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-rwxr-xr-xwqflask/base/trait.py28
-rwxr-xr-xwqflask/maintenance/gen_select_dataset.py52
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py29
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py128
-rwxr-xr-xwqflask/wqflask/static/new/javascript/dataset_menu_structure.json696
-rwxr-xr-xwqflask/wqflask/static/new/javascript/histogram.coffee27
-rwxr-xr-xwqflask/wqflask/static/new/javascript/histogram.js245
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.coffee1
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait.js1
-rwxr-xr-xwqflask/wqflask/templates/index_page.html12
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html10
-rwxr-xr-xwqflask/wqflask/templates/show_trait_details.html6
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html118
14 files changed, 473 insertions, 882 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index f3648b80..8930c917 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -53,7 +53,8 @@ class GeneralTrait(object):
self.pvalue = None
self.mean = None
self.num_overlap = None
-
+ self.strand_probe = None
+ self.symbol = None
if kw.get('fullname'):
name2 = value.split("::")
@@ -533,12 +534,27 @@ class GeneralTrait(object):
return setDescription
@property
+ def name_header_fmt(self):
+ '''Return a human-readable name for use in page header'''
+ if self.dataset.type == 'ProbeSet':
+ return self.symbol
+ elif self.dataset.type == 'Geno':
+ return self.name
+ elif self.dataset.type == 'Publish':
+ return self.post_publication_abbreviation
+ else:
+ return "unnamed"
+
+ @property
def description_fmt(self):
'''Return a text formated description'''
- if self.description:
- formatted = self.description
- if self.probe_target_description:
- formatted += "; " + self.probe_target_description
+ if self.dataset.type == 'ProbeSet':
+ if self.description:
+ formatted = self.description
+ if self.probe_target_description:
+ formatted += "; " + self.probe_target_description
+ elif self.dataset.type == 'Publish':
+ formatted = self.post_publication_description
else:
formatted = "Not available"
return formatted.capitalize()
@@ -652,4 +668,4 @@ def get_sample_data():
# jsonable_sample_data[sample] = trait_ob.data[sample].value
#
#return jsonable_sample_data
- \ No newline at end of file
+
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 694efeca..a2ad8c91 100755
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -35,7 +35,9 @@ from __future__ import print_function, division
#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
#print("cdict is:", cdict)
-import our_settings
+import sys
+sys.path.append("/home/zas1024/")
+import zach_settings
import MySQLdb
@@ -47,7 +49,7 @@ import urlparse
from pprint import pformat as pf
-#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI)
+#Engine = sa.create_engine(zach_settings.SQLALCHEMY_DATABASE_URI)
# build MySql database connection
@@ -60,7 +62,7 @@ from pprint import pformat as pf
def parse_db_uri(db_uri):
"""Converts a database URI to the db name, host name, user name, and password"""
- parsed_uri = urlparse.urlparse(our_settings.DB_URI)
+ parsed_uri = urlparse.urlparse(zach_settings.DB_URI)
db_conn_info = dict(
db = parsed_uri.path[1:],
@@ -104,12 +106,48 @@ def get_types(groups):
types[species] = {}
for group_name, _group_full_name in group_dict:
# make group an alias to shorten the code
- types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
- types[species][group_name] += build_types(species, group_name)
+ #types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
+ if phenotypes_exist(group_name):
+ types[species][group_name] = [("Phenotypes", "Phenotypes")]
+ if genotypes_exist(group_name):
+ if group_name in types[species]:
+ types[species][group_name] += [("Genotypes", "Genotypes")]
+ else:
+ types[species][group_name] = [("Genotypes", "Genotypes")]
+ if group_name in types[species]:
+ types[species][group_name] += build_types(species, group_name)
+ else:
+ types[species][group_name] = build_types(species, group_name)
return types
+def phenotypes_exist(group_name):
+ print("group_name:", group_name)
+ Cursor.execute("""select Name from PublishFreeze
+ where PublishFreeze.Name = %s""", (group_name+"Publish"))
+
+ results = Cursor.fetchone()
+ print("RESULTS:", results)
+
+ if results != None:
+ return True
+ else:
+ return False
+
+def genotypes_exist(group_name):
+ print("group_name:", group_name)
+ Cursor.execute("""select Name from GenoFreeze
+ where GenoFreeze.Name = %s""", (group_name+"Geno"))
+
+ results = Cursor.fetchone()
+ print("RESULTS:", results)
+
+ if results != None:
+ return True
+ else:
+ return False
+
def build_types(species, group):
"""Fetches tissues
@@ -196,7 +234,7 @@ def build_datasets(species, group, type_name):
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
- parse_db_uri(our_settings.DB_URI)
+ parse_db_uri(zach_settings.DB_URI)
species = get_species()
groups = get_groups(species)
@@ -236,6 +274,6 @@ def _test_it():
#print("build_datasets:", pf(datasets))
if __name__ == '__main__':
- Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI))
+ Conn = MySQLdb.Connect(**parse_db_uri(zach_settings.DB_URI))
Cursor = Conn.cursor()
main()
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 1cd3fc80..4b4b7f73 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -24,9 +24,6 @@ from base import data_set
from base import species
from base import webqtlConfig
from utility import webqtlUtil
-# from wqflask.my_pylmm.data import prep_data
-# from wqflask.my_pylmm.pyLMM import lmm
-# from wqflask.my_pylmm.pyLMM import input
from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
@@ -223,32 +220,6 @@ class IntervalMapping(object):
"cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive}
self.qtl_results.append(qtl)
- def gen_pylmm_results(self, tempdata):
- print("USING PYLMM")
- self.dataset.group.get_markers()
