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authorLei Yan2017-04-06 18:20:51 +0000
committerLei Yan2017-04-06 18:20:51 +0000
commit67218be3a181de7aad617237c11ee33436b8d762 (patch)
treed999c5a59bda8d82f04cfb151fb4bba57f2f19be
parent0b25ab1565faf3824d591c545dfe71dbd28c38ee (diff)
parentf419b8bc824303009817ad9d52e1452b870b0039 (diff)
downloadgenenetwork2-67218be3a181de7aad617237c11ee33436b8d762.tar.gz
Merge branch 'master' of github.com:genenetwork/genenetwork2
-rw-r--r--wqflask/base/data_set.py35
-rw-r--r--wqflask/base/trait.py16
-rw-r--r--wqflask/base/webqtlConfig.py2
-rw-r--r--wqflask/runserver.py2
-rw-r--r--wqflask/wqflask/collect.py18
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py9
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py87
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py12
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py98
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py63
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py35
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py19
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py174
-rw-r--r--wqflask/wqflask/static/new/images/a1.gifbin0 -> 430 bytes
-rw-r--r--wqflask/wqflask/static/new/images/arrowdown.gifbin0 -> 844 bytes
-rw-r--r--wqflask/wqflask/static/new/images/step1.gifbin0 -> 758 bytes
-rw-r--r--wqflask/wqflask/static/new/images/step2.gifbin0 -> 826 bytes
-rw-r--r--wqflask/wqflask/static/new/images/step3.gifbin0 -> 818 bytes
-rw-r--r--wqflask/wqflask/static/new/javascript/draw_probability_plot.js10
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js2
-rw-r--r--wqflask/wqflask/static/new/packages/nvd3/nv.d3.css1188
-rw-r--r--wqflask/wqflask/templates/correlation_page.html125
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html12
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html14
-rw-r--r--wqflask/wqflask/templates/show_trait.html4
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html7
-rw-r--r--wqflask/wqflask/templates/submit_trait.html2
-rw-r--r--wqflask/wqflask/views.py33
29 files changed, 1081 insertions, 888 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..7f08135f 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -61,14 +61,17 @@ logger = getLogger(__name__ )
# Each subclass will add to this
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
- return dataset_class(dataset_name, get_samplelist)
+ if dataset_type == "Temp":
+ return dataset_class(dataset_name, get_samplelist, group_name)
+ else:
+ return dataset_class(dataset_name, get_samplelist)
class Dataset_Types(object):
@@ -261,10 +264,13 @@ class DatasetGroup(object):
has multiple datasets associated with it.
"""
- def __init__(self, dataset):
+ def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
- self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ if name == None:
+ self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ else:
+ self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
@@ -304,7 +310,7 @@ class DatasetGroup(object):
elif mapping_id == "2":
mapping_names = ["GEMMA"]
elif mapping_id == "4":
- mapping_names = ["PLINK"]
+ mapping_names = ["GEMMA", "PLINK"]
else:
mapping_names = []
@@ -319,9 +325,7 @@ class DatasetGroup(object):
def check_plink_gemma():
if flat_file_exists("mapping"):
MAPPING_PATH = flat_files("mapping")+"/"
- if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
- (os.path.isfile(MAPPING_PATH+self.name+".map") or
- os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+ if os.path.isfile(MAPPING_PATH+self.name+".bed"):
return True
return False
@@ -481,7 +485,7 @@ class DataSet(object):
"""
- def __init__(self, name, get_samplelist = True):
+ def __init__(self, name, get_samplelist = True, group_name = None):
assert name, "Need a name"
self.name = name
@@ -493,11 +497,12 @@ class DataSet(object):
self.setup()
- self.check_confidentiality()
-
- self.retrieve_other_names()
-
- self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ if self.type == "Temp": #Need to supply group name as input if temp trait
+ self.group = DatasetGroup(self, group_name) # sets self.group and self.group_id and gets genotype
+ else:
+ self.check_confidentiality()
+ self.retrieve_other_names()
+ self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
@@ -1156,6 +1161,8 @@ class MrnaAssayDataSet(DataSet):
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
+ DS_NAME_MAP['Temp'] = 'TempDataSet'
+
def setup(self):
self.search_fields = ['name',
'description']
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bf87e879..e22a51e4 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -62,6 +62,11 @@ class GeneralTrait(object):
self.strand_probe = None
self.symbol = None
+ self.LRS_score_repr = "N/A"
+ self.LRS_score_value = 0
+ self.LRS_location_repr = "N/A"
+ self.LRS_location_value = 1000000
+
if kw.get('fullname'):
name2 = value.split("::")
if len(name2) == 2:
@@ -72,9 +77,10 @@ class GeneralTrait(object):
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
- self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
- if get_sample_info != False:
- self = retrieve_sample_data(self, self.dataset)
+ if self.dataset.type != "Temp":
+ self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+ if get_sample_info != False:
+ self = retrieve_sample_data(self, self.dataset)
def get_name(self):
@@ -315,12 +321,12 @@ def get_sample_data():
#
#return jsonable_sample_data
-def jsonable(trait, dataset_name):
+def jsonable(trait):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name)
+ dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..1e47e183 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -65,7 +65,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
# want to reach this base dir
assert_writable_dir(TEMPDIR)
-TMPDIR = mk_dir(TEMPDIR+'/gn2/')
+TMPDIR = mk_dir(TEMPDIR+'gn2')
assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR+'/cache/')
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 0342b7ad..a6ae28af 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -50,5 +50,5 @@ else: # staging/production modes
debug=False,
use_debugger=False,
threaded=True,
- processes=8,
+ processes=0,
use_reloader=True)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index ba555094..478dbcaa 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -203,7 +203,8 @@ def process_traits(unprocessed_traits):
data, _separator, hmac = trait.rpartition(':')
data = data.strip()
assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
- traits.add (str(data))
+ traits.add(str(data))
+
return traits
def report_change(len_before, len_now):
@@ -244,7 +245,6 @@ def collections_new():
if "sign_in" in params:
return redirect(url_for('login'))
-
if "create_new" in params:
print("in create_new")
collection_name = params['new_collection']
@@ -376,13 +376,17 @@ def view_collection():
for atrait in traits:
name, dataset_name = atrait.split(':')
- dataset = create_dataset(dataset_name)
-
- trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
- trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
+ if dataset_name == "Temp":
+ group = name.split("_")[2]
+ dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group)
+ trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
+ else:
+ dataset = create_dataset(dataset_name)
+ trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
+ trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
trait_obs.append(trait_ob)
- json_version.append(trait.jsonable(trait_ob, dataset_name))
+ json_version.append(trait.jsonable(trait_ob))
if "uc_id" in params:
collection_info = dict(trait_obs=trait_obs,
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index cc21d1bf..7957e643 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,7 +96,14 @@ class CorrelationResults(object):
print("TESTING...")
with Bench("Doing correlations"):
- helper_functions.get_species_dataset_trait(self, start_vars)
+ if start_vars['dataset'] == "Temp":
+ self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
+ self.trait_id = "Temp"
+ self.this_trait = GeneralTrait(dataset=self.dataset,
+ name=self.trait_id,
+ cellid=None)
+ else:
+ helper_functions.get_species_dataset_trait(self, start_vars)
self.dataset.group.read_genotype_file()
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 630980c7..95a5f6a6 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -33,6 +33,9 @@ import math
import collections
import resource
+import numarray
+import numarray.linear_algebra as la
+import numpy as np
import scipy
from rpy2.robjects.packages import importr
@@ -91,31 +94,40 @@ class CorrelationMatrix(object):
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
+ if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples
+ return False
+
self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
self.corr_results = []
self.pca_corr_results = []
+ self.trait_data_array = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
this_db = trait_db[1]
- this_db_samples = this_db.group.samplelist
+ this_db_samples = this_db.group.all_samples_ordered()
this_sample_data = this_trait.data
+ this_trait_vals = []
+ for index, sample in enumerate(this_db_samples):
+ if (sample in this_sample_data):
+ sample_value = this_sample_data[sample].value
+ this_trait_vals.append(sample_value)
+ self.trait_data_array.append(this_trait_vals)
+
corr_result_row = []
pca_corr_result_row = []
is_spearman = False #ZS: To determine if it's above or below the diagonal
for target in self.trait_list:
target_trait = target[0]
target_db = target[1]
- target_samples = target_db.group.samplelist
-
+ target_samples = target_db.group.all_samples_ordered()
target_sample_data = target_trait.data
this_trait_vals = []
target_vals = []
for index, sample in enumerate(target_samples):
-
if (sample in this_sample_data) and (sample in target_sample_data):
sample_value = this_sample_data[sample].value
target_sample_value = target_sample_data[sample].value
@@ -144,13 +156,14 @@ class CorrelationMatrix(object):
self.corr_results.append(corr_result_row)
self.pca_corr_results.append(pca_corr_result_row)
- print("corr_results:", pf(self.corr_results))
+ corr_result_eigen = la.eigenvectors(numarray.array(self.pca_corr_results))
+ corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen)
groups = []
for sample in self.all_sample_list:
groups.append(1)
- pca = self.calculate_pca(self.pca_corr_results, range(len(self.traits)))
+ pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
self.loadings_array = self.process_loadings()
@@ -180,31 +193,34 @@ class CorrelationMatrix(object):
#print("trait_list:", self.trait_list)
- def calculate_pca(self, corr_results, cols):
+ def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
base = importr('base')
stats = importr('stats')
- print("checking:", pf(stats.rnorm(100)))
- corr_results_to_list = robjects.FloatVector([item for sublist in corr_results for item in sublist])
- print("corr_results:", pf(corr_results_to_list))
+ corr_results_to_list = robjects.FloatVector([item for sublist in self.pca_corr_results for item in sublist])
m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
eigen = base.eigen(m)
- print("eigen:", eigen)
pca = stats.princomp(m, cor = "TRUE")
- print("pca:", pca)
self.loadings = pca.rx('loadings')
self.scores = pca.rx('scores')
self.scale = pca.rx('scale')
- print("scores:", pca.rx('scores'))
- print("scale:", pca.rx('scale'))
+ trait_array = zScore(self.trait_data_array)
+ trait_array = np.array(trait_array)
+ trait_array_vectors = np.dot(corr_eigen_vectors, trait_array)
+
+ pca_traits = []
+ for i, vector in enumerate(trait_array_vectors):
+ if corr_eigen_value[i-1] < 100.0/len(self.trait_list):
+ pca_traits.append(vector*-1.0)
+
+ print("pca_traits:", pca_traits)
return pca
def process_loadings(self):
loadings_array = []
loadings_row = []
- print("before loop:", self.loadings[0])
for i in range(len(self.trait_list)):
loadings_row = []
if len(self.trait_list) > 2:
@@ -215,6 +231,45 @@ class CorrelationMatrix(object):
position = i + len(self.trait_list)*j
loadings_row.append(self.loadings[0][position])
loadings_array.append(loadings_row)
- print("loadings:", loadings_array)
return loadings_array
+def zScore(trait_data_array):
+ NN = len(trait_data_array[0])
+ if NN < 10:
+ return trait_data_array
+ else:
+ i = 0
+ for data in trait_data_array:
+ N = len(data)
+ S = reduce(lambda x,y: x+y, data, 0.)
