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-rw-r--r--wqflask/maintenance/gen_select_dataset.py4
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py9
-rw-r--r--wqflask/wqflask/static/new/css/network_graph.css2
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json178
-rw-r--r--wqflask/wqflask/static/new/javascript/network_graph.js11
-rw-r--r--wqflask/wqflask/templates/network_graph.html7
6 files changed, 128 insertions, 83 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 23adc4f9..542c0d83 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -49,7 +49,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
import MySQLdb
-# import simplejson as json
+import simplejson as json
import urlparse
@@ -289,7 +289,7 @@ def main():
#print("data:", data)
- output_file = """./wqflask/wqflask/static/new/javascript/dataset_menu_structure.json"""
+ output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json"""
with open(output_file, 'w') as fh:
json.dump(data, fh, indent=" ", sort_keys=True)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 1d725c4c..cebe5c03 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -167,9 +167,9 @@ class NetworkGraph(object):
if abs(sample_r) > max_corr:
max_corr = abs(sample_r)
- edge_data = {'id' : this_trait.name + '_to_' + target_trait.name,
- 'source' : this_trait.name + ":" + this_trait.dataset.name,
- 'target' : target_trait.name + ":" + target_trait.dataset.name,
+ edge_data = {'id' : str(this_trait.name) + '_to_' + str(target_trait.name),
+ 'source' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
+ 'target' : str(target_trait.name) + ":" + str(target_trait.dataset.name),
'correlation' : round(sample_r, 3),
'abs_corr' : abs(round(sample_r, 3)),
'p_value' : round(sample_p, 3),
@@ -181,8 +181,9 @@ class NetworkGraph(object):
self.edges_list.append(edge_dict)
- node_dict = { 'data' : {'id' : this_trait.name + ":" + this_trait.dataset.name,
+ node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
'label' : this_trait.name,
+ 'symbol' : this_trait.symbol,
'geneid' : this_trait.geneid,
'omim' : this_trait.omim,
'max_corr' : max_corr } }
diff --git a/wqflask/wqflask/static/new/css/network_graph.css b/wqflask/wqflask/static/new/css/network_graph.css
index c01c0d24..1cba546a 100644
--- a/wqflask/wqflask/static/new/css/network_graph.css
+++ b/wqflask/wqflask/static/new/css/network_graph.css
@@ -13,7 +13,7 @@
#secondaryContent {
position: relative;
float: left;
- width: 16.5em;
+ width: 18.5em;
padding: 1em 1em 1em 1em;
background: #fff url('/static/new/images/a1.gif') top right repeat-y;
}
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 750a9118..d3db1853 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -317,6 +317,30 @@
]
},
"GTEx": {
+ "Adipose tissue, subcutaneous mRNA": [
+ [
+ "580",
+ "GTEx_log2_Subcu_0314",
+ "GTEx Human Subcutaneous (Mar14) RPKM Log2"
+ ],
+ [
+ "530",
+ "GTEx_Subcu_0414",
+ "GTEx Human Subcutaneous (Apr14) RPKM"
+ ]
+ ],
+ "Adipose tissue, visceral mRNA": [
+ [
+ "587",
+ "GTEx_log2_Visce_0314",