-
- pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
- if self.dataset.group.species == "human":
- p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
- else:
- genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-
- no_val_samples = self.identify_empty_samples()
- trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
- genotype_matrix = np.array(trimmed_genotype_data).T
-
- t_stats, p_values = lmm.run(
- pheno_vector,
- genotype_matrix,
- restricted_max_likelihood=True,
- refit=False,
- temp_data=tempdata
- )
-
- print("p_values:", p_values)
- self.dataset.group.markers.add_pvalues(p_values)
- self.qtl_results = self.dataset.group.markers.markers
def gen_qtl_results_2(self, tempdata):
"""Generates qtl results for plotting interval map"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 76d05bd8..999a32b8 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -120,57 +120,83 @@ class MarkerRegression(object):
else:
print("RUNNING NOTHING")
- self.lod_cutoff = 2
- self.filtered_markers = []
- highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
- for marker in qtl_results:
- if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
- if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
- highest_chr = marker['chr']
- if 'lod_score' in marker:
- self.filtered_markers.append(marker)
-
- self.json_data['chr'] = []
- self.json_data['pos'] = []
- self.json_data['lod.hk'] = []
- 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
- self.qtl_results = []
- for index,qtl in enumerate(self.filtered_markers):
- if index<40:
- print("lod score is:", qtl['lod_score'])
- if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
- print("changing to X")
- self.json_data['chr'].append("X")
- else:
- self.json_data['chr'].append(str(qtl['chr']))
- self.json_data['pos'].append(qtl['Mb'])
- self.json_data['lod.hk'].append(str(qtl['lod_score']))
- self.json_data['markernames'].append(qtl['name'])
-
- #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
-
- # print("json_data:", self.json_data)
-
-
- self.js_data = dict(
- json_data = self.json_data,
- this_trait = self.this_trait.name,
- data_set = self.dataset.name,
- maf = self.maf,
- manhattan_plot = self.manhattan_plot,
- chromosomes = chromosome_mb_lengths,
- qtl_results = self.filtered_markers,
- )
+ if self.pair_scan == True:
+ self.filtered_markers = []
+ highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ for marker in qtl_results:
+ if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ highest_chr = marker['chr1']
+ if 'lod_score' in marker:
+ self.filtered_markers.append(marker)
+
+ for qtl in enumerate(self.filtered_markers):
+ self.json_data['chr1'].append(str(qtl['chr1']))
+ self.json_data['chr2'].append(str(qtl['chr2']))
+ self.json_data['Mb'].append(qtl['Mb'])
+ self.json_data['markernames'].append(qtl['name'])
+
+ self.js_data = dict(
+ json_data = self.json_data,
+ this_trait = self.this_trait.name,
+ data_set = self.dataset.name,
+ maf = self.maf,
+ manhattan_plot = self.manhattan_plot,
+ qtl_results = self.filtered_markers,
+ )
+
+ else:
+ self.lod_cutoff = 2
+ self.filtered_markers = []
+ highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ for marker in qtl_results:
+ if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ highest_chr = marker['chr']
+ if 'lod_score' in marker:
+ self.filtered_markers.append(marker)
+
+ self.json_data['chr'] = []
+ self.json_data['pos'] = []
+ self.json_data['lod.hk'] = []
+ 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
+ self.qtl_results = []
+ for index, qtl in enumerate(self.filtered_markers):
+ if index<40:
+ print("lod score is:", qtl['lod_score'])
+ if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+ print("changing to X")
+ self.json_data['chr'].append("X")
+ else:
+ self.json_data['chr'].append(str(qtl['chr']))
+ self.json_data['pos'].append(qtl['Mb'])
+ self.json_data['lod.hk'].append(str(qtl['lod_score']))
+ self.json_data['markernames'].append(qtl['name'])
+
+ #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
+
+ # print("json_data:", self.json_data)
+
+
+ self.js_data = dict(
+ json_data = self.json_data,
+ this_trait = self.this_trait.name,
+ data_set = self.dataset.name,
+ maf = self.maf,
+ manhattan_plot = self.manhattan_plot,
+ chromosomes = chromosome_mb_lengths,
+ qtl_results = self.filtered_markers,
+ )
def run_gemma(self):
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index fabf3998..e790c9c0 100755
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -56,12 +56,6 @@
},
"barley": {
"QSM": {
- "Genotypes": [
- [
- "QSMGeno",
- "QSM Genotypes"
- ]
- ],
"Leaf mRNA": [
[
"B1LI0809R",
@@ -79,12 +73,6 @@
"B1MI0809R",
"Barley1 Leaf MOCK TTKS (Aug09) RMA"
]
- ],
- "Phenotypes": [
- [
- "QSMPublish",
- "QSM Published Phenotypes"
- ]
]
},
"SXM": {
@@ -114,12 +102,12 @@
"Barley1 Leaf MAS 5.0 SCRI (Dec06)"
],
[
- "B30_K_1206_Rn",
- "Barley1 Leaf gcRMAn SCRI (Dec06)"
- ],
- [
"B30_K_1206_R",
"Barley1 Leaf gcRMA SCRI (Dec06)"
+ ],
+ [
+ "B30_K_1206_Rn",
+ "Barley1 Leaf gcRMAn SCRI (Dec06)"
]
],
"Phenotypes": [
@@ -132,18 +120,6 @@
},
"drosophila": {
"DGRP": {
- "Genotypes": [
- [
- "DGRPGeno",
- "DGRP Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "DGRPPublish",
- "DGRP Published Phenotypes"
- ]
- ],
"Whole Body mRNA": [
[
"NCSU_DrosWB_LC_RMA_0111",
@@ -152,18 +128,6 @@
]
},
"Oregon-R_x_2b3": {
- "Genotypes": [
- [
- "Oregon-R_x_2b3Geno",
- "Oregon-R_x_2b3 Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "Oregon-R_x_2b3Publish",
- "Oregon-R_x_2b3 Published Phenotypes"
- ]
- ],
"Whole Body mRNA": [
[
"UAB_DrosWB_LC_RMA_1009",
@@ -195,18 +159,6 @@
"GSE5281_RMA0709",
"GSE5281 Human Brain Best 102 Liang (Jul09) RMA"
]
- ],
- "Genotypes": [
- [
- "AD-cases-controlsGeno",
- "AD-cases-controls Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "AD-cases-controlsPublish",
- "AD-cases-controls Published Phenotypes"
- ]
]