+ SS = reduce(lambda x,y: x+y*y, data, 0.)
+ mean = S/N
+ var = SS - S*S/N
+ stdev = math.sqrt(var/(N-1))
+ if stdev == 0:
+ stdev = 1e-100
+ data2 = map(lambda x:(x-mean)/stdev,data)
+ trait_data_array[i] = data2
+ i += 1
+ return trait_data_array
+
+def sortEigenVectors(vector):
+ try:
+ eigenValues = vector[0].tolist()
+ eigenVectors = vector[1].tolist()
+ combines = []
+ i = 0
+ for item in eigenValues:
+ combines.append([eigenValues[i],eigenVectors[i]])
+ i += 1
+ combines.sort(webqtlUtil.cmpEigenValue)
+ A = []
+ B = []
+ for item in combines:
+ A.append(item[0])
+ B.append(item[1])
+ sum = reduce(lambda x,y: x+y, A, 0.0)
+ A = map(lambda x:x*100.0/sum, A)
+ return [A,B]
+ except:
+ return [] \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 3bde61cd..6e2cb972 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,22 +1,22 @@
import os, math
from base import webqtlConfig
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_RESULTS_PATH
+from utility.tools import flat_files, GEMMA_COMMAND
def run_gemma(this_dataset, samples, vals):
"""Generates p-values for each marker using GEMMA"""
print("INSIDE GEMMA_MAPPING")
- gen_pheno_txt_file(this_dataset, samples, vals)
+ gen_pheno_txt_file(this_dataset, vals)
# use GEMMA_RUN in the next one, create a unique temp file
- gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -outdir %s/output -o %s_output' % (flat_files('mapping'),
+ gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
this_dataset.group.name,
flat_files('mapping'),
this_dataset.group.name,
- GEMMA_RESULTS_PATH,
+ webqtlConfig.GENERATED_IMAGE_DIR,
this_dataset.group.name)
print("gemma_command:" + gemma_command)
@@ -26,7 +26,7 @@ def run_gemma(this_dataset, samples, vals):
return marker_obs
-def gen_pheno_txt_file(this_dataset, samples, vals):
+def gen_pheno_txt_file(this_dataset, vals):
"""Generates phenotype file for GEMMA"""
current_file_data = []
@@ -47,7 +47,7 @@ def parse_gemma_output(this_dataset):
included_markers = []
p_values = []
marker_obs = []
- with open("{}/output/{}_output.assoc.txt".format(GEMMA_RESULTS_PATH, this_dataset.group.name)) as output_file:
+ with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name)) as output_file:
for line in output_file:
if line.startswith("chr"):
continue
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index b1d2f811..87532445 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -211,6 +211,8 @@ class MarkerRegression(object):
self.control_marker,
self.manhattan_plot)
elif self.mapping_method == "plink":
+ self.score_type = "-log(p)"
+ self.manhattan_plot = True
results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf)
#results = self.run_plink()
elif self.mapping_method == "pylmm":
@@ -263,52 +265,53 @@ class MarkerRegression(object):
self.trimmed_markers = trim_markers_for_table(results)
- self.json_data['chr'] = []
- self.json_data['pos'] = []
- self.json_data['lod.hk'] = []
- self.json_data['markernames'] = []
-
- self.json_data['suggestive'] = self.suggestive
- self.json_data['significant'] = self.significant
-
- #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
- for index, qtl in enumerate(self.qtl_results):
- #if index<40:
- # logger.debug("lod score is:", qtl['lod_score'])
- if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
- #logger.debug("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'])
- if 'lrs_value' in qtl.keys():
- self.json_data['lod.hk'].append(str(qtl['lrs_value']))
- else:
- self.json_data['lod.hk'].append(str(qtl['lod_score']))
- self.json_data['markernames'].append(qtl['name'])
-
- #Get chromosome lengths for drawing the interval map plot
- chromosome_mb_lengths = {}
- 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
-
- # logger.debug("json_data:", self.json_data)
-
- self.js_data = dict(
- result_score_type = self.score_type,
- json_data = self.json_data,
- this_trait = self.this_trait.name,
- data_set = self.dataset.name,
- maf = self.maf,
- manhattan_plot = self.manhattan_plot,
- mapping_scale = self.mapping_scale,
- chromosomes = chromosome_mb_lengths,
- qtl_results = self.qtl_results,
- num_perm = self.num_perm,
- perm_results = self.perm_output,
- )
+ if self.mapping_method != "gemma":
+ self.json_data['chr'] = []
+ self.json_data['pos'] = []
+ self.json_data['lod.hk'] = []
+ self.json_data['markernames'] = []
+
+ self.json_data['suggestive'] = self.suggestive
+ self.json_data['significant'] = self.significant
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ for index, qtl in enumerate(self.qtl_results):
+ #if index<40:
+ # logger.debug("lod score is:", qtl['lod_score'])
+ if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+ #logger.debug("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'])
+ if 'lrs_value' in qtl.keys():
+ self.json_data['lod.hk'].append(str(qtl['lrs_value']))
+ else:
+ self.json_data['lod.hk'].append(str(qtl['lod_score']))
+ self.json_data['markernames'].append(qtl['name'])
+
+ #Get chromosome lengths for drawing the interval map plot
+ chromosome_mb_lengths = {}
+ 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
+
+ # logger.debug("json_data:", self.json_data)
+
+ self.js_data = dict(
+ result_score_type = self.score_type,
+ json_data = self.json_data,
+ this_trait = self.this_trait.name,
+ data_set = self.dataset.name,
+ maf = self.maf,
+ manhattan_plot = self.manhattan_plot,
+ mapping_scale = self.mapping_scale,
+ chromosomes = chromosome_mb_lengths,
+ qtl_results = self.qtl_results,
+ num_perm = self.num_perm,
+ perm_results = self.perm_output,
+ )
def run_rqtl_plink(self):
# os.chdir("") never do this inside a webserver!!
@@ -599,8 +602,7 @@ def trim_markers_for_table(markers):
#ZS: So we end up with a list of just 200 markers
if len(sorted_markers) >= 200:
- trimming_factor = 200 / len(sorted_markers)
- trimmed_sorted_markers = sorted_markers[:int(len(sorted_markers) * trimming_factor)]
+ trimmed_sorted_markers = sorted_markers[:200]
return trimmed_sorted_markers
else:
return sorted_markers
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 392ad745..49959a74 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -181,7 +181,8 @@ class MarkerRegression(object):
self.mapmodel_rqtl_geno = start_vars['model']
self.pair_scan = start_vars['pair_scan']
- self.js_data = start_vars['js_data']
+ if self.mapping_method != "gemma" and self.mapping_method != "plink":
+ self.js_data = start_vars['js_data']
self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
#ZS: Think I can just get all this from dataset object now
@@ -564,7 +565,6 @@ class MarkerRegression(object):
gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
self.gifmap = gifmap.__str__()
- #print("GIFMAP:", gifmap.__str__())
self.filename= webqtlUtil.genRandStr("Itvl_")
intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg')
@@ -847,8 +847,7 @@ class MarkerRegression(object):
pass
#draw position, no need to use a separate function
- if self.genotype.Mbmap:
- self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
+ self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
return gifmap
@@ -1010,35 +1009,34 @@ class MarkerRegression(object):
locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
else:
locPixel = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- if _chr.name != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ for i, _chr in enumerate(self.ChrList[1:]):
+ if _chr[0] != Chr:
+ locPixel += (self.ChrLengthDistList[i-1] + self.GraphInterval)*plotXScale
else:
locPixel += Mb*plotXScale
break
else:
if self.selectedChr > -1:
- if self.genotype[0].name != Chr:
- return
- else:
- for i, _locus in enumerate(self.genotype[0]):
- #the trait's position is on the left of the first genotype
- if i==0 and _locus.Mb >= Mb:
- locPixel=-1
- break
+ for i, qtlresult in enumerate(self.qtlresults):
+ if qtlresult['Chr'] != self.selectedChr:
+ continue
- #the trait's position is between two traits
- if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
- locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
- break
+ if i==0 and qtlresult['Mb'] >= Mb:
+ locPixel=-1
+ break
+
+ #the trait's position is between two traits
+ if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
+ locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['cM']+(qtlresult['cM']-self.qtlresults[i-1]['cM'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+ break
- #the trait's position is on the right of the last genotype
- if i==len(self.genotype[0]) and Mb>=_locus.Mb:
- locPixel = -1
+ #the trait's position is on the right of the last genotype
+ if i==len(self.qtlresults) and Mb>=qtlresult['Mb']:
+ locPixel = -1
else:
locPixel = xLeftOffset
- for i, _chr in enumerate(self.genotype):
- if _chr.name != Chr:
+ for i, _chr in enumerate(self.ChrList):
+ if _chr != Chr:
locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
else:
locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
@@ -1190,13 +1188,16 @@ class MarkerRegression(object):
else:
if self.mapping_method == "gemma":
string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+ elif self.mapping_method == "plink":
+ string2 = 'Using PLINK mapping method with no control for other QTLs.'
