<br>
@@ -196,6 +164,13 @@
<tr><td>Intercept</td> <td>{{'%0.3f' % jsdata.intercept}}</td></tr>
<tr><td>r value</td> <td>{{'%0.3f' % jsdata.r_value}}</td></tr>
<tr><td>P value</td> <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td></tr>
+ <tr>
+ <td style="text-align: left;" colspan="2">
+ Regression Line
+ <br>
+ y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
+ </td>
+ </tr>
</tbody>
</table>
@@ -204,54 +179,12 @@
<div class="tab-pane" id="tp2">
<br>
-<table class="table">
- <tr>
-
- <td>Width</td>
- <td><input class="srchartupdatewh" id="srwidth" type="text" value="1000" style="width: 44px;"> px</td>
-
- <td>Height</td>
- <td><input class="srchartupdatewh" id="srheight" type="text" value="800" style="width: 44px;"> px</td>
-
- <td>Size</td>
- <td>
- <select class="srchartupdatedata" id="srmarksize" style="width: 100px;">
- <option value="0">0</option>
- <option value="1">1</option>
- <option value="2">2</option>
- <option value="3">3</option>
- <option value="4">4</option>
- <option value="5" selected>5</option>
- <option value="6">6</option>
- <option value="7">7</option>
- <option value="8">8</option>
- <option value="9">9</option>
- <option value="10">10</option>
- </select>
- </td>
-
- <td>Shape</td>
- <td>
- <select class="srchartupdatedata" id="srmarkshape" style="width: 100px;">
- <option value="circle" selected>Circle</option>
- <option value="cross">Cross</option>
- <option value="triangle-up">Triangle-up</option>
- <option value="triangle-down">Triangle-down</option>
- <option value="diamond">Diamond</option>
- <option value="square">Square</option>
- </select>
- </td>
-
- </tr>
-</table>
<div><a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a></div>
<div style="width: 1000px; text-align: center;"><h2>Spearman Rank Correlation Scatterplot</h2></div>
-<div id="srscatterplot2">
- <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-</div>
+<div id="srscatterplot2"><svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
<br>
@@ -287,5 +220,4 @@
<script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.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/draw_corr_scatterplot-2.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2_sr.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index ab793d58..d27788a8 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -61,6 +61,7 @@
<br>
<button class="btn btn-default" id="short_labels">Short Labels</button>
<button class="btn btn-default" id="long_labels">Long Labels</button>
+{% if pca_works == "True" %}
<br>
<br>
<h2>Factor Loadings Plot</h2>
@@ -93,7 +94,7 @@
</tbody>
</table>
</div>
-
+{% endif %}
{% endblock %}
{% block js %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index fa9e3585..fb4e19a1 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,8 +1,7 @@
{% extends "base.html" %}
{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/tabulator/css/tabulator.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/packages/DataTables/extensions/buttons.bootstrap.css" />
{% endblock %}
{% block content %}
@@ -63,15 +62,15 @@
</div>
<div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
- <table id="trait_table" class="display dataTable nowrap" style="float: left;">
+ <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;">
<thead>
<tr>
- <th style="width: 30px;"></th>
+ <th></th>
{% for header in target_dataset.header_fields %}
{% if header == 'Year' %}
<th>{{header}}</th>
{% elif header == 'Max LRS' %}
- <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ <th>Max LRS</th>
{% elif header == 'Max LRS Location' %}
<th>{{header}}</th>
{% elif header == 'Location' %}
@@ -79,7 +78,7 @@
{% elif header == 'Mean' %}
<th>{{header}}</th>
{% elif header == 'Additive Effect' %}
- <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ <th>Additive Effect</th>
{% elif header == 'Index' %}
<th>{{header}}</th>
{% elif header == 'N' %}
@@ -91,7 +90,7 @@
{% if target_dataset.type == "ProbeSet" %}
{% if corr_method == 'pearson' %}
<th>Sample r</th>
- <th>&nbsp;&nbsp;N</th>
+ <th>N</th>
<th>Sample p(r)</th>
<th>Lit r</th>
<th>Tissue r</th>
@@ -129,8 +128,8 @@
<tbody>
{% for trait in correlation_results %}
<tr>
- <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
- <td align="right">{{ loop.index }}</td>
+ <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
+ <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;">{{ loop.index }}</td>
<td>
<a href="{{ url_for('show_trait_page',
trait_id = trait.name,
@@ -191,13 +190,15 @@
{% block js %}
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
<script type="text/javascript" charset="utf-8">
function getValue(x) {
if (x.indexOf('input') >= 0) {
@@ -213,7 +214,8 @@
}
return parseFloat(x);
}
-
+
+
jQuery.fn.dataTableExt.oSort['numeric-html-asc'] = function(a,b) {