},
"AD-cases-controls-Myers": {
@@ -229,12 +181,6 @@
"AD-cases-controls-MyersGeno",
"AD-cases-controls-Myers Genotypes"
]
- ],
- "Phenotypes": [
- [
- "AD-cases-controls-MyersPublish",
- "AD-cases-controls-Myers Published Phenotypes"
- ]
]
},
"Aging-Brain-UCI": {
@@ -244,24 +190,12 @@
"GSE11882 UCI Human Entorhinal Cortex Affy U133 Plus2 (Sep13) RMA"
]
],
- "Genotypes": [
- [
- "Aging-Brain-UCIGeno",
- "Aging-Brain-UCI Genotypes"
- ]
- ],
"Hippocampus mRNA": [
[
"UCI_HC_0913",
"GSE11882 UCI Human Hippocampus Affy U133 Plus2 (Sep13) RMA"
]
],
- "Phenotypes": [
- [
- "Aging-Brain-UCIPublish",
- "Aging-Brain-UCI Published Phenotypes"
- ]
- ],
"Postcentral Gyrus mRNA": [
[
"UCI_PCG_0913",
@@ -282,18 +216,6 @@
"GSE15745 NIH Human Brain Cerebellum ILM humanRef-8 v2.0 (May10) RankInv"
]
],
- "Genotypes": [
- [
- "Brain-Normal-NIH-GibbsGeno",
- "Brain-Normal-NIH-Gibbs Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "Brain-Normal-NIH-GibbsPublish",
- "Brain-Normal-NIH-Gibbs Published Phenotypes"
- ]
- ],
"Pons mRNA": [
[
"GSE15745-GPL6104_Po0510",
@@ -314,12 +236,6 @@
]
},
"CANDLE": {
- "Genotypes": [
- [
- "CANDLEGeno",
- "CANDLE Genotypes"
- ]
- ],
"Methylation": [
[
"CANDLE_Meth27_0313",
@@ -344,12 +260,6 @@
]
},
"CEPH-2004": {
- "Genotypes": [
- [
- "CEPH-2004Geno",
- "CEPH-2004 Genotypes"
- ]
- ],
"Lymphoblast B-cell mRNA": [
[
"UT_CEPH_RankInv0909",
@@ -359,12 +269,6 @@
"Human_1008",
"Monks CEPH B-cells Agilent (Dec04) Log10Ratio"
]
- ],
- "Phenotypes": [
- [
- "CEPH-2004Publish",
- "CEPH-2004 Published Phenotypes"
- ]
]
},
"GTEx": {
@@ -558,12 +462,6 @@
"GTEx Human Frontal Cortex (Apr14) RPKM"
]
],
- "Genotypes": [
- [
- "GTExGeno",
- "GTEx Genotypes"
- ]
- ],
"Heart - Atrial Appendage mRNA": [
[
"GTEx_log2_HeartAt_0314",
@@ -684,12 +582,6 @@
"GTEx Human Pancreas (Apr14) RPKM"
]
],
- "Phenotypes": [
- [
- "GTExPublish",
- "GTEx Published Phenotypes"
- ]
- ],
"Pituitary Gland mRNA": [
[
"GTEx_log2_Pitui_0314",
@@ -870,18 +762,6 @@
"HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio"
]
],
- "Genotypes": [
- [
- "HBGeno",
- "HB Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "HBPublish",
- "HB Published Phenotypes"
- ]
- ],
"Prefrontal Cortex mRNA": [
[
"HBTRC-MLPFC_0611",
@@ -920,12 +800,6 @@
]
},
"HCP": {
- "Genotypes": [
- [
- "HCPGeno",
- "HCP Genotypes"
- ]
- ],
"Phenotypes": [
[
"HCPPublish",
@@ -934,12 +808,6 @@
]
},
"HLC": {
- "Genotypes": [
- [
- "HLCGeno",
- "HLC Genotypes"
- ]
- ],
"Liver mRNA": [
[
"HLC_0311",
@@ -962,12 +830,6 @@
]
},
"HLT": {
- "Genotypes": [
- [
- "HLTGeno",
- "HLT Genotypes"
- ]
- ],
"Lung mRNA": [
[
"GSE23546HLT0613",
@@ -985,12 +847,6 @@
"GRNG-GSE23545HLT0613",
"GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA"
]
- ],
- "Phenotypes": [
- [
- "HLTPublish",
- "HLT Published Phenotypes"
- ]
]
},
"HSB": {
@@ -1012,12 +868,6 @@
"Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
]
],
- "Genotypes": [
- [
- "HSBGeno",
- "HSB Genotypes"
- ]
- ],
"Hippocampus mRNA": [
[
"KIN_YSM_HIP_0711",
@@ -1048,12 +898,6 @@
"Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile"
]
],
- "Phenotypes": [
- [
- "HSBPublish",
- "HSB Published Phenotypes"
- ]
- ],
"Posterior Inferior Parietal Cortex mRNA": [
[
"KIN_YSM_IPC_0711",
@@ -1118,12 +962,6 @@
"INIA Macaca fasicularis Brain (Jan10) RMA **"
]
],
- "Genotypes": [
- [
- "Macaca-fasicularisGeno",
- "Macaca-fasicularis Genotypes"
- ]
- ],
"Hippocampus mRNA": [
[
"INIA_MacFas_Hc_RMA_0110",
@@ -1136,12 +974,6 @@
"INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **"
]
],
- "Phenotypes": [
- [
- "Macaca-fasicularisPublish",
- "Macaca-fasicularis Published Phenotypes"
- ]
- ],
"Prefrontal Cortex mRNA": [
[
"INIA_MacFas_Pf_RMA_0110",
@@ -1164,18 +996,12 @@
"NCI Mammary LMT miRNA v2 (Apr09) RMA"
],
[
- "MA_M_0704_R",
- "NCI Mammary mRNA M430 (July04) RMA"
- ],
- [
"MA_M_0704_M",
"NCI Mammary mRNA M430 (July04) MAS5"
- ]
- ],
- "Phenotypes": [
+ ],
[
- "AKXDPublish",
- "AKXD Published Phenotypes"
+ "MA_M_0704_R",
+ "NCI Mammary mRNA M430 (July04) RMA"
]
]
},
@@ -1226,12 +1052,12 @@
],
"Liver mRNA": [
[
- "LVF2_M_0704_R",
- "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
- ],
- [
"LVF2_M_0704_M",
"(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
+ ],
+ [
+ "LVF2_M_0704_R",
+ "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
]
],
"Phenotypes": [
@@ -1244,10 +1070,6 @@
"B6D2F2": {
"Brain mRNA": [
[
- "BRF2_M_0805_M",
- "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
- ],
- [
"BRF2_M_0805_P",
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
],
@@ -1256,16 +1078,20 @@
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
],
[
- "BRF2_M_0304_P",
- "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
+ "BRF2_M_0805_M",
+ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
],
[
- "BRF2_M_0304_R",
- "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
+ "BRF2_M_0304_P",
+ "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
],
[
"BRF2_M_0304_M",
"OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
+ ],
+ [
+ "BRF2_M_0304_R",
+ "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
]
],
"Genotypes": [
@@ -1273,12 +1099,6 @@
"B6D2F2Geno",
"B6D2F2 Genotypes"
]
- ],
- "Phenotypes": [
- [
- "B6D2F2Publish",
- "B6D2F2 Published Phenotypes"
- ]
]
},
"B6D2F2-PSU": {
@@ -1305,32 +1125,14 @@
"PSU-B6D2F2_M2000812",
"PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200 **"
]
- ],
- "Phenotypes": [
- [
- "B6D2F2-PSUPublish",
- "B6D2F2-PSU Published Phenotypes"
- ]
]
},
"B6D2RI": {
- "Genotypes": [
- [
- "B6D2RIGeno",
- "B6D2RI Genotypes"
- ]
- ],
"Hippocampus mRNA": [
[
"UTHSC_B6D2RI_H_0912",
"UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **"
]
- ],
- "Phenotypes": [
- [
- "B6D2RIPublish",
- "B6D2RI Published Phenotypes"
- ]
]
},
"BDF2-1999": {
@@ -1345,12 +1147,6 @@
"UCLA_BDF2_LIVER_1999",
"UCLA BDF2 Liver (1999) mlratio"
]
- ],
- "Phenotypes": [
- [
- "BDF2-1999Publish",