else:
string2 = 'Using Haldane mapping function with no control for other QTLs'
- d = 4+ max(canvas.stringWidth(string1,font=labelFont),canvas.stringWidth(string2,font=labelFont))
if self.this_trait.name:
identification = "Trait ID: %s : %s" % (self.dataset.fullname, self.this_trait.name)
+ d = 4+ max(canvas.stringWidth(identification, font=labelFont), canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
canvas.drawString(identification,canvas.size[0] - xRightOffset-d,20*fontZoom,font=labelFont,color=labelColor)
-
+ else:
+ d = 4+ max(canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35*fontZoom,font=labelFont,color=labelColor)
canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50*fontZoom,font=labelFont,color=labelColor)
@@ -1915,7 +1916,7 @@ class MarkerRegression(object):
if self.lrsMax <= 0: #sliding scale
if "lrs_value" in self.qtlresults[0]:
LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
- if self.LRS_LOD == "LOD":
+ if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
@@ -2118,7 +2119,7 @@ class MarkerRegression(object):
# fix the over limit LRS graph issue since genotype trait may give infinite LRS;
# for any lrs is over than 460(LRS max in this system), it will be reset to 460
if 'lrs_value' in qtlresult:
- if self.LRS_LOD == "LOD":
+ if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
else:
@@ -2143,7 +2144,11 @@ class MarkerRegression(object):
# Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
if self.manhattan_plot == True:
- canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)
+ if previous_chr_as_int % 2 == 1:
+ point_color = pid.grey
+ else:
+ point_color = pid.black
+ canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont)
else:
LRSCoordXY.append((Xc, Yc))
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index b457b9a0..3d31da1a 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -3,7 +3,7 @@ import os
from base.webqtlConfig import TMPDIR
from utility import webqtlUtil
-from utility.tools import PLINK_COMMAND
+from utility.tools import flat_files, PLINK_COMMAND
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -11,12 +11,11 @@ logger = utility.logger.getLogger(__name__ )
def run_plink(this_trait, dataset, species, vals, maf):
plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name))
- gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
+ gen_pheno_txt_file(dataset, vals)
+ #gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
- plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (
- PLINK_PATH, dataset.group.name, PLINK_PATH, dataset.group.name,
- TMPDIR, plink_output_filename, this_trait.name, maf, TMPDIR,
- plink_output_filename)
+ plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-fid --no-parents --no-sex --maf %s --missing-phenotype -9 --out %s/%s --assoc ' % (
+ flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename)
logger.debug("plink_command:", plink_command)
os.system(plink_command)
@@ -29,11 +28,27 @@ def run_plink(this_trait, dataset, species, vals, maf):
# self.dataset.group.markers.markers.remove(marker)
# #del self.dataset.group.markers.markers[marker]
- logger.debug("p_values:", pf(p_values))
+ logger.debug("p_values:", p_values)
dataset.group.markers.add_pvalues(p_values)
return dataset.group.markers.markers
+def gen_pheno_txt_file(this_dataset, vals):
+ """Generates phenotype file for GEMMA/PLINK"""
+
+ current_file_data = []
+ with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
+ for i, line in enumerate(outfile):
+ split_line = line.split()
+ current_file_data.append(split_line)
+
+ with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
+ for i, line in enumerate(current_file_data):
+ if vals[i] == "x":
+ this_val = -9
+ else:
+ this_val = vals[i]
+ outfile.write(line[1] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
ped_sample_list = get_samples_from_ped_file(dataset)
@@ -71,7 +86,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
# get strain name from ped file in order
def get_samples_from_ped_file(dataset):
- ped_file= open("{}/{}.ped".format(PLINK_PATH, dataset.group.name),"r")
+ ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
line = ped_file.readline()
sample_list=[]
@@ -89,9 +104,9 @@ def get_samples_from_ped_file(dataset):
def parse_plink_output(output_filename, species):
plink_results={}
- threshold_p_value = 0.01
+ threshold_p_value = 1
- result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb")
+ result_fp = open("%s/%s.qassoc"% (TMPDIR, output_filename), "rb")
header_line = result_fp.readline()# read header line
line = result_fp.readline()
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 7e7503d4..6d84a960 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -32,7 +32,6 @@ class SampleList(object):
self.sample_attribute_values = {}
self.get_attributes()
- # logger.debug("camera: attributes are:", pf(self.attributes))
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
self.get_extra_attribute_values()
@@ -40,12 +39,18 @@ class SampleList(object):
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
- #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
- try:
- sample = self.this_trait.data[sample_name]
- except KeyError:
- logger.debug("No sample %s, let's create it now" % sample_name)
- sample = webqtlCaseData.webqtlCaseData(sample_name)
+ if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+ if counter <= len(self.this_trait) and self.this_trait[counter-1] != 'X':
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
+ else:
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+ else:
+ #ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
+ try:
+ sample = self.this_trait.data[sample_name]
+ except KeyError:
+ logger.debug("No sample %s, let's create it now" % sample_name)
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name)
#sampleNameAdd = ''
#if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 5d55ebe1..b2dfc4ac 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -2,6 +2,7 @@ from __future__ import absolute_import, print_function, division
import string
import os
+import datetime
import cPickle
import uuid
import json as json
@@ -9,6 +10,9 @@ import json as json
from collections import OrderedDict
+import redis
+Redis = redis.StrictRedis()
+
from flask import Flask, g
from htmlgen import HTMLgen2 as HT
@@ -42,16 +46,33 @@ class ShowTrait(object):
def __init__(self, kw):
logger.debug("in ShowTrait, kw are:", kw)
- if kw['trait_id'] != None:
+ if 'trait_id' in kw and kw['dataset'] != "Temp":
self.temp_trait = False
self.trait_id = kw['trait_id']
helper_functions.get_species_dataset_trait(self, kw)
- else:
+ elif 'group' in kw:
self.temp_trait = True
- self.trait_vals = kw['trait_paste'].split()
- self.temp_group = kw['group']
+ self.trait_id = "Temp_"+kw['species']+ "_" + kw['group'] + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
self.temp_species = kw['species']
- #self.create_temp_trait()
+ self.temp_group = kw['group']
+ self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
+ self.this_trait = GeneralTrait(dataset=self.dataset,
+ name=self.trait_id,
+ cellid=None)
+ self.trait_vals = kw['trait_paste'].split()
+
+ # Put values in Redis so they can be looked up later if added to a collection
+ Redis.set(self.trait_id, kw['trait_paste'])
+ else:
+ self.temp_trait = True
+ self.trait_id = kw['trait_id']
+ self.temp_species = self.trait_id.split("_")[1]
+ self.temp_group = self.trait_id.split("_")[2]
+ self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
+ self.this_trait = GeneralTrait(dataset=self.dataset,
+ name=self.trait_id,
+ cellid=None)
+ self.trait_vals = Redis.get(self.trait_id).split()
#self.dataset.group.read_genotype_file()
@@ -64,17 +85,17 @@ class ShowTrait(object):
self.build_correlation_tools()
#Get nearest marker for composite mapping
+ if not self.temp_trait:
+ if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+ self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
+ #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
+ #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
+ else:
+ self.nearest_marker = ""
+ #self.nearest_marker1 = ""
+ #self.nearest_marker2 = ""
- if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
- self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
- #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
- #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
- else:
- self.nearest_marker = ""
- #self.nearest_marker1 = ""
- #self.nearest_marker2 = ""
-
- self.make_sample_lists(self.this_trait)
+ self.make_sample_lists()
# Todo: Add back in the ones we actually need from below, as we discover we need them
hddn = OrderedDict()
@@ -84,17 +105,22 @@ class ShowTrait(object):
hddn['trait_id'] = self.trait_id
hddn['dataset'] = self.dataset.name
+ hddn['temp_trait'] = False
+ if self.temp_trait:
+ hddn['temp_trait'] = True
+ hddn['group'] = self.temp_group
+ hddn['species'] = self.temp_species
hddn['use_outliers'] = False
hddn['method'] = "pylmm"
hddn['mapping_display_all'] = True
hddn['suggestive'] = 0
hddn['num_perm'] = 0
hddn['manhattan_plot'] = ""
- if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
- hddn['control_marker'] = self.nearest_marker
- #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
- else:
- hddn['control_marker'] = ""