a = Math.abs(parseFloat($(a).text()));
b = Math.abs(parseFloat($(b).text()));
@@ -263,6 +265,8 @@
$(document).ready( function () {
+ var table_json = {{ json_results | safe }}
+
$('#trait_table tr').click(function(event) {
if (event.target.type !== 'checkbox') {
$(':checkbox', this).trigger('click');
diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html
new file mode 100644
index 00000000..d1b779ef
--- /dev/null
+++ b/wqflask/wqflask/templates/empty_collection.html
@@ -0,0 +1,15 @@
+{% extends "base.html" %}
+{% block title %}{{ tool }}{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ {{ header("Error") }}
+
+ <div class="container">
+ <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
+ <p>You must select at least two traits to use the {{ tool }}.</p>
+ </div>
+
+
+<!-- End of body -->
+
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index c5f815ce..ef233333 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,9 +1,10 @@
<div>
+ <div class="col-xs-7">
<div style="padding: 20px" class="form-horizontal">
<div class="form-group">
- <label for="corr_type" class="col-xs-1 control-label">Method</label>
- <div class="col-xs-2 controls">
+ <label for="corr_type" class="col-xs-2 control-label">Method</label>
+ <div class="col-xs-3 controls">
<select name="corr_type" class="form-control">
<option value="sample">Sample r</option>
<option value="lit">Literature r</option>
@@ -13,8 +14,8 @@
</div>
<div class="form-group">
- <label for="corr_dataset" class="col-xs-1 control-label">Database</label>
- <div class="col-xs-6 controls">
+ <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+ <div class="col-xs-10 controls">
<select name="corr_dataset" class="form-control">
{% for tissue in corr_tools.dataset_menu %}
{% if tissue.tissue %}
@@ -37,8 +38,8 @@
</div>
<div class="form-group">
- <label for="corr_return_results" class="col-xs-1 control-label">Return</label>
- <div class="col-xs-2 controls">
+ <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+ <div class="col-xs-3 controls">
<select name="corr_return_results" class="form-control">
{% for return_result in corr_tools.return_results_menu %}
<option value="{{ return_result }}"
@@ -53,8 +54,8 @@
</div>
<div class="form-group">
- <label for="corr_samples_group" class="col-xs-1 control-label">Samples</label>
- <div class="col-xs-2 controls">
+ <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+ <div class="col-xs-3 controls">
<select name="corr_samples_group" class="form-control">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
@@ -64,8 +65,8 @@
</div>
<div id="corr_sample_method" class="form-group">
- <label for="corr_sample_method" class="col-xs-1 control-label">Type</label>
- <div class="col-xs-2 controls">
+ <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
+ <div class="col-xs-3 controls">
<select name="corr_sample_method" class="form-control">
<option value="pearson">Pearson</option>
<option value="spearman">Spearman Rank</option>
@@ -73,14 +74,14 @@
</div>
</div>
<div class="form-group">
- <label class="col-xs-1 control-label">Min Expr</label>
- <div class="col-xs-2 controls">
+ <label class="col-xs-2 control-label">Min Expr</label>
+ <div class="col-xs-3 controls">
<input name="min_expr" value="" type="text" class="form-control" style="width: 50px;">
</div>
</div>
<div class="form-group">
- <label class="col-xs-1 control-label">Location</label>
- <div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label">Location</label>
+ <div class="col-xs-5 controls">
<span>
Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">&nbsp;&nbsp;&nbsp;
Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
@@ -89,8 +90,8 @@
</div>
</div>
<div class="form-group">
- <label class="col-xs-1 control-label">Range</label>
- <div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label">Range</label>
+ <div class="col-xs-5 controls">
<input name="p_range_lower" value="" type="hidden">
<input name="p_range_upper" value="" type="hidden">
<span style="display: inline;">
@@ -103,48 +104,45 @@
</div>
<div class="form-group">
- <label for="corr_sample_method" class="col-xs-1 control-label"></label>
- <div class="col-xs-4 controls">
+ <label for="corr_sample_method" class="col-xs-2 control-label"></label>
+ <div class="col-xs-3 controls">
<button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
-
- <div class="form-group">
- <label for="descriptions" class="col-xs-1 control-label"></label>
- <div class="col-xs-6 controls">
- <span id="sample_r_desc" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
- is computed
- between trait data and any
- other traits in the sample database selected above. Use
- <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
- Rank</a>
- when the sample size is small (&lt;20) or when there are influential outliers.