- "BDF2-1999 Published Phenotypes"
- ]
]
},
"BDF2-2005": {
@@ -1360,52 +1156,46 @@
"BDF2-2005 Genotypes"
]
],
- "Phenotypes": [
- [
- "BDF2-2005Publish",
- "BDF2-2005 Published Phenotypes"
- ]
- ],
"Striatum mRNA": [
[
- "SA_M2_0905_R",
- "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
- ],
- [
"SA_M2_0905_M",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
],
[
"SA_M2_0905_P",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
+ ],
+ [
+ "SA_M2_0905_R",
+ "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
]
]
},
"BHF2": {
"Adipose mRNA": [
[
- "UCLA_BHF2_ADIPOSE_MALE",
- "UCLA BHF2 Adipose Male mlratio"
- ],
- [
"UCLA_BHF2_ADIPOSE_FEMALE",
"UCLA BHF2 Adipose Female mlratio"
],
[
+ "UCLA_BHF2_ADIPOSE_MALE",
+ "UCLA BHF2 Adipose Male mlratio"
+ ],
+ [
"UCLA_BHF2_ADIPOSE_0605",
"UCLA BHF2 Adipose (June05) mlratio"
]
],
"Brain mRNA": [
[
- "UCLA_BHF2_BRAIN_MALE",
- "UCLA BHF2 Brain Male mlratio"
- ],
- [
"UCLA_BHF2_BRAIN_FEMALE",
"UCLA BHF2 Brain Female mlratio"
],
[
+ "UCLA_BHF2_BRAIN_MALE",
+ "UCLA BHF2 Brain Male mlratio"
+ ],
+ [
"UCLA_BHF2_BRAIN_0605",
"UCLA BHF2 Brain (June05) mlratio"
]
@@ -1418,37 +1208,31 @@
],
"Liver mRNA": [
[
- "UCLA_BHF2_LIVER_MALE",
- "UCLA BHF2 Liver Male mlratio"
- ],
- [
"UCLA_BHF2_LIVER_FEMALE",
"UCLA BHF2 Liver Female mlratio"
],
[
+ "UCLA_BHF2_LIVER_MALE",
+ "UCLA BHF2 Liver Male mlratio"
+ ],
+ [
"UCLA_BHF2_LIVER_0605",
"UCLA BHF2 Liver (June05) mlratio"
]
],
"Muscle mRNA": [
[
- "UCLA_BHF2_MUSCLE_MALE",
- "UCLA BHF2 Muscle Male mlratio **"
- ],
- [
"UCLA_BHF2_MUSCLE_FEMALE",
"UCLA BHF2 Muscle Female mlratio **"
],
[
+ "UCLA_BHF2_MUSCLE_MALE",
+ "UCLA BHF2 Muscle Male mlratio **"
+ ],
+ [
"UCLA_BHF2_MUSCLE_0605",
"UCLA BHF2 Muscle (June05) mlratio **"
]
- ],
- "Phenotypes": [
- [
- "BHF2Publish",
- "BHF2 Published Phenotypes"
- ]
]
},
"BHHBF2": {
@@ -1513,12 +1297,6 @@
"UCLA_BHHBF2_MUSCLE_FEMALE",
"UCLA BHHBF2 Muscle Female Only"
]
- ],
- "Phenotypes": [
- [
- "BHHBF2Publish",
- "BHHBF2 Published Phenotypes"
- ]
]
},
"BXD": {
@@ -1604,14 +1382,14 @@
"UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 2.0"
],
[
- "UTHSC_BXD_WB_RNASeq1112",
- "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
- ],
- [
"UTHSC_BXD_WB_RNASeqtrim1_1112",
"UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 1.0"
],
[
+ "UTHSC_BXD_WB_RNASeq1112",
+ "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
+ ],
+ [
"UTHSC_BXD_WB_RNASeqEx1112",
"UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM"
],
@@ -1624,6 +1402,10 @@
"UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
],
[
+ "BR_U_0805_P",
+ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
+ ],
+ [
"BR_U_0805_M",
"UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
],
@@ -1632,10 +1414,6 @@
"UTHSC Brain mRNA U74Av2 (Aug05) RMA"
],
[
- "BR_U_0805_P",
- "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
- ],
- [
"CB_M_0204_P",
"INIA Brain mRNA M430 (Feb04) PDNN"
]
@@ -1746,10 +1524,6 @@
"Eye M430v2 WT Gpnmb (Sep08) RMA **"
],
[
- "Eye_M2_0908_R_MT",
- "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **"
- ],
- [
"Eye_M2_0908_WTWT",
"Eye M430v2 WT WT (Sep08) RMA **"
],
@@ -1758,6 +1532,10 @@
"Eye M430v2 WT Tyrp1 (Sep08) RMA **"
],
[
+ "Eye_M2_0908_R_MT",
+ "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **"
+ ],
+ [
"DBA2J-ONH-1212",
"Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
],
@@ -1962,12 +1740,12 @@
"Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
],
[
- "MA_M2_0706_P",
- "Mouse Kidney M430v2 (Jul06) PDNN"
- ],
- [
"MA_M2_0706_R",
"Mouse Kidney M430v2 (Jul06) RMA"
+ ],
+ [
+ "MA_M2_0706_P",
+ "Mouse Kidney M430v2 (Jul06) PDNN"
]
],
"Leucocytes mRNA": [
@@ -1988,14 +1766,14 @@
],
"Liver Proteome": [
[
- "EPFLETHZBXDprotHFD0514",
- "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **"
- ],
- [
"EPFLETHZBXDprotCD0514",
"EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH **"
],
[
+ "EPFLETHZBXDprotHFD0514",
+ "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **"
+ ],
+ [
"EPFLBXDprotHFDRPN0214",
"EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM **"
],
@@ -2132,14 +1910,14 @@
],
"Neocortex mRNA": [
[
- "DevNeocortex_ILM6.2P14RInv_1111",
- "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
- ],
- [
"DevNeocortex_ILM6.2P3RInv_1111",
"BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
],
[
+ "DevNeocortex_ILM6.2P14RInv_1111",
+ "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+ ],
+ [
"HQFNeoc_1210v2_RankInv",
"HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
],
@@ -2152,12 +1930,12 @@
"HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
],
[
- "DevNeocortex_ILM6.2P3RInv_1110",
- "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
- ],
- [
"DevNeocortex_ILM6.2P14RInv_1110",
"BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
+ ],
+ [
+ "DevNeocortex_ILM6.2P3RInv_1110",
+ "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
]
],
"Nucleus Accumbens mRNA": [
@@ -2256,14 +2034,14 @@
"ONC HEI Retina (April 2012) RankInv"
],
[
- "DoDTATRCRetMoGene2_1313",
- "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA"
- ],
- [
"DoDTATRCRetExMoGene2_1313",
"DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA Exon Level"
],
[
+ "DoDTATRCRetMoGene2_1313",
+ "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA"
+ ],
+ [
"ONCRetMoGene2_0413",
"DoD TATRC Retina Affy MoGene 2.0 ST (Oct13) RMA **"
],
@@ -2284,12 +2062,12 @@
"B6D2 ONC Retina (April 2012) RankInv **"
],
[
- "HEIONCvsCRetILM6_0911",
- "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **"
- ],
- [
"G2HEIONCRetILM6_0911",
"G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **"
+ ],
+ [
+ "HEIONCvsCRetILM6_0911",
+ "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **"
]
],
"Spleen mRNA": [
@@ -2376,12 +2154,12 @@
"BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **"
],
[
- "DevStriatum_ILM6.2P14RInv_1110",