+ hddn['control_marker'] = ""
+ if not self.temp_trait:
+ if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
+ hddn['control_marker'] = self.nearest_marker
+ #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
hddn['do_control'] = False
hddn['maf'] = 0.01
hddn['compare_traits'] = []
@@ -118,11 +144,12 @@ class ShowTrait(object):
self.trait_table_width = get_trait_table_width(self.sample_groups)
- if self.this_trait.symbol:
- trait_symbol = self.this_trait.symbol
- else:
- trait_symbol = None
- js_data = dict(trait_id = self.this_trait.name,
+ trait_symbol = None
+ if not self.temp_trait:
+ if self.this_trait.symbol:
+ trait_symbol = self.this_trait.symbol
+
+ js_data = dict(trait_id = self.trait_id,
trait_symbol = trait_symbol,
dataset_type = self.dataset.type,
data_scale = self.dataset.data_scale,
@@ -149,7 +176,7 @@ class ShowTrait(object):
else:
return False
- self.genofiles = get_genofiles(self.this_trait)
+ self.genofiles = get_genofiles(self.dataset)
self.use_plink_gemma = check_plink_gemma()
self.use_pylmm_rqtl = check_pylmm_rqtl()
@@ -173,8 +200,8 @@ class ShowTrait(object):
dataset_menu = data_set.datasets(this_group, self.dataset.group)
dataset_menu_selected = None
if len(dataset_menu):
- if self.this_trait and self.this_trait.dataset:
- dataset_menu_selected = self.this_trait.dataset.name
+ if self.dataset:
+ dataset_menu_selected = self.dataset.name
return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
return_results_menu_selected = 500
@@ -185,52 +212,57 @@ class ShowTrait(object):
return_results_menu_selected = return_results_menu_selected,)
- def make_sample_lists(self, this_trait):
+ def make_sample_lists(self):
all_samples_ordered = self.dataset.group.all_samples_ordered()
primary_sample_names = list(all_samples_ordered)
- other_sample_names = []
- for sample in this_trait.data.keys():
- if (this_trait.data[sample].name2 in primary_sample_names) and (this_trait.data[sample].name not in primary_sample_names):
- primary_sample_names.append(this_trait.data[sample].name)
- primary_sample_names.remove(this_trait.data[sample].name2)
- elif sample not in all_samples_ordered:
- all_samples_ordered.append(sample)
- other_sample_names.append(sample)
-
- if self.dataset.group.species == "human":
- primary_sample_names += other_sample_names
-
- primary_samples = SampleList(dataset = self.dataset,
- sample_names=primary_sample_names,
- this_trait=this_trait,
- sample_group_type='primary',
- header="%s Only" % (self.dataset.group.name))
- logger.debug("primary_samples is: ", pf(primary_samples))
-
- logger.debug("other_sample_names2:", other_sample_names)
- if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
- parent_f1_samples = None
- if self.dataset.group.parlist and self.dataset.group.f1list:
- parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
-
- other_sample_names.sort() #Sort other samples
- if parent_f1_samples:
- other_sample_names = parent_f1_samples + other_sample_names
-
- logger.debug("other_sample_names:", other_sample_names)
-
- other_samples = SampleList(dataset=self.dataset,
- sample_names=other_sample_names,
- this_trait=this_trait,
- sample_group_type='other',
- header="Non-%s" % (self.dataset.group.name))
-
- self.sample_groups = (primary_samples, other_samples)
+ if not self.temp_trait:
+ other_sample_names = []
+ for sample in self.this_trait.data.keys():
+ if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
+ primary_sample_names.append(self.this_trait.data[sample].name)
+ primary_sample_names.remove(self.this_trait.data[sample].name2)
+ elif sample not in all_samples_ordered:
+ all_samples_ordered.append(sample)
+ other_sample_names.append(sample)
+
+ if self.dataset.group.species == "human":
+ primary_sample_names += other_sample_names
+
+ primary_samples = SampleList(dataset = self.dataset,
+ sample_names=primary_sample_names,
+ this_trait=self.this_trait,
+ sample_group_type='primary',
+ header="%s Only" % (self.dataset.group.name))
+
+ if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
+ parent_f1_samples = None
+ if self.dataset.group.parlist and self.dataset.group.f1list:
+ parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
+
+ other_sample_names.sort() #Sort other samples
+ if parent_f1_samples:
+ other_sample_names = parent_f1_samples + other_sample_names
+
+ logger.debug("other_sample_names:", other_sample_names)
+
+ other_samples = SampleList(dataset=self.dataset,
+ sample_names=other_sample_names,
+ this_trait=self.this_trait,
+ sample_group_type='other',
+ header="Non-%s" % (self.dataset.group.name))
+
+ self.sample_groups = (primary_samples, other_samples)
+ else:
+ self.sample_groups = (primary_samples,)
else:
+ primary_samples = SampleList(dataset = self.dataset,
+ sample_names=primary_sample_names,
+ this_trait=self.trait_vals,
+ sample_group_type='primary',
+ header="%s Only" % (self.dataset.group.name))
self.sample_groups = (primary_samples,)
-
#TODO: Figure out why this if statement is written this way - Zach
#if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
# or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
@@ -261,8 +293,8 @@ def get_nearest_marker(this_trait, this_db):
return result[0][0]
#return result[0][0], result[1][0]
-def get_genofiles(this_trait):
- jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_trait.dataset.group.name)
+def get_genofiles(this_dataset):
+ jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_dataset.group.name)
try:
f = open(jsonfile)
except:
@@ -271,7 +303,7 @@ def get_genofiles(this_trait):
return jsondata['genofile']
def get_trait_table_width(sample_groups):
- table_width = 20
+ table_width = 25
if sample_groups[0].se_exists():
table_width += 15
if (table_width + len(sample_groups[0].attributes)*10) > 100:
diff --git a/wqflask/wqflask/static/new/images/a1.gif b/wqflask/wqflask/static/new/images/a1.gif
new file mode 100644
index 00000000..283921a0
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/a1.gif
Binary files differ
diff --git a/wqflask/wqflask/static/new/images/arrowdown.gif b/wqflask/wqflask/static/new/images/arrowdown.gif
new file mode 100644
index 00000000..577e5476
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/arrowdown.gif
Binary files differ
diff --git a/wqflask/wqflask/static/new/images/step1.gif b/wqflask/wqflask/static/new/images/step1.gif
new file mode 100644
index 00000000..42d2bc7d
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step1.gif
Binary files differ
diff --git a/wqflask/wqflask/static/new/images/step2.gif b/wqflask/wqflask/static/new/images/step2.gif
new file mode 100644
index 00000000..b3dca656
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step2.gif
Binary files differ
diff --git a/wqflask/wqflask/static/new/images/step3.gif b/wqflask/wqflask/static/new/images/step3.gif
new file mode 100644
index 00000000..0e0c7ea2
--- /dev/null
+++ b/wqflask/wqflask/static/new/images/step3.gif
Binary files differ
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index e5787564..f23dad0c 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -45,7 +45,7 @@
chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range());
chart.pointRange([50, 50]);
chart.legend.updateState(false);
- chart.xAxis.axisLabel("Expected Z score").tickFormat(d3.format('.02f'));
+ chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f'));
chart.tooltipContent(function(obj) {
return '<b style="font-size: 20px">' + obj.point.name + '</b>';
});
@@ -78,13 +78,19 @@
}
return results;
})();
- chart.yAxis.axisLabel("Trait value").tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
+ //ZS: 0.1 indicates buffer, increase to increase buffer
+ y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1]
+ chart.yDomain(y_domain)
+ chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
sw_result = ShapiroWilkW(sorted_values);
W = sw_result.w.toFixed(3);
pvalue = sw_result.p.toFixed(3);
pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
z_scores = get_z_scores(sorted_values.length);
+ //ZS: 0.1 indicates buffer, increase to increase buffer
+ x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1]
+ chart.xDomain(x_domain)
slope = jStat.stdev(sorted_values);
intercept = jStat.mean(sorted_values);
make_data = function(group_name) {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8223a38c..bb1af326 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -195,7 +195,7 @@
}
row_line = "<tr>";
if (row.url != null) {
- row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
+ row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\" style=\"color: #000000;\">" + row.pretty + "</a></td>";
} else {
row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
}
diff --git a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
index 694b9218..593d3889 100644
--- a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
+++ b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
@@ -1,96 +1,96 @@
/* nvd3 version 1.8.1 (https://github.com/novus/nvd3) 2015-05-25 */
-.nvd3 .nv-axis {
- pointer-events:none;
- opacity: 1;
-}
-
-.nvd3 .nv-axis path {
- fill: none;
- stroke: #000;
- stroke-opacity: .75;
- shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-axis path.domain {
- stroke-opacity: .75;
-}
-
-.nvd3 .nv-axis.nv-x path.domain {
- stroke-opacity: 1;