- </span>
- <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
- (Lit r) between
- this gene and all other genes is computed<br>
- using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
- Semantic Gene Organizer</a>
- and human, rat, and mouse data from PubMed.
- Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
- <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
- </span>
- <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
- The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
- (Tissue r)
- estimates the similarity of expression of two genes
- or transcripts across different cells, tissues, or organs
- (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
- Tissue correlations
- are generated by analyzing expression in multiple samples usually taken from single cases.<br>
- <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
- computed for all pairs of genes using data from mouse samples.<br>
- </span>
- </div>
- </div>
</div>
+ </div>
+ <div class="col-xs-5">
+ <span id="sample_r_desc" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
+ is computed
+ between trait data and any
+ other traits in the sample database selected above. Use
+ <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
+ Rank</a>
+ when the sample size is small (&lt;20) or when there are influential outliers.
+ </span>
+ <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
+ (Lit r) between
+ this gene and all other genes is computed<br>
+ using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
+ Semantic Gene Organizer</a>
+ and human, rat, and mouse data from PubMed.
+ Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
+ <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
+ </span>
+ <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
+ The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
+ (Tissue r)
+ estimates the similarity of expression of two genes
+ or transcripts across different cells, tissues, or organs
+ (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
+ Tissue correlations
+ are generated by analyzing expression in multiple samples usually taken from single cases.<br>
+ <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
+ computed for all pairs of genes using data from mouse samples.<br>
+ </span>
+ </div>
</div> \ 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 dcec2b9e..03590c2c 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,6 +1,6 @@
<div>
- {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
- <div class="col-xs-4">
+ {% if dataset.group.mapping_names|length > 0 %}
+ <div class="col-xs-5">
<div class="tabbable"> <!-- Only required for left/right tabs -->
<ul class="nav nav-pills">
@@ -38,11 +38,11 @@
{# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
{% if dataset.group.mapping_id == "1" %}
<div class="tab-pane active" id="gemma">
- <div style="padding-top: 10px;" class="form-horizontal">
+ <div style="padding-top: 20px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -52,50 +52,72 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
- <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-4 control-label">Use LOCO</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
<label class="radio-inline">
- <input type="radio" name="use_loco" value="True">
+ <input type="radio" name="use_loco" value="True" checked="">
Yes
</label>
<label class="radio-inline">
- <input type="radio" name="use_loco" value="False" checked="">
+ <input type="radio" name="use_loco" value="False">
No
</label>
</div>
</div>
+ <!--
</div>
<div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+ -->
<div class="mapping_method_fields form-group">
- <button type="button" id="select_covariates" class="btn btn-default">
- Select Covariates
- </button>
- <button type="button" id="remove_covariates" class="btn btn-default">
- Remove Covariates
+ <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
+ <div style="margin-left:20px;" class="col-xs-7">
+ {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% elif g.cookie_session.display_num_collections() == "" %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+ <div style="margin-bottom: 10px;" class="btn-group" role="group">
+ <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+ <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+ </div>
+ <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+ {% endif %}
+ </div>
+ </div>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+ Compute
</button>
+ </div>
</div>
</div>
-
+<!--
<div class="form-group">
<div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label"></label>
+ <div class="col-xs-4">
<button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
+ </div>
</div>
</div>
+-->
</div>
<div class="tab-pane" id="interval_mapping">
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<select id="genofile_reaper" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -105,20 +127,20 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
- <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<input name="num_bootstrap" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -162,8 +184,8 @@
<div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_reaper" value="True">
Yes
@@ -174,11 +196,12 @@
</label>
</div>
</div>
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
</div>
</div>
<!--<div id="alert_placeholder"></div>-->
@@ -189,8 +212,8 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<select id="genofile_rqtl_geno" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -200,17 +223,14 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- <input name="num_perm_rqtl_geno" value="" type="text" class="form-control">