- "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **"
- ],
- [
"DevStriatum_ILM6.2P3RInv_1110",
"BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **"
+ ],
+ [
+ "DevStriatum_ILM6.2P14RInv_1110",
+ "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **"
]
],
"T Cell (helper) mRNA": [
@@ -2404,16 +2182,16 @@
],
"Ventral Tegmental Area mRNA": [
[
- "VCUEtOH_0609_R",
- "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
- ],
- [
"VCUSal_0609_R",
"VCU BXD VTA Sal M430 2.0 (Jun09) RMA **"
],
[
"VCUEtvsSal_0609_R",
"VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **"
+ ],
+ [
+ "VCUEtOH_0609_R",
+ "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
]
]
},
@@ -2550,12 +2328,12 @@
],
"Hippocampus mRNA": [
[
- "HC_M2CB_1205_R",
- "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
- ],
- [
"HC_M2CB_1205_P",
"Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
+ ],
+ [
+ "HC_M2CB_1205_R",
+ "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
]
],
"Phenotypes": [
@@ -2572,12 +2350,6 @@
]
},
"HS": {
- "Genotypes": [
- [
- "HSGeno",
- "HS Genotypes"
- ]
- ],
"Hippocampus mRNA": [
[
"OXUKHS_ILMHipp_RI0510",
@@ -2604,18 +2376,6 @@
]
},
"HS-CC": {
- "Genotypes": [
- [
- "HS-CCGeno",
- "HS-CC Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "HS-CCPublish",
- "HS-CC Published Phenotypes"
- ]
- ],
"Striatum mRNA": [
[
"OHSU_HS-CC_ILMStr_0211",
@@ -2660,14 +2420,6 @@
"Hippocampus Illumina (May07) RankInv"
],
[
- "Illum_LXS_Hipp_NON_1008",
- "Hippocampus Illumina NON (Oct08) RankInv beta"
- ],
- [
- "Illum_LXS_Hipp_RSE_1008",
- "Hippocampus Illumina RSE (Oct08) RankInv beta"
- ],
- [
"Illum_LXS_Hipp_NOE_1008",
"Hippocampus Illumina NOE (Oct08) RankInv beta"
],
@@ -2678,6 +2430,14 @@
[
"Illum_LXS_Hipp_NOS_1008",
"Hippocampus Illumina NOS (Oct08) RankInv beta"
+ ],
+ [
+ "Illum_LXS_Hipp_NON_1008",
+ "Hippocampus Illumina NON (Oct08) RankInv beta"
+ ],
+ [
+ "Illum_LXS_Hipp_RSE_1008",
+ "Hippocampus Illumina RSE (Oct08) RankInv beta"
]
],
"Phenotypes": [
@@ -2688,16 +2448,16 @@
],
"Prefrontal Cortex mRNA": [
[
- "VCUEtOH_0806_R",
- "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
- ],
- [
"VCUSal_0806_R",
"VCU LXS PFC Sal M430A 2.0 (Aug06) RMA"
],
[
"VCUEt_vs_Sal_0806_R",
"VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **"
+ ],
+ [
+ "VCUEtOH_0806_R",
+ "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
]
]
},
@@ -2736,12 +2496,12 @@
],
"Hippocampus mRNA": [
[
- "UMUTAffyExon_0209_RMA_MDP",
- "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
- ],
- [
"HC_M2_0606_MDP",
"Hippocampus Consortium M430v2 (Jun06) RMA MDP"
+ ],
+ [
+ "UMUTAffyExon_0209_RMA_MDP",
+ "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
]
],
"Liver mRNA": [
@@ -2774,12 +2534,6 @@
]
},
"NZBXFVB-N2": {
- "Genotypes": [
- [
- "NZBXFVB-N2Geno",
- "NZBXFVB-N2 Genotypes"
- ]
- ],
"Mammary Tumors mRNA": [
[
"NCI_Mam_Tum_RMA_0409",
@@ -2799,12 +2553,6 @@
"SOTNOT-OHSUGeno",
"SOTNOT-OHSU Genotypes"
]
- ],
- "Phenotypes": [
- [
- "SOTNOT-OHSUPublish",
- "SOTNOT-OHSU Published Phenotypes"
- ]
]
},
"Scripps-2013": {
@@ -2817,29 +2565,11 @@
"ScrBXDACC4GEx0513",
"Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level **"
]
- ],
- "Genotypes": [
- [
- "Scripps-2013Geno",
- "Scripps-2013 Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "Scripps-2013Publish",
- "Scripps-2013 Published Phenotypes"
- ]
]
}
},
"rat": {
"HSNIH": {
- "Genotypes": [
- [
- "HSNIHGeno",
- "HSNIH Genotypes"
- ]
- ],
"Phenotypes": [
[
"HSNIHPublish",
@@ -2915,18 +2645,6 @@
"UIOWA_Eye_RMA_0906",
"UIOWA Eye mRNA RAE230v2 (Sep06) RMA"
]
- ],
- "Genotypes": [
- [
- "SRxSHRSPF2Geno",
- "SRxSHRSPF2 Genotypes"
- ]
- ],
- "Phenotypes": [
- [
- "SRxSHRSPF2Publish",
- "SRxSHRSPF2 Published Phenotypes"
- ]
]
}
},
@@ -2946,12 +2664,6 @@
]
},
"J12XJ58F2": {
- "Genotypes": [
- [
- "J12XJ58F2Geno",
- "J12XJ58F2 Genotypes"
- ]
- ],
"Phenotypes": [
[
"J12XJ58F2Publish",
@@ -2962,12 +2674,6 @@
},
"tomato": {
"LXP": {
- "Genotypes": [
- [
- "LXPGeno",
- "LXP Genotypes"
- ]
- ],
"Phenotypes": [
[
"LXPPublish",
@@ -3285,14 +2991,6 @@
"barley": {
"QSM": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Leaf mRNA",
"Leaf mRNA"
]
@@ -3319,28 +3017,12 @@
"drosophila": {
"DGRP": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Whole Body mRNA",
"Whole Body mRNA"
]
],
"Oregon-R_x_2b3": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Whole Body mRNA",
"Whole Body mRNA"
]
@@ -3349,24 +3031,12 @@
"human": {
"AD-cases-controls": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Brain mRNA",
"Brain mRNA"
]
],
"AD-cases-controls-Myers": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3377,14 +3047,6 @@
],
"Aging-Brain-UCI": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Entorhinal Cortex mRNA",
"Entorhinal Cortex mRNA"
],
@@ -3403,14 +3065,6 @@
],
"Brain-Normal-NIH-Gibbs": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Cerebellum mRNA",
"Cerebellum mRNA"
],
@@ -3433,10 +3087,6 @@
"Phenotypes"
],
[
- "Genotypes",
- "Genotypes"
- ],
- [
"Methylation",
"Methylation"
],
@@ -3447,28 +3097,12 @@
],
"CEPH-2004": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Lymphoblast B-cell mRNA",
"Lymphoblast B-cell mRNA"
]
],
"GTEx": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Adrenal Gland mRNA",
"Adrenal Gland mRNA"
],
@@ -3659,14 +3293,6 @@
],
"HB": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Cerebellum mRNA",
"Cerebellum mRNA"
],
@@ -3683,10 +3309,6 @@
[
"Phenotypes",
"Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
]
],
"HLC": [
@@ -3695,38 +3317,18 @@
"Phenotypes"
],
[
- "Genotypes",
- "Genotypes"
- ],
- [
"Liver mRNA",
"Liver mRNA"
]
],
"HLT": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Lung mRNA",
"Lung mRNA"
]
],
"HSB": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Amygdala mRNA",
"Amygdala mRNA"
],
@@ -3795,14 +3397,6 @@
"macaque monkey": {
"Macaca-fasicularis": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Amygdala mRNA",