-}
-
-.nvd3 .nv-axis line {
- fill: none;
- stroke: #e5e5e5;
- shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-axis .zero line,
- /*this selector may not be necessary*/ .nvd3 .nv-axis line.zero {
- stroke-opacity: .75;
-}
-
-.nvd3 .nv-axis .nv-axisMaxMin text {
- font-weight: bold;
-}
-
-.nvd3 .x .nv-axis .nv-axisMaxMin text,
-.nvd3 .x2 .nv-axis .nv-axisMaxMin text,
-.nvd3 .x3 .nv-axis .nv-axisMaxMin text {
- text-anchor: middle
-}
-
-.nvd3 .nv-axis.nv-disabled {
- opacity: 0;
-}
-
-.nvd3 .nv-bars rect {
- fill-opacity: .75;
-
- transition: fill-opacity 250ms linear;
- -moz-transition: fill-opacity 250ms linear;
- -webkit-transition: fill-opacity 250ms linear;
-}
-
-.nvd3 .nv-bars rect.hover {
- fill-opacity: 1;
-}
-
-.nvd3 .nv-bars .hover rect {
- fill: lightblue;
-}
-
-.nvd3 .nv-bars text {
- fill: rgba(0,0,0,0);
-}
-
-.nvd3 .nv-bars .hover text {
- fill: rgba(0,0,0,1);
-}
-
-.nvd3 .nv-multibar .nv-groups rect,
-.nvd3 .nv-multibarHorizontal .nv-groups rect,
-.nvd3 .nv-discretebar .nv-groups rect {
- stroke-opacity: 0;
-
- transition: fill-opacity 250ms linear;
- -moz-transition: fill-opacity 250ms linear;
- -webkit-transition: fill-opacity 250ms linear;
-}
-
-.nvd3 .nv-multibar .nv-groups rect:hover,
-.nvd3 .nv-multibarHorizontal .nv-groups rect:hover,
-.nvd3 .nv-candlestickBar .nv-ticks rect:hover,
-.nvd3 .nv-discretebar .nv-groups rect:hover {
- fill-opacity: 1;
-}
-
-.nvd3 .nv-discretebar .nv-groups text,
-.nvd3 .nv-multibarHorizontal .nv-groups text {
- font-weight: bold;
- fill: rgba(0,0,0,1);
- stroke: rgba(0,0,0,0);
-}
+.nvd3 .nv-axis {
+ pointer-events:none;
+ opacity: 1;
+}
+
+.nvd3 .nv-axis path {
+ fill: none;
+ stroke: #000;
+ stroke-opacity: .75;
+ shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-axis path.domain {
+ stroke-opacity: .75;
+}
+
+.nvd3 .nv-axis.nv-x path.domain {
+ stroke-opacity: 1;
+}
+
+.nvd3 .nv-axis line {
+ fill: none;
+ stroke: #e5e5e5;
+ shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-axis .zero line,
+ /*this selector may not be necessary*/ .nvd3 .nv-axis line.zero {
+ stroke-opacity: .75;
+}
+
+.nvd3 .nv-axis .nv-axisMaxMin text {
+ font-weight: bold;
+}
+
+.nvd3 .x .nv-axis .nv-axisMaxMin text,
+.nvd3 .x2 .nv-axis .nv-axisMaxMin text,
+.nvd3 .x3 .nv-axis .nv-axisMaxMin text {
+ text-anchor: middle
+}
+
+.nvd3 .nv-axis.nv-disabled {
+ opacity: 0;
+}
+
+.nvd3 .nv-bars rect {
+ fill-opacity: .75;
+
+ transition: fill-opacity 250ms linear;
+ -moz-transition: fill-opacity 250ms linear;
+ -webkit-transition: fill-opacity 250ms linear;
+}
+
+.nvd3 .nv-bars rect.hover {
+ fill-opacity: 1;
+}
+
+.nvd3 .nv-bars .hover rect {
+ fill: lightblue;
+}
+
+.nvd3 .nv-bars text {
+ fill: rgba(0,0,0,0);
+}
+
+.nvd3 .nv-bars .hover text {
+ fill: rgba(0,0,0,1);
+}
+
+.nvd3 .nv-multibar .nv-groups rect,
+.nvd3 .nv-multibarHorizontal .nv-groups rect,
+.nvd3 .nv-discretebar .nv-groups rect {
+ stroke-opacity: 0;
+
+ transition: fill-opacity 250ms linear;
+ -moz-transition: fill-opacity 250ms linear;
+ -webkit-transition: fill-opacity 250ms linear;
+}
+
+.nvd3 .nv-multibar .nv-groups rect:hover,
+.nvd3 .nv-multibarHorizontal .nv-groups rect:hover,
+.nvd3 .nv-candlestickBar .nv-ticks rect:hover,
+.nvd3 .nv-discretebar .nv-groups rect:hover {
+ fill-opacity: 1;
+}
+
+.nvd3 .nv-discretebar .nv-groups text,
+.nvd3 .nv-multibarHorizontal .nv-groups text {
+ font-weight: bold;
+ fill: rgba(0,0,0,1);
+ stroke: rgba(0,0,0,0);
+}
/* boxplot CSS */
.nvd3 .nv-boxplot circle {
@@ -112,57 +112,57 @@
.nv-boxplot-tick:hover {
stroke-width: 2.5px;
}
-/* bullet */
-.nvd3.nv-bullet { font: 10px sans-serif; }
-.nvd3.nv-bullet .nv-measure { fill-opacity: .8; }
-.nvd3.nv-bullet .nv-measure:hover { fill-opacity: 1; }
-.nvd3.nv-bullet .nv-marker { stroke: #000; stroke-width: 2px; }
-.nvd3.nv-bullet .nv-markerTriangle { stroke: #000; fill: #fff; stroke-width: 1.5px; }
-.nvd3.nv-bullet .nv-tick line { stroke: #666; stroke-width: .5px; }
-.nvd3.nv-bullet .nv-range.nv-s0 { fill: #eee; }
-.nvd3.nv-bullet .nv-range.nv-s1 { fill: #ddd; }
-.nvd3.nv-bullet .nv-range.nv-s2 { fill: #ccc; }
-.nvd3.nv-bullet .nv-title { font-size: 14px; font-weight: bold; }
-.nvd3.nv-bullet .nv-subtitle { fill: #999; }
-
-
-.nvd3.nv-bullet .nv-range {
- fill: #bababa;
- fill-opacity: .4;
-}
-.nvd3.nv-bullet .nv-range:hover {
- fill-opacity: .7;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick {
- stroke-width: 1px;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.hover {
- stroke-width: 2px;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.positive rect {
- stroke: #2ca02c;
- fill: #2ca02c;
-}
-
-.nvd3.nv-candlestickBar .nv-ticks .nv-tick.negative rect {
- stroke: #d62728;
- fill: #d62728;
-}
-
-.with-transitions .nv-candlestickBar .nv-ticks .nv-tick {
- transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
- -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
- -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-candlestickBar .nv-ticks line {
- stroke: #333;
-}
-
+/* bullet */
+.nvd3.nv-bullet { font: 10px sans-serif; }
+.nvd3.nv-bullet .nv-measure { fill-opacity: .8; }
+.nvd3.nv-bullet .nv-measure:hover { fill-opacity: 1; }
+.nvd3.nv-bullet .nv-marker { stroke: #000; stroke-width: 2px; }
+.nvd3.nv-bullet .nv-markerTriangle { stroke: #000; fill: #fff; stroke-width: 1.5px; }
+.nvd3.nv-bullet .nv-tick line { stroke: #666; stroke-width: .5px; }
+.nvd3.nv-bullet .nv-range.nv-s0 { fill: #eee; }
+.nvd3.nv-bullet .nv-range.nv-s1 { fill: #ddd; }
+.nvd3.nv-bullet .nv-range.nv-s2 { fill: #ccc; }
+.nvd3.nv-bullet .nv-title { font-size: 14px; font-weight: bold; }
+.nvd3.nv-bullet .nv-subtitle { fill: #999; }
+
+
+.nvd3.nv-bullet .nv-range {
+ fill: #bababa;
+ fill-opacity: .4;
+}
+.nvd3.nv-bullet .nv-range:hover {
+ fill-opacity: .7;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick {
+ stroke-width: 1px;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.hover {
+ stroke-width: 2px;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.positive rect {
+ stroke: #2ca02c;
+ fill: #2ca02c;
+}
+
+.nvd3.nv-candlestickBar .nv-ticks .nv-tick.negative rect {
+ stroke: #d62728;
+ fill: #d62728;
+}
+
+.with-transitions .nv-candlestickBar .nv-ticks .nv-tick {
+ transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-candlestickBar .nv-ticks line {
+ stroke: #333;
+}
+
.nvd3 .nv-legend .nv-disabled rect {
/*fill-opacity: 0;*/
@@ -187,455 +187,455 @@
opacity: 0;
}
-/* line plus bar */
-.nvd3.nv-linePlusBar .nv-bar rect {
- fill-opacity: .75;
-}
-
-.nvd3.nv-linePlusBar .nv-bar rect:hover {
- fill-opacity: 1;
-}
-.nvd3 .nv-groups path.nv-line {
- fill: none;
-}
-
-.nvd3 .nv-groups path.nv-area {
- stroke: none;
-}
-
-.nvd3.nv-line .nvd3.nv-scatter .nv-groups .nv-point {
- fill-opacity: 0;
- stroke-opacity: 0;
-}
-
-.nvd3.nv-scatter.nv-single-point .nv-groups .nv-point {
- fill-opacity: .5 !important;
- stroke-opacity: .5 !important;
-}
-
-
-.with-transitions .nvd3 .nv-groups .nv-point {
- transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
- -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
- -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-scatter .nv-groups .nv-point.hover,
-.nvd3 .nv-groups .nv-point.hover {
- stroke-width: 7px;
- fill-opacity: .95 !important;
- stroke-opacity: .95 !important;
-}
-
-
-.nvd3 .nv-point-paths path {
- stroke: #aaa;
- stroke-opacity: 0;
- fill: #eee;
- fill-opacity: 0;
-}
-
-
-
-.nvd3 .nv-indexLine {
- cursor: ew-resize;
-}
-
-/********************
- * SVG CSS
- */
-
-/********************
- Default CSS for an svg element nvd3 used
-*/
-svg.nvd3-svg {
- -webkit-touch-callout: none;
- -webkit-user-select: none;
- -khtml-user-select: none;
- -ms-user-select: none;
- -moz-user-select: none;
- user-select: none;
- display: block;
- width:100%;
- height:100%;
-}
-
-/********************
- Box shadow and border radius styling
-*/
-.nvtooltip.with-3d-shadow, .with-3d-shadow .nvtooltip {
- -moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
- -webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
- box-shadow: 0 5px 10px rgba(0,0,0,.2);
-
- -webkit-border-radius: 5px;
- -moz-border-radius: 5px;
- border-radius: 5px;
-}
-
-
-.nvd3 text {
- font: normal 12px Arial;
-}
-
-.nvd3 .title {
- font: bold 14px Arial;
-}
-
-.nvd3 .nv-background {
- fill: white;
- fill-opacity: 0;
-}
-
-.nvd3.nv-noData {
- font-size: 18px;
- font-weight: bold;
-}
-
-
-/**********
-* Brush
-*/
-
-.nv-brush .extent {
- fill-opacity: .125;
- shape-rendering: crispEdges;
-}
-
-.nv-brush .resize path {
- fill: #eee;
- stroke: #666;
-}
-
-
-/**********
-* Legend
-*/
-
-.nvd3 .nv-legend .nv-series {
- cursor: pointer;
-}
-
-.nvd3 .nv-legend .nv-disabled circle {
- fill-opacity: 0;
-}
-
-/* focus */
-.nvd3 .nv-brush .extent {
- fill-opacity: 0 !important;
-}
-
-.nvd3 .nv-brushBackground rect {
- stroke: #000;
- stroke-width: .4;
- fill: #fff;
- fill-opacity: .7;
-}
-
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick {
- stroke-width: 1px;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.hover {
- stroke-width: 2px;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.positive {
- stroke: #2ca02c;
-}
-
-.nvd3.nv-ohlcBar .nv-ticks .nv-tick.negative {
- stroke: #d62728;
-}
-
-
-.nvd3 .background path {
- fill: none;
- stroke: #EEE;
- stroke-opacity: .4;
