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-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py15
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json284
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html5
5 files changed, 245 insertions, 62 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 49959a74..82a44796 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1018,7 +1018,7 @@ class MarkerRegression(object):
else:
if self.selectedChr > -1:
for i, qtlresult in enumerate(self.qtlresults):
- if qtlresult['Chr'] != self.selectedChr:
+ if qtlresult['chr'] != self.selectedChr:
continue
if i==0 and qtlresult['Mb'] >= Mb:
@@ -1027,7 +1027,7 @@ class MarkerRegression(object):
#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']))
+ locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(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
@@ -1036,11 +1036,12 @@ class MarkerRegression(object):
else:
locPixel = xLeftOffset
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
- break
+ if i < (len(self.ChrList)-1):
+ if _chr != Chr:
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ else:
+ locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+ break
if locPixel >= 0 and self.plotScale == 'physic':
traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 861af3d6..f3712b5d 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1340,14 +1340,14 @@
"GSE9588 Human Liver Normal (Mar11) Both Sexes"
],
[
- "384",
- "HLCF_0311",
- "GSE9588 Human Liver Normal (Mar11) Females"
- ],
- [
"383",
"HLCM_0311",
"GSE9588 Human Liver Normal (Mar11) Males"
+ ],
+ [
+ "384",
+ "HLCF_0311",
+ "GSE9588 Human Liver Normal (Mar11) Females"
]
],
"Phenotypes": [
@@ -1493,6 +1493,15 @@
]
]
},
+ "Islets-Gerling": {
+ "Phenotypes": [
+ [
+ "None",
+ "Islets-GerlingPublish",
+ "Islets-Gerling Published Phenotypes"