"Amygdala mRNA"
],
@@ -3827,10 +3421,6 @@
"mouse": {
"AKXD": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3881,10 +3471,6 @@
],
"B6D2F2": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3895,10 +3481,6 @@
],
"B6D2F2-PSU": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3909,24 +3491,12 @@
],
"B6D2RI": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Hippocampus mRNA",
"Hippocampus mRNA"
]
],
"BDF2-1999": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3937,10 +3507,6 @@
],
"BDF2-2005": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3951,10 +3517,6 @@
],
"BHF2": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -3977,10 +3539,6 @@
],
"BHHBF2": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
],
@@ -4233,10 +3791,6 @@
"Phenotypes"
],
[
- "Genotypes",
- "Genotypes"
- ],
- [
"Hippocampus mRNA",
"Hippocampus mRNA"
],
@@ -4251,14 +3805,6 @@
],
"HS-CC": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Striatum mRNA",
"Striatum mRNA"
]
@@ -4323,34 +3869,18 @@
"Phenotypes"
],
[
- "Genotypes",
- "Genotypes"
- ],
- [
"Mammary Tumors mRNA",
"Mammary Tumors mRNA"
]
],
"SOTNOT-OHSU": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
"Genotypes",
"Genotypes"
]
],
"Scripps-2013": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Anterior Cingulate Cortex mRNA",
"Anterior Cingulate Cortex mRNA"
]
@@ -4361,10 +3891,6 @@
[
"Phenotypes",
"Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
]
],
"HXBBXH": [
@@ -4403,14 +3929,6 @@
],
"SRxSHRSPF2": [
[
- "Phenotypes",
- "Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
- ],
- [
"Eye mRNA",
"Eye mRNA"
]
@@ -4431,10 +3949,6 @@
[
"Phenotypes",
"Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
]
]
},
@@ -4443,10 +3957,6 @@
[
"Phenotypes",
"Phenotypes"
- ],
- [
- "Genotypes",
- "Genotypes"
]
]
}
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 98f89ac6..68d9b5a2 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -4,7 +4,6 @@ class Histogram
constructor: (@sample_list, @sample_group) ->
@sort_by = "name"
@format_count = d3.format(",.0f") #a formatter for counts
- @get_sample_vals()
@margin = {top: 10, right: 30, bottom: 30, left: 30}
@plot_width = 960 - @margin.left - @margin.right
@@ -12,21 +11,25 @@ class Histogram
@x_buffer = @plot_width/20
@y_buffer = @plot_height/20
+ @plot_height -= @y_buffer
+
+ @get_sample_vals(@sample_list)
+ @redraw(@sample_vals)
+ redraw: (@sample_vals) ->
@y_min = d3.min(@sample_vals)
@y_max = d3.max(@sample_vals) * 1.1
-
- @plot_height -= @y_buffer
+
@create_x_scale()
@get_histogram_data()
@create_y_scale()
+ $("#histogram").empty()
@svg = @create_svg()
-
@create_graph()
- get_sample_vals: () ->
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
+ get_sample_vals: (sample_list) ->
+ @sample_vals = (sample.value for sample in sample_list when sample.value != null)
create_svg: () ->
svg = d3.select("#histogram")
@@ -53,8 +56,9 @@ class Histogram
get_histogram_data: () ->
console.log("sample_vals:", @sample_vals)
+ n_bins = Math.sqrt(@sample_vals.length)
@histogram_data = d3.layout.histogram()
- .bins(@x_scale.ticks(20))(@sample_vals)
+ .bins(@x_scale.ticks(n_bins))(@sample_vals)
console.log("histogram_data:", @histogram_data[0])
create_y_scale: () ->
@@ -112,17 +116,20 @@ class Histogram
.attr("class", "bar")
.attr("transform", (d) =>
return "translate(" + @x_scale(d.x) + "," + @y_scale(d.y) + ")")
+
+ rect_width = @x_scale(@histogram_data[0].x + @histogram_data[0].dx) -
+ @x_scale(@histogram_data[0].x)
bar.append("rect")
.attr("x", 1)
- .attr("width", @x_scale(@histogram_data[0].x + @histogram_data[0].dx) - 1)
+ .attr("width", rect_width - 1)
.attr("height", (d) =>
return @plot_height - @y_scale(d.y)
)
bar.append("text")
.attr("dy", ".75em")
.attr("y", 6)
- .attr("x", @x_scale(@histogram_data[0].dx)/2)
+ .attr("x", rect_width / 2)
.attr("text-anchor", "middle")
.style("fill", "#fff")
.text((d) =>
@@ -131,4 +138,4 @@ class Histogram
return @format_count(d.y)
)
-root.Histogram = Histogram \ No newline at end of file
+root.Histogram = Histogram
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 561a3068..d872a3ba 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -1,124 +1,135 @@
-// Generated by CoffeeScript 1.8.0
-var Histogram, root;
-
-root = typeof exports !== "undefined" && exports !== null ? exports : this;
-
-Histogram = (function() {
- function Histogram(sample_list, sample_group) {
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.sort_by = "name";
- this.format_count = d3.format(",.0f");
- this.get_sample_vals();
- this.margin = {
- top: 10,
- right: 30,
- bottom: 30,
- left: 30
+// Generated by CoffeeScript 1.9.2
+(function() {
+ var Histogram, root;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+ Histogram = (function() {
+ function Histogram(sample_list1, sample_group) {
+ this.sample_list = sample_list1;
+ this.sample_group = sample_group;
+ this.sort_by = "name";
+ this.format_count = d3.format(",.0f");
+ this.margin = {
+ top: 10,
+ right: 30,
+ bottom: 30,
+ left: 30
+ };
+ this.plot_width = 960 - this.margin.left - this.margin.right;
+ this.plot_height = 500 - this.margin.top - this.margin.bottom;
+ this.x_buffer = this.plot_width / 20;
+ this.y_buffer = this.plot_height / 20;
+ this.plot_height -= this.y_buffer;
+ this.get_sample_vals(this.sample_list);
+ this.redraw(this.sample_vals);
+ }
+
+ Histogram.prototype.redraw = function(sample_vals) {
+ this.sample_vals = sample_vals;
+ this.y_min = d3.min(this.sample_vals);
+ this.y_max = d3.max(this.sample_vals) * 1.1;
+ this.create_x_scale();
+ this.get_histogram_data();
+ this.create_y_scale();
+ $("#histogram").empty();
+ this.svg = this.create_svg();
+ return this.create_graph();
};
- this.plot_width = 960 - this.margin.left - this.margin.right;
- this.plot_height = 500 - this.margin.top - this.margin.bottom;
- this.x_buffer = this.plot_width / 20;
- this.y_buffer = this.plot_height / 20;