- shape-rendering: crispEdges;
-}
-
-.nvd3 .foreground path {
- fill: none;
- stroke-opacity: .7;
-}
-
-.nvd3 .nv-parallelCoordinates-brush .extent
-{
- fill: #fff;
- fill-opacity: .6;
- stroke: gray;
- shape-rendering: crispEdges;
-}
-
-.nvd3 .nv-parallelCoordinates .hover {
- fill-opacity: 1;
- stroke-width: 3px;
-}
-
-
-.nvd3 .missingValuesline line {
- fill: none;
- stroke: black;
- stroke-width: 1;
- stroke-opacity: 1;
- stroke-dasharray: 5, 5;
-}
-.nvd3.nv-pie path {
- stroke-opacity: 0;
- transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
- -moz-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
- -webkit-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
-
-}
-
-.nvd3.nv-pie .nv-pie-title {
- font-size: 24px;
- fill: rgba(19, 196, 249, 0.59);
-}
-
-.nvd3.nv-pie .nv-slice text {
- stroke: #000;
- stroke-width: 0;
-}
-
-.nvd3.nv-pie path {
- stroke: #fff;
- stroke-width: 1px;
- stroke-opacity: 1;
-}
-
-.nvd3.nv-pie .hover path {
- fill-opacity: .7;
-}
-.nvd3.nv-pie .nv-label {
- pointer-events: none;
-}
-.nvd3.nv-pie .nv-label rect {
- fill-opacity: 0;
- stroke-opacity: 0;
-}
-
-/* scatter */
-.nvd3 .nv-groups .nv-point.hover {
- stroke-width: 20px;
- stroke-opacity: .5;
-}
-
-.nvd3 .nv-scatter .nv-point.hover {
- fill-opacity: 1;
-}
-.nv-noninteractive {
- pointer-events: none;
-}
-
-.nv-distx, .nv-disty {
- pointer-events: none;
-}
-
-/* sparkline */
-.nvd3.nv-sparkline path {
- fill: none;
-}
-
-.nvd3.nv-sparklineplus g.nv-hoverValue {
- pointer-events: none;
-}
-
-.nvd3.nv-sparklineplus .nv-hoverValue line {
- stroke: #333;
- stroke-width: 1.5px;
-}
-
-.nvd3.nv-sparklineplus,
-.nvd3.nv-sparklineplus g {
- pointer-events: all;
-}
-
-.nvd3 .nv-hoverArea {
- fill-opacity: 0;
- stroke-opacity: 0;
-}
-
-.nvd3.nv-sparklineplus .nv-xValue,
-.nvd3.nv-sparklineplus .nv-yValue {
- stroke-width: 0;
- font-size: .9em;
- font-weight: normal;
-}
-
-.nvd3.nv-sparklineplus .nv-yValue {
- stroke: #f66;
-}
-
-.nvd3.nv-sparklineplus .nv-maxValue {
- stroke: #2ca02c;
- fill: #2ca02c;
-}
-
-.nvd3.nv-sparklineplus .nv-minValue {
- stroke: #d62728;
- fill: #d62728;
-}
-
-.nvd3.nv-sparklineplus .nv-currentValue {
- font-weight: bold;
- font-size: 1.1em;
-}
-/* stacked area */
-.nvd3.nv-stackedarea path.nv-area {
- fill-opacity: .7;
- stroke-opacity: 0;
- transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
- -moz-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
- -webkit-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
-}
-
-.nvd3.nv-stackedarea path.nv-area.hover {
- fill-opacity: .9;
-}
-
-
-.nvd3.nv-stackedarea .nv-groups .nv-point {
- stroke-opacity: 0;
- fill-opacity: 0;
-}
-
-
-.nvtooltip {
- position: absolute;
- background-color: rgba(255,255,255,1.0);
- color: rgba(0,0,0,1.0);
- padding: 1px;
- border: 1px solid rgba(0,0,0,.2);
- z-index: 10000;
- display: block;
-
- font-family: Arial;
- font-size: 13px;
- text-align: left;
- pointer-events: none;
-
- white-space: nowrap;
-
- -webkit-touch-callout: none;
- -webkit-user-select: none;
- -khtml-user-select: none;
- -moz-user-select: none;
- -ms-user-select: none;
- user-select: none;
-}
-
-.nvtooltip {
- background: rgba(255,255,255, 0.8);
- border: 1px solid rgba(0,0,0,0.5);
- border-radius: 4px;
-}
-
-/*Give tooltips that old fade in transition by
- putting a "with-transitions" class on the container div.
-*/
-.nvtooltip.with-transitions, .with-transitions .nvtooltip {
- transition: opacity 50ms linear;
- -moz-transition: opacity 50ms linear;
- -webkit-transition: opacity 50ms linear;
-
- transition-delay: 200ms;
- -moz-transition-delay: 200ms;
- -webkit-transition-delay: 200ms;
-}
-
-.nvtooltip.x-nvtooltip,
-.nvtooltip.y-nvtooltip {
- padding: 8px;
-}
-
-.nvtooltip h3 {
- margin: 0;
- padding: 4px 14px;
- line-height: 18px;
- font-weight: normal;
- background-color: rgba(247,247,247,0.75);
- color: rgba(0,0,0,1.0);
- text-align: center;
-
- border-bottom: 1px solid #ebebeb;
-
- -webkit-border-radius: 5px 5px 0 0;
- -moz-border-radius: 5px 5px 0 0;
- border-radius: 5px 5px 0 0;
-}
-
-.nvtooltip p {
- margin: 0;
- padding: 5px 14px;
- text-align: center;
-}
-
-.nvtooltip span {
- display: inline-block;
- margin: 2px 0;
-}
-
-.nvtooltip table {
- margin: 6px;
- border-spacing:0;
-}
-
-
-.nvtooltip table td {
- padding: 2px 9px 2px 0;
- vertical-align: middle;
-}
-
-.nvtooltip table td.key {
- font-weight:normal;
-}
-.nvtooltip table td.value {
- text-align: right;
- font-weight: bold;
-}
-
-.nvtooltip table tr.highlight td {
- padding: 1px 9px 1px 0;
- border-bottom-style: solid;
- border-bottom-width: 1px;
- border-top-style: solid;
- border-top-width: 1px;
-}
-
-.nvtooltip table td.legend-color-guide div {
- width: 8px;
- height: 8px;
- vertical-align: middle;
-}
-
-.nvtooltip table td.legend-color-guide div {
- width: 12px;
- height: 12px;
- border: 1px solid #999;
-}
-
-.nvtooltip .footer {
- padding: 3px;
- text-align: center;
-}
-
-.nvtooltip-pending-removal {
- pointer-events: none;
- display: none;
-}
-
-
-/****
-Interactive Layer
-*/
-.nvd3 .nv-interactiveGuideLine {
- pointer-events:none;
-}
-.nvd3 line.nv-guideline {
- stroke: #ccc;
+/* line plus bar */
+.nvd3.nv-linePlusBar .nv-bar rect {
+ fill-opacity: .75;
+}
+
+.nvd3.nv-linePlusBar .nv-bar rect:hover {
+ fill-opacity: 1;
+}
+.nvd3 .nv-groups path.nv-line {
+ fill: none;
+}
+
+.nvd3 .nv-groups path.nv-area {
+ stroke: none;
+}
+
+.nvd3.nv-line .nvd3.nv-scatter .nv-groups .nv-point {
+ fill-opacity: 0;
+ stroke-opacity: 0;
+}
+
+.nvd3.nv-scatter.nv-single-point .nv-groups .nv-point {
+ fill-opacity: .5 !important;
+ stroke-opacity: .5 !important;
+}
+
+
+.with-transitions .nvd3 .nv-groups .nv-point {
+ transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -moz-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -webkit-transition: stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-scatter .nv-groups .nv-point.hover,
+.nvd3 .nv-groups .nv-point.hover {
+ stroke-width: 7px;
+ fill-opacity: .95 !important;
+ stroke-opacity: .95 !important;
+}
+
+
+.nvd3 .nv-point-paths path {
+ stroke: #aaa;
+ stroke-opacity: 0;
+ fill: #eee;
+ fill-opacity: 0;
+}
+
+
+
+.nvd3 .nv-indexLine {
+ cursor: ew-resize;
+}
+
+/********************
+ * SVG CSS
+ */
+
+/********************
+ Default CSS for an svg element nvd3 used
+*/
+svg.nvd3-svg {
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -ms-user-select: none;
+ -moz-user-select: none;
+ user-select: none;
+ display: block;
+ width:100%;
+ height:100%;
+}
+
+/********************
+ Box shadow and border radius styling
+*/
+.nvtooltip.with-3d-shadow, .with-3d-shadow .nvtooltip {
+ -moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
+ -webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
+ box-shadow: 0 5px 10px rgba(0,0,0,.2);
+
+ -webkit-border-radius: 5px;
+ -moz-border-radius: 5px;
+ border-radius: 5px;
+}
+
+
+.nvd3 text {
+ font: normal 14px Arial;
+}
+
+.nvd3 .title {
+ font: bold 14px Arial;
+}
+
+.nvd3 .nv-background {
+ fill: white;
+ fill-opacity: 0;
+}
+
+.nvd3.nv-noData {
+ font-size: 18px;
+ font-weight: bold;
+}
+
+
+/**********
+* Brush
+*/
+
+.nv-brush .extent {
+ fill-opacity: .125;
+ shape-rendering: crispEdges;
+}
+
+.nv-brush .resize path {
+ fill: #eee;
+ stroke: #666;
+}
+
+
+/**********
+* Legend
+*/
+
+.nvd3 .nv-legend .nv-series {
+ cursor: pointer;
+}
+
+.nvd3 .nv-legend .nv-disabled circle {
+ fill-opacity: 0;
+}
+
+/* focus */
+.nvd3 .nv-brush .extent {
+ fill-opacity: 0 !important;
+}
+
+.nvd3 .nv-brushBackground rect {
+ stroke: #000;
+ stroke-width: .4;
+ fill: #fff;
+ fill-opacity: .7;
+}
+
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick {
+ stroke-width: 1px;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.hover {
+ stroke-width: 2px;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.positive {
+ stroke: #2ca02c;
+}
+
+.nvd3.nv-ohlcBar .nv-ticks .nv-tick.negative {
+ stroke: #d62728;
+}
+
+
+.nvd3 .background path {
+ fill: none;
+ stroke: #EEE;
+ stroke-opacity: .4;
+ shape-rendering: crispEdges;
+}
+
+.nvd3 .foreground path {
+ fill: none;
+ stroke-opacity: .7;
+}
+
+.nvd3 .nv-parallelCoordinates-brush .extent
+{
+ fill: #fff;
+ fill-opacity: .6;
+ stroke: gray;
+ shape-rendering: crispEdges;
+}
+
+.nvd3 .nv-parallelCoordinates .hover {
+ fill-opacity: 1;
+ stroke-width: 3px;
+}
+
+
+.nvd3 .missingValuesline line {
+ fill: none;
+ stroke: black;
+ stroke-width: 1;
+ stroke-opacity: 1;
+ stroke-dasharray: 5, 5;
+}
+.nvd3.nv-pie path {
+ stroke-opacity: 0;
+ transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -moz-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+ -webkit-transition: fill-opacity 250ms linear, stroke-width 250ms linear, stroke-opacity 250ms linear;
+
+}
+
+.nvd3.nv-pie .nv-pie-title {
+ font-size: 24px;
+ fill: rgba(19, 196, 249, 0.59);
+}
+
+.nvd3.nv-pie .nv-slice text {
+ stroke: #000;
+ stroke-width: 0;
+}
+
+.nvd3.nv-pie path {
+ stroke: #fff;
+ stroke-width: 1px;
+ stroke-opacity: 1;
+}
+
+.nvd3.nv-pie .hover path {
+ fill-opacity: .7;
+}
+.nvd3.nv-pie .nv-label {
+ pointer-events: none;
+}
+.nvd3.nv-pie .nv-label rect {
+ fill-opacity: 0;
+ stroke-opacity: 0;
+}
+
+/* scatter */
+.nvd3 .nv-groups .nv-point.hover {
+ stroke-width: 20px;
+ stroke-opacity: .5;
+}
+
+.nvd3 .nv-scatter .nv-point.hover {
+ fill-opacity: 1;