+ "GTEx Human Visceral (Mar14) RPKM Log2"
+ ],
+ [
+ "537",
+ "GTEx_Visce_0414",
+ "GTEx Human Visceral (Apr14) RPKM"
+ ]
+ ],
"Adrenal Gland mRNA": [
[
"545",
@@ -773,18 +797,6 @@
"GTEx Human Stomach (Apr14) RPKM"
]
],
- "Subcutaneous mRNA": [
- [
- "580",
- "GTEx_log2_Subcu_0314",
- "GTEx Human Subcutaneous (Mar14) RPKM Log2"
- ],
- [
- "530",
- "GTEx_Subcu_0414",
- "GTEx Human Subcutaneous (Apr14) RPKM"
- ]
- ],
"Substantia Nigra mRNA": [
[
"581",
@@ -857,18 +869,6 @@
"GTEx Human Vagina (Apr14) RPKM"
]
],
- "Visceral mRNA": [
- [
- "587",
- "GTEx_log2_Visce_0314",
- "GTEx Human Visceral (Mar14) RPKM Log2"
- ],
- [
- "537",
- "GTEx_Visce_0414",
- "GTEx Human Visceral (Apr14) RPKM"
- ]
- ],
"Whole Blood mRNA": [
[
"588",
@@ -883,6 +883,20 @@
]
},
"GTEx_v5": {
+ "Adipose tissue, subcutaneous mRNA": [
+ [
+ "718",
+ "GTEXv5_AdipSub_0915",
+ "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2"
+ ]
+ ],
+ "Adipose tissue, visceral mRNA": [
+ [
+ "719",
+ "GTEXv5_AdiVis_0915",
+ "GTEXv5 Human Adipose Visceral Omentum RefSeq (Sep15) RPKM log2"
+ ]
+ ],
"Adrenal Gland mRNA": [
[
"720",
@@ -1191,13 +1205,6 @@
"GTEXv5 Human Stomach RefSeq (Sep15) RPKM log2"
]
],
- "Subcutaneous mRNA": [
- [
- "718",
- "GTEXv5_AdipSub_0915",
- "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2"
- ]
- ],
"Substantia Nigra mRNA": [
[
"737",
@@ -1240,13 +1247,6 @@
"GTEXv5 Human Vagina RefSeq (Sep15) RPKM log2"
]
],
- "Visceral mRNA": [
- [
- "719",
- "GTEXv5_AdiVis_0915",
- "GTEXv5 Human Adipose Visceral Omentum RefSeq (Sep15) RPKM log2"
- ]
- ],
"Whole Blood mRNA": [
[
"770",
@@ -1609,9 +1609,30 @@
]
]
},
+ "B6D2": {
+ "Phenotypes": [
+ [
+ "None",
+ "B6D2Publish",
+ "B6D2 Published Phenotypes"
+ ]
+ ],
+ "Retina mRNA": [
+ [
+ "803",
+ "UTHSC_mm9_B6D2_Ret_0916",
+ "UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA"
+ ]
+ ]
+ },
"B6D2F2": {
"Brain mRNA": [
[
+ "78",
+ "BRF2_M_0805_P",
+ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
+ ],
+ [
"77",
"BRF2_M_0805_R",
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
@@ -1622,11 +1643,6 @@
"OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
],
[
- "78",
- "BRF2_M_0805_P",
- "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
- ],
- [
"33",
"BRF2_M_0304_P",
"OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
@@ -2306,16 +2322,16 @@
],
"Kidney mRNA": [
[
- "239",
- "MA_M2F_0706_R",
- "Mouse kidney M430v2 Female (Aug06) RMA"
- ],
- [
"240",
"MA_M2M_0706_R",
"Mouse kidney M430v2 Male (Aug06) RMA"
],
[
+ "239",
+ "MA_M2F_0706_R",
+ "Mouse kidney M430v2 Female (Aug06) RMA"
+ ],
+ [
"118",
"MA_M2_0806_R",
"Mouse kidney M430v2 Sex Balanced (Aug06) RMA"
@@ -2495,16 +2511,16 @@
],
"Neocortex mRNA": [
[
- "375",
- "DevNeocortex_ILM6.2P14RInv_1111",
- "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
- ],
- [
"374",
"DevNeocortex_ILM6.2P3RInv_1111",
"BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
],
[
+ "375",
+ "DevNeocortex_ILM6.2P14RInv_1111",
+ "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+ ],
+ [
"284",
"HQFNeoc_1210v2_RankInv",
"HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -3017,6 +3033,11 @@
],
"Hippocampus mRNA": [
[
+ "214",
+ "Illum_LXS_Hipp_NOE_1008",
+ "Hippocampus Illumina NOE (Oct08) RankInv beta"
+ ],
+ [
"211",
"Illum_LXS_Hipp_RSS_1008",
"Hippocampus Illumina RSS (Oct08) RankInv beta"
@@ -3037,11 +3058,6 @@
"Hippocampus Illumina RSE (Oct08) RankInv beta"
],
[
- "214",
- "Illum_LXS_Hipp_NOE_1008",
- "Hippocampus Illumina NOE (Oct08) RankInv beta"
- ],
- [
"143",
"Illum_LXS_Hipp_loess0807",
"Hippocampus Illumina (Aug07) LOESS"
@@ -3472,6 +3488,10 @@
"B6BTBRF2"
],
[
+ "B6D2",
+ "Glaucoma and Aged Retina, UTHSC"
+ ],
+ [
"B6D2F2",
"B6D2F2"
],
@@ -3793,6 +3813,14 @@
],
"GTEx": [
[
+ "Adipose tissue, subcutaneous mRNA",
+ "Adipose tissue, subcutaneous mRNA"
+ ],
+ [
+ "Adipose tissue, visceral mRNA",
+ "Adipose tissue, visceral mRNA"
+ ],
+ [
"Adrenal Gland mRNA",
"Adrenal Gland mRNA"
],
@@ -3945,10 +3973,6 @@
"Stomach mRNA"
],
[
- "Subcutaneous mRNA",
- "Subcutaneous mRNA"
- ],
- [
"Substantia Nigra mRNA",
"Substantia Nigra mRNA"
],
@@ -3973,16 +3997,20 @@
"Vagina mRNA"
],
[
- "Visceral mRNA",
- "Visceral mRNA"
- ],
- [
"Whole Blood mRNA",
"Whole Blood mRNA"
]
],
"GTEx_v5": [
[
+ "Adipose tissue, subcutaneous mRNA",
+ "Adipose tissue, subcutaneous mRNA"
+ ],
+ [
+ "Adipose tissue, visceral mRNA",
+ "Adipose tissue, visceral mRNA"
+ ],
+ [
"Adrenal Gland mRNA",
"Adrenal Gland mRNA"
],
@@ -4159,10 +4187,6 @@
"Stomach mRNA"
],
[
- "Subcutaneous mRNA",
- "Subcutaneous mRNA"
- ],
- [
"Substantia Nigra mRNA",
"Substantia Nigra mRNA"
],
@@ -4187,10 +4211,6 @@
"Vagina mRNA"
],
[
- "Visceral mRNA",
- "Visceral mRNA"
- ],
- [
"Whole Blood mRNA",
"Whole Blood mRNA"
]
@@ -4363,6 +4383,16 @@
"Liver mRNA"
]
],
+ "B6D2": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ],
+ [
+ "Retina mRNA",
+ "Retina mRNA"
+ ]
+ ],
"B6D2F2": [
[
"Genotypes",
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index da90ae26..e8ca6be0 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -12,7 +12,7 @@ window.onload=function() {
selector: 'node',
style: {
'background-color': '#666',
- 'label': 'data(id)',
+ 'label': 'data(symbol)',
'font-size': 10
}
},
@@ -154,6 +154,15 @@ window.onload=function() {
});
+ $('#reset_graph').click(function() {
+ eles.restore()
+ $('#slide').val(0)
+ cy.layout({ name: $('select[name=layout_select]').val(),
+ fit: true, // whether to fit the viewport to the graph
+ padding: 25 // the padding on fit
+ });
+ });
+
$('select[name=focus_select]').change(function() {
focus_trait = $(this).val()
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index ec3a7971..57426af7 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -22,6 +22,11 @@
<tbody>
<tr>
<td>
+ <button id="reset_graph">Reset Graph</button>
+ </td>
+ </tr>
+ <tr>
+ <td>
Focus Trait
</td>
</tr>
@@ -29,7 +34,7 @@
<td>
<select name="focus_select">
{% for trait in traits %}
- <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.name }}</option>
+ <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.symbol }} ({{ trait.name }})</option>
{% endfor %}
</select>
</td>