- this.y_min = d3.min(this.sample_vals);
- this.y_max = d3.max(this.sample_vals) * 1.1;
- this.plot_height -= this.y_buffer;
- this.create_x_scale();
- this.get_histogram_data();
- this.create_y_scale();
- this.svg = this.create_svg();
- this.create_graph();
- }
-
- Histogram.prototype.get_sample_vals = function() {
- var sample;
- return this.sample_vals = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sample_list;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- if (sample.value !== null) {
- _results.push(sample.value);
+
+ Histogram.prototype.get_sample_vals = function(sample_list) {
+ var sample;
+ return this.sample_vals = (function() {
+ var i, len, results;
+ results = [];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
+ if (sample.value !== null) {
+ results.push(sample.value);
+ }
}
- }
- return _results;
- }).call(this);
- };
-
- Histogram.prototype.create_svg = function() {
- var svg;
- svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
- return svg;
- };
-
- Histogram.prototype.create_x_scale = function() {
- var x0;
- console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
- x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
- return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
- };
-
- Histogram.prototype.get_histogram_data = function() {
- console.log("sample_vals:", this.sample_vals);
- this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
- return console.log("histogram_data:", this.histogram_data[0]);
- };
-
- Histogram.prototype.create_y_scale = function() {
- return this.y_scale = d3.scale.linear().domain([
- 0, d3.max(this.histogram_data, (function(_this) {
+ return results;
+ })();
+ };
+
+ Histogram.prototype.create_svg = function() {
+ var svg;
+ svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
+ return svg;
+ };
+
+ Histogram.prototype.create_x_scale = function() {
+ var x0;
+ console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
+ x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+ return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
+ };
+
+ Histogram.prototype.get_histogram_data = function() {
+ var n_bins;
+ console.log("sample_vals:", this.sample_vals);
+ n_bins = Math.sqrt(this.sample_vals.length);
+ this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals);
+ return console.log("histogram_data:", this.histogram_data[0]);
+ };
+
+ Histogram.prototype.create_y_scale = function() {
+ return this.y_scale = d3.scale.linear().domain([
+ 0, d3.max(this.histogram_data, (function(_this) {
+ return function(d) {
+ return d.y;
+ };
+ })(this))
+ ]).range([this.plot_height, 0]);
+ };
+
+ Histogram.prototype.create_graph = function() {
+ this.add_x_axis();
+ this.add_y_axis();
+ return this.add_bars();
+ };
+
+ Histogram.prototype.add_x_axis = function() {
+ var x_axis;
+ x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
+ return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
+ };
+
+ Histogram.prototype.add_y_axis = function() {
+ var yAxis;
+ yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+ return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+ };
+
+ Histogram.prototype.add_bars = function() {
+ var bar, rect_width;
+ console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
+ bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
return function(d) {
- return d.y;
+ return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
};
- })(this))
- ]).range([this.plot_height, 0]);
- };
-
- Histogram.prototype.create_graph = function() {
- this.add_x_axis();
- this.add_y_axis();
- return this.add_bars();
- };
-
- Histogram.prototype.add_x_axis = function() {
- var x_axis;
- x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
- return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
- };
-
- Histogram.prototype.add_y_axis = function() {
- var yAxis;
- yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
- return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
- };
-
- Histogram.prototype.add_bars = function() {
- var bar;
- console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
- bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
- return function(d) {
- return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
- };
- })(this));
- bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
- return function(d) {
- return _this.plot_height - _this.y_scale(d.y);
- };
- })(this));
- return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
- return function(d) {
- var bar_height;
- bar_height = _this.plot_height - _this.y_scale(d.y);
- if (bar_height > 20) {
- return _this.format_count(d.y);
- }
- };
- })(this));
- };
+ })(this));
+ rect_width = this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - this.x_scale(this.histogram_data[0].x);
+ bar.append("rect").attr("x", 1).attr("width", rect_width - 1).attr("height", (function(_this) {
+ return function(d) {
+ return _this.plot_height - _this.y_scale(d.y);
+ };
+ })(this));
+ return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", rect_width / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
+ return function(d) {
+ var bar_height;
+ bar_height = _this.plot_height - _this.y_scale(d.y);
+ if (bar_height > 20) {
+ return _this.format_count(d.y);
+ }
+ };
+ })(this));
+ };
+
+ return Histogram;
- return Histogram;
+ })();
-})();
+ root.Histogram = Histogram;
-root.Histogram = Histogram;
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index ee57831f..1d3123ba 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -238,6 +238,7 @@ $ ->
sample_sets['samples_all'].add_value(real_value)
already_seen[name] = true
console.log("towards end:", sample_sets)
+ root.histogram.redraw(sample_sets['samples_primary'].the_values)
update_stat_values(sample_sets)
show_hide_outliers = ->
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c2dc07ee..9323862a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -265,6 +265,7 @@