+}
+.nv-noninteractive {
+ pointer-events: none;
+}
+
+.nv-distx, .nv-disty {
+ pointer-events: none;
+}
+
+/* sparkline */
+.nvd3.nv-sparkline path {
+ fill: none;
+}
+
+.nvd3.nv-sparklineplus g.nv-hoverValue {
+ pointer-events: none;
+}
+
+.nvd3.nv-sparklineplus .nv-hoverValue line {
+ stroke: #333;
+ stroke-width: 1.5px;
+}
+
+.nvd3.nv-sparklineplus,
+.nvd3.nv-sparklineplus g {
+ pointer-events: all;
+}
+
+.nvd3 .nv-hoverArea {
+ fill-opacity: 0;
+ stroke-opacity: 0;
+}
+
+.nvd3.nv-sparklineplus .nv-xValue,
+.nvd3.nv-sparklineplus .nv-yValue {
+ stroke-width: 0;
+ font-size: .9em;
+ font-weight: normal;
+}
+
+.nvd3.nv-sparklineplus .nv-yValue {
+ stroke: #f66;
+}
+
+.nvd3.nv-sparklineplus .nv-maxValue {
+ stroke: #2ca02c;
+ fill: #2ca02c;
+}
+
+.nvd3.nv-sparklineplus .nv-minValue {
+ stroke: #d62728;
+ fill: #d62728;
+}
+
+.nvd3.nv-sparklineplus .nv-currentValue {
+ font-weight: bold;
+ font-size: 1.1em;
+}
+/* stacked area */
+.nvd3.nv-stackedarea path.nv-area {
+ fill-opacity: .7;
+ stroke-opacity: 0;
+ transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+ -moz-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+ -webkit-transition: fill-opacity 250ms linear, stroke-opacity 250ms linear;
+}
+
+.nvd3.nv-stackedarea path.nv-area.hover {
+ fill-opacity: .9;
+}
+
+
+.nvd3.nv-stackedarea .nv-groups .nv-point {
+ stroke-opacity: 0;
+ fill-opacity: 0;
+}
+
+
+.nvtooltip {
+ position: absolute;
+ background-color: rgba(255,255,255,1.0);
+ color: rgba(0,0,0,1.0);
+ padding: 1px;
+ border: 1px solid rgba(0,0,0,.2);
+ z-index: 10000;
+ display: block;
+
+ font-family: Arial;
+ font-size: 13px;
+ text-align: left;
+ pointer-events: none;
+
+ white-space: nowrap;
+
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+.nvtooltip {
+ background: rgba(255,255,255, 0.8);
+ border: 1px solid rgba(0,0,0,0.5);
+ border-radius: 4px;
+}
+
+/*Give tooltips that old fade in transition by
+ putting a "with-transitions" class on the container div.
+*/
+.nvtooltip.with-transitions, .with-transitions .nvtooltip {
+ transition: opacity 50ms linear;
+ -moz-transition: opacity 50ms linear;
+ -webkit-transition: opacity 50ms linear;
+
+ transition-delay: 200ms;
+ -moz-transition-delay: 200ms;
+ -webkit-transition-delay: 200ms;
+}
+
+.nvtooltip.x-nvtooltip,
+.nvtooltip.y-nvtooltip {
+ padding: 8px;
+}
+
+.nvtooltip h3 {
+ margin: 0;
+ padding: 4px 14px;
+ line-height: 18px;
+ font-weight: normal;
+ background-color: rgba(247,247,247,0.75);
+ color: rgba(0,0,0,1.0);
+ text-align: center;
+
+ border-bottom: 1px solid #ebebeb;
+
+ -webkit-border-radius: 5px 5px 0 0;
+ -moz-border-radius: 5px 5px 0 0;
+ border-radius: 5px 5px 0 0;
+}
+
+.nvtooltip p {
+ margin: 0;
+ padding: 5px 14px;
+ text-align: center;
+}
+
+.nvtooltip span {
+ display: inline-block;
+ margin: 2px 0;
+}
+
+.nvtooltip table {
+ margin: 6px;
+ border-spacing:0;
+}
+
+
+.nvtooltip table td {
+ padding: 2px 9px 2px 0;
+ vertical-align: middle;
+}
+
+.nvtooltip table td.key {
+ font-weight:normal;
+}
+.nvtooltip table td.value {
+ text-align: right;
+ font-weight: bold;
+}
+
+.nvtooltip table tr.highlight td {
+ padding: 1px 9px 1px 0;
+ border-bottom-style: solid;
+ border-bottom-width: 1px;
+ border-top-style: solid;
+ border-top-width: 1px;
+}
+
+.nvtooltip table td.legend-color-guide div {
+ width: 8px;
+ height: 8px;
+ vertical-align: middle;
+}
+
+.nvtooltip table td.legend-color-guide div {
+ width: 12px;
+ height: 12px;
+ border: 1px solid #999;
+}
+
+.nvtooltip .footer {
+ padding: 3px;
+ text-align: center;
+}
+
+.nvtooltip-pending-removal {
+ pointer-events: none;
+ display: none;
+}
+
+
+/****
+Interactive Layer
+*/
+.nvd3 .nv-interactiveGuideLine {
+ pointer-events:none;
+}
+.nvd3 line.nv-guideline {
+ stroke: #ccc;
} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index cedb65a1..3bde7dc7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -32,65 +32,65 @@
<br />
<br />
- <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1200px{% else %}800px{% endif %}; background-color: #eeeeee; border: 1px solid black;">
+ <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
<table width="1600px" id="trait_table" class="table table-hover table-striped">
<thead>
<tr>
- <th style="width: 30px; background-color: #eeeeee;"></th>
+ <th style="width: 30px;"></th>
{% for header in target_dataset.header_fields %}
{% if header == 'Year' %}
- <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% elif header == 'Max LRS' %}
- <th style="text-align: right; background-color: #eeeeee;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
{% elif header == 'Max LRS Location' %}
- <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% elif header == 'Location' %}
- <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% elif header == 'Mean' %}
- <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% elif header == 'Additive Effect' %}
- <th style="text-align: right; background-color: #eeeeee;">Add&nbsp;&nbsp;<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+ <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
{% elif header == 'Index' %}
- <th style="text-align: right; background-color: #eeeeee; padding-left: 0px; margin-left: 0px;">{{header}}</th>
+ <th>{{header}}</th>
{% elif header == 'N' %}
- <th style="text-align: right; background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% else %}
- <th style="background-color: #eeeeee;">{{header}}</th>
+ <th>{{header}}</th>
{% endif %}
{% endfor %}
{% if target_dataset.type == "ProbeSet" %}
{% if corr_method == 'pearson' %}
- <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
- <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
- <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
- <th style="text-align: right; background-color: #eeeeee;">Tissue r</th>
+ <th>Sample r</th>
+ <th>&nbsp;&nbsp;N</th>
+ <th>Sample p(r)</th>
+ <th>Lit r</th>
+ <th>Tissue r</th>
{% else %}
- <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
- <th style="text-align: right; background-color: #eeeeee;">N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
- <th style="text-align: right; background-color: #eeeeee;">Lit r</th>
- <th style="text-align: right; background-color: #eeeeee;">Tissue rho</th>
+ <th>Sample rho</th>
+ <th>N</th>
+ <th>Sample p(rho)</th>
+ <th>Lit r</th>
+ <th>Tissue rho</th>
{% endif %}
{% elif target_dataset.type == "Publish" %}
{% if corr_method == 'pearson' %}
- <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
- <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+ <th>Sample r</th>
+ <th>&nbsp;&nbsp;N</th>
+ <th>Sample p(r)</th>
{% else %}
- <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
- <th style="text-align: right; background-color: #eeeeee;">&nbsp;&nbsp;N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+ <th>Sample rho</th>
+ <th>&nbsp;&nbsp;N</th>
+ <th>Sample p(rho)</th>
{% endif %}
{% elif target_dataset.type == "Geno" %}
{% if corr_method == 'pearson' %}
- <th style="text-align: right; background-color: #eeeeee;">Sample r</th>
- <th style="text-align: right; background-color: #eeeeee;">N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(r)</th>
+ <th>Sample r</th>
+ <th>N</th>
+ <th>Sample p(r)</th>
{% else %}
- <th style="text-align: right; background-color: #eeeeee;">Sample rho</th>
- <th style="text-align: right; background-color: #eeeeee;">N</th>
- <th style="text-align: right; background-color: #eeeeee;">Sample p(rho)</th>
+ <th>Sample rho</th>
+ <th>N</th>
+ <th>Sample p(rho)</th>
{% endif %}
{% endif %}
</tr>
@@ -99,7 +99,7 @@
<tbody>
{% for trait in correlation_results %}
<tr>
- <td>&nbsp;<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
+ <td align="center" style="padding-right: 0px;">&nbsp;<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>
<a href="{{ url_for('show_trait_page',
@@ -114,21 +114,21 @@
<td>{{ trait.description_display }}</TD>
<td align="right"style="white-space: nowrap;">{{ trait.location_repr }}</td>
<td align="right">{{ '%0.3f' % trait.mean|float }}</td>
- <td align="right" style="padding-right: 15px;">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
- <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
- <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
- <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
- <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
- <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+ <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
+ <td align="right">{{ trait.LRS_location_repr }}</td>
+ <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+ <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+ <td align="right">{{ trait.num_overlap }}</td>
+ <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
{% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
- <td align="right" style="padding-right: 15px;">--</td>
+ <td align="right">--</td>
{% else %}
- <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.lit_corr)}}</td>
+ <td align="right">{{'%0.3f'|format(trait.lit_corr)}}</td>
{% endif %}
{% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
- <td align="right" style="padding-right: 15px;">--</td>
+ <td align="right">--</td>
{% else %}
- <td align="right" style="padding-right: 15px;">{{'%0.3f'|format(trait.tissue_corr)}}</td>
+ <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
{% endif %}
{% elif target_dataset.type == "Publish" %}
<td>{{ trait.description_display }}</td>
@@ -138,17 +138,17 @@
{{ trait.pubmed_text }}
</a>
</td>
- <td align="right" style="padding-right: 15px;">{{ trait.LRS_score_repr }}</td>
- <td align="right" style="padding-right: 15px;">{{ trait.LRS_location_repr }}</td>
- <td align="right" style="padding-right: 15px;">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
- <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
- <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
- <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+ <td align="right">{{ trait.LRS_score_repr }}</td>
+ <td align="right">{{ trait.LRS_location_repr }}</td>
+ <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+ <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+ <td align="right">{{ trait.num_overlap }}</td>
+ <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
{% elif target_dataset.type == "Geno" %}
- <td align="right" style="padding-right: 15px;">{{ trait.location_repr }}</TD>
- <td align="right" style="padding-right: 15px;"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
- <td align="right" style="padding-right: 15px;">{{ trait.num_overlap }}</td>
- <td align="right" style="padding-right: 15px;">{{'%0.3e'|format(trait.sample_p)}}</td>
+ <td align="right">{{ trait.location_repr }}</TD>
+ <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
+ <td align="right">{{ trait.num_overlap }}</td>
+ <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
{% endif %}
</tr>
{% endfor %}
@@ -278,6 +278,13 @@
{ "type": "natural" },
{ "type": "natural" }
],
+ "createdRow": function ( row, data, index ) {
+ $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+ if ($('td', row).eq(4).text().length > 60) {
+ $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+ $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+ }
+ },
"order": [[12, "asc" ]],
"sDom": "Btir",
"autoWidth": false,
@@ -287,7 +294,6 @@
} );
var table = $('#trait_table').DataTable();
- new $.fn.dataTable.FixedHeader( table );
{% elif target_dataset.type == "Publish" %}
$('#trait_table').dataTable( {
@@ -311,7 +317,7 @@
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural", "width": "25%" },
- { "type": "natural", "width": "10%" },
+ { "type": "natural", "width": "15%" },
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural" },
@@ -320,6 +326,13 @@
{ "type": "natural" },
{ "type": "scientific" }
],
+ "createdRow": function ( row, data, index ) {
+ $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+ if ($('td', row).eq(4).text().length > 60) {
+ $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+ $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+ }
+ },
"order": [[11, "asc" ]],
"sDom": "Btir",
"autoWidth": false,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 1694eae5..72ced084 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -173,6 +173,16 @@
</div>
<div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
+ <section id="websites">
+ <div class="page-header">
+ <h1>Github</h1>
+ </div>
+ <ul>
+ <li><a href="https://github.com/genenetwork/genenetwork2">GN2 Source Code</a></li>
+ <li><a href="https://github.com/genenetwork/sysmaintenance">System Maintenance Code</a></li>
+ <li><a href="https://github.com/genenetwork/genenetwork">GN1 Source Code</a></li>
+ </ul>
+ </section>
<section id="news-section">
<div class="page-header">
<h1>News</h1>
@@ -212,7 +222,7 @@
<section id="websites">
<div class="page-header">
- <h2>Links</h2>
+ <h1>Links</h1>
</div>
<h3>GeneNetwork v2:</h3>
<ul>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 6d3f9326..4cea51b2 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -137,9 +137,9 @@
<li id="gn1_map_tab">
<a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
</li>
- {% if mapping_method != "gemma" %}
+ {% if mapping_method != "gemma" and mapping_method != "plink" %}
<li id="vector_map_tab">
- <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+ <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" and mapping_method != "plink" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
</li>
{% endif %}
</ul>
@@ -161,7 +161,7 @@
{% endif %}
</div>
</div>
- {% if mapping_method != "gemma" %}
+ {% if mapping_method != "gemma" and mapping_method != "plink" %}
<div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
<div id="chart_container">
<div class="qtlcharts" id="topchart"></div>
@@ -277,11 +277,13 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+ {% if mapping_method != "gemma" and mapping_method != "plink" %}
<script>
js_data = {{ js_data | safe }}
</script>
+ {% endif %}
- {% if mapping_method != "gemma" %}
+ {% if mapping_method != "gemma" and mapping_method != "plink" %}
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
@@ -385,6 +387,7 @@
return $('#marker_regression_form').submit();
};
+ {% if mapping_method != "gemma" and mapping_method != "plink" %}
export_perm_data = function() {
var num_perm, perm_data;
num_perm = js_data.num_perm
@@ -393,7 +396,8 @@
$('input[name=perm_results]').val(json_perm_data);
$('#marker_regression_form').attr('action', '/export_perm_data');
return $('#marker_regression_form').submit();
- };
+ }
+ {% endif %}
</script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 772c4314..56b6cc62 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -17,7 +17,9 @@
{% block content %} <!-- Start of body -->
<!--
- {% if this_trait.dataset.type != 'Geno' %}
+ {% if dataset.type == 'Temp' %}
+ {{ header("{}".format("Temporary Trait")) }}
+ {% elif dataset.type != 'Geno' %}
{{ header("{}".format(this_trait.name_header_fmt),
'{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
{% else %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 547c3c27..a0c40c7f 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -3,10 +3,12 @@
<td>Species and Group</td>
<td>{{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}</td>
</tr>
+ {% if this_trait.dataset.type == 'Publish' %}
<tr>
<td>Tissue</td>
<td>{{ this_trait.dataset.tissue }}</td>
</tr>
+ {% endif %}
{% if this_trait.dataset.type == 'ProbeSet' %}
{% if this_trait.symbol != None %}
<tr>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 12ba80b9..23c09d05 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -17,16 +17,17 @@
</li>
{% endif %}
{# if use_plink_gemma #}
- {% if dataset.group.mapping_id == "2" or dataset.group.mapping_id == "4" %}
+ {% for mapping_method in dataset.group.mapping_names %}
+ {% if mapping_method == "GEMMA" %}
<li class="active">
<a href="#gemma" data-toggle="tab">GEMMA</a>
</li>
- {% if dataset.group.mapping_id == "4" %}
+ {% elif mapping_method == "PLINK" %}
<li>
<a href="#plink" data-toggle="tab">PLINK</a>
</li>
{% endif %}
- {% endif %}
+ {% endfor %}
<!--<li>
<a href="#pair_scan" data-toggle="tab">Pair Scan</a>
</li>-->
diff --git a/wqflask/wqflask/templates/submit_trait.html b/wqflask/wqflask/templates/submit_trait.html
index 2529a4f4..8d624ffd 100644
--- a/wqflask/wqflask/templates/submit_trait.html
+++ b/wqflask/wqflask/templates/submit_trait.html
@@ -2,7 +2,7 @@
{% block title %}Trait Submission{% endblock %}
{% block content %}
<!-- Start of body -->
- <form method="post" action="/show_trait">
+ <form method="post" action="/show_temp_trait">
<div class="container-fluid">
{{ flash_me() }}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ab6c433d..39f4a686 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -389,6 +389,20 @@ def export_perm_data():
mimetype='text/csv',
headers={"Content-Disposition":"attachment;filename=perm_data.csv"})
+@app.route("/show_temp_trait", methods=('POST',))
+def show_temp_trait_page():
+ template_vars = show_trait.ShowTrait(request.form)
+ #logger.info("js_data before dump:", template_vars.js_data)
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+ # Sorting the keys messes up the ordered dictionary, so don't do that
+ #sort_keys=True)
+
+ #logger.info("js_data after dump:", template_vars.js_data)
+ #logger.info("show_trait template_vars:", pf(template_vars.__dict__))
+ return render_template("show_trait.html", **template_vars.__dict__)
+
@app.route("/show_trait")
def show_trait_page():
template_vars = show_trait.ShowTrait(request.args)
@@ -575,9 +589,10 @@ def marker_regression_page():
with Bench("Total time in MarkerRegression"):
template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
+ if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
result = template_vars.__dict__
@@ -598,13 +613,15 @@ def marker_regression_page():
# logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
-
- pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- logger.info("pickled result length:", len(pickled_result))
- Redis.set(key, pickled_result)
- Redis.expire(key, 1*60)
+ #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+ #logger.info("pickled result length:", len(pickled_result))
+ #Redis.set(key, pickled_result)
+ #Redis.expire(key, 1*60)
with Bench("Rendering template"):
+ if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
+ gn1_template_vars.pop('qtlresults', None)
+ print("TEMPLATE KEYS:", list(gn1_template_vars.keys()))
rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
# with Bench("Rendering template"):