+ <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
+ <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
</div>
</div>
- <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
- Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
- </div>
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -228,8 +248,8 @@
</div>
<div class="mapping_method_fields form-group">
- <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label>
- <div class="col-xs-4 controls">
+ <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<select name="mapmethod_rqtl_geno" class="form-control">
<option value="em">em</option>
<option value="imp">imp</option>
@@ -243,8 +263,8 @@
</div>
<div class="mapping_method_fields form-group">
- <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label>
- <div class="col-xs-4 controls">
+ <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
+ <div style="margin-left:20px;" class="col-xs-4 controls">
<select name="mapmodel_rqtl_geno" class="form-control">
<option value="normal">normal</option>
<!--<option value="binary">binary</option>
@@ -269,8 +289,8 @@
</div>
-->
<div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
- <div class="col-xs-12 controls">
+ <label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_rqtl" value="True">
Yes
@@ -282,11 +302,12 @@
</div>
</div>
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
</div>
</div>
</div>
@@ -295,8 +316,8 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<select id="genofile_pylmm" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -305,44 +326,12 @@
</div>
</div>
{% endif %}
-<!--
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
- {% else %}
- <input name="control_pylmm" value="" type="text" />
- {% endif %}
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="true">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="false" checked="">
- No
- </label>
- </div>
- </div>
- <div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
- <div class="col-xs-12 controls">
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="True">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
- No
- </label>
- </div>
- </div>
--->
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
+ <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
+ Compute
+ </button>
</div>
</div>
</div>
@@ -354,8 +343,8 @@
<div style="padding-top: 10px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -365,29 +354,34 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
- <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
- </div>
-
- <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <button type="button" id="select_covariates" class="btn btn-default">
- Select Covariates
- </button>
- <button type="button" id="remove_covariates" class="btn btn-default">
- Remove Covariates
- </button>
+ <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
+ <div style="margin-left:20px;" class="col-xs-7">
+ {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% elif g.cookie_session.display_num_collections() == "" %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+ <div style="margin-bottom: 10px;" class="btn-group" role="group">
+ <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+ <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+ </div>
+ <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
+ {% endif %}
+ </div>
</div>
- </div>
-
- <div class="form-group">
- <div class="col-xs-4 controls">
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6">
<button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
+ </div>
</div>
</div>
</div>
@@ -395,16 +389,16 @@
<div class="tab-pane" id="plink">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="maf_plink" value="0.01" type="text" class="form-control">
</div>
</div>
</div>
<div class="form-group">
- <label for="plink_compute" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
+ <label style="text-align: right;" class="col-xs-3 control-label"></label>
+ <div style="margin-left:20px;" class="col-xs-6 controls">
<button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
@@ -416,25 +410,29 @@
</div>
</div>
</div>
- <div class="col-xs-6">
+ <div class="col-xs-5">
{% if dataset.group.mapping_id == "1" %}
<dl>
+ <dt>GEMMA</dt>
+ <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd>
<dt>Interval Mapping</dt>
<dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
- <dt>pyLMM</dt>
- <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
<dt>R/qtl</dt>
<dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+ <dt>pyLMM</dt>
+ <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
</dl>
{% else %}
<dl>
+ {% if mapping_method == "GEMMA" %}
<dt>GEMMA</dt>
<dd>
GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br>
- Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you receive an error, please wait a few minutes and try again.
</dd>
+ {% elif mapping_method == "PLINK" %}
<dt>PLINK</dt>
<dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
+ {% endif %}
</dl>
{% endif %}
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8476b6c5..3ebef046 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -582,7 +582,7 @@ def marker_regression_page():
'control_marker',
'control_marker_db',
'do_control',
- 'genofile',
+ 'genofile_string',
'pair_scan',
'startMb',
'endMb',
@@ -743,7 +743,7 @@ def corr_matrix_page():
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
- if traits[0] != "":
+ if len(traits) > 1:
template_vars = show_corr_matrix.CorrelationMatrix(start_vars)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 03:34:38 +0000