}
}
console.log("towards end:", sample_sets);
+ root.histogram.redraw(sample_sets['samples_primary'].the_values);
return update_stat_values(sample_sets);
};
show_hide_outliers = function() {
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 5e0a92e3..cb29a07c 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -206,12 +206,12 @@
<h3>GN1 Mirror and development sites</h3>
<ul>
- <li><a href="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN1 site at UTHSC</a> (main site)</li>
- <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
- <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
- <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
- <li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
- <li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
+ <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li>
+ <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">Australia at the UWA</a></li>
+ <li><a href="http://gn.genetics.ucla.edu/" target="_blank">California at UCLA</a></li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li>
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li>
+ <li><a href="http://genenetwork.epfl.ch/" target="_blank">Switzerland at the EPFL</a></li>
</ul>
</section>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f46d7cbf..ab4a36bb 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -44,7 +44,7 @@
</tr>
</thead>
<tbody>
- {% for marker in pair_scan_results %}
+ {% for marker in filtered_markers %}
<tr>
<td>{{loop.index}}</td>
<td>{{marker.name}}</td>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a1723ef8..d6f22f41 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -13,8 +13,12 @@
{% endblock %}
{% block content %} <!-- Start of body -->
- {{ header("{}".format(this_trait.symbol),
- '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% if this_trait.dataset.type != 'Geno' %}
+ {{ header("{}".format(this_trait.name_header_fmt),
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+ {% else %}
+ {{ header("{}".format(this_trait.name_header_fmt)) }}
+ {% endif %}
<form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
@@ -31,7 +35,7 @@
<div class="page-header">
<h1>{{ dataset.group.species.capitalize() }} -
{{ dataset.group.name }} -
- {{ this_trait.symbol }}
+ {{ this_trait.name_header_fmt }}
</h1>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 0afac1f7..e1780e42 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,9 +1,13 @@
<dl class="dl-horizontal">
+ {% if this_trait.dataset.type == 'ProbeSet' %}
<dt>Aliases</dt>
<dd>{{ this_trait.alias_fmt }}</dd>
+ {% endif %}
+ {% if this_trait.dataset.type != 'Publish' %}
<dt>Location</dt>
<dd>{{ this_trait.location_fmt }}</dd>
+ {% endif %}
<dt>Database</dt>
<dd>
@@ -16,7 +20,7 @@
<dt>
<a href="/blatInfo.html" target="_blank"
title="Values higher than 2 for the specificity are good">
- BLAT Specifity
+ BLAT Specificity
</a>
</dt>
<dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27504e51..bd1e6f1e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -4,14 +4,16 @@
<ul class="nav nav-pills">
<li class="active">
- <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
- </li>
- <li>
<a href="#pylmm" data-toggle="tab">pyLMM</a>
</li>
<li>
<a href="#rqtl_geno" data-toggle="tab">rqtl</a>
</li>
+ {% if dataset.group.species != 'human' %}
+ <li>
+ <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+ </li>
+ {% endif %}
{% if dataset.group.species == 'human' %}
<li>
<a href="#plink" data-toggle="tab">PLINK</a>
@@ -26,60 +28,7 @@
</ul>
<div class="tab-content">
- <div class="tab-pane active" id="interval_mapping">
- <div style="padding: 20px" class="form-horizontal">
- <div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-2 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-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- <input name="mapping_bootstraps" value="2000" type="text" class="form-control">
- </div>
- </div>
-
- <div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
- <div class="col-xs-12 controls" id="display_additive_effect">
- <label class="radio-inline">
- <input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="display_additive" id="display_additive" value="no">
- 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_reaper" value="true">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
- No
- </label>
- </div>
- </div>
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
- <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
- </button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="tab-pane" id="pylmm">
+ <div class="tab-pane active" id="pylmm">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
@@ -211,7 +160,60 @@
</div>
</div>
</div>
-
+ {% if dataset.group.species != 'human' %}
+ <div class="tab-pane" id="interval_mapping">
+ <div style="padding: 20px" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <label for="mapping_permutations" class="col-xs-2 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-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <input name="mapping_bootstraps" value="2000" type="text" class="form-control">
+ </div>
+ </div>
+
+ <div class="mapping_method_fields form-group">
+ <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
+ <div class="col-xs-12 controls" id="display_additive_effect">
+ <label class="radio-inline">
+ <input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="display_additive" id="display_additive" value="no">
+ 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_reaper" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
+ No
+ </label>
+ </div>
+ </div>
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+ {% endif %}
{% if dataset.group.species == 'human' %}
<div class="tab-pane" id="plink">
<div style="padding: 20px" class="form-horizontal">
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 18:45:14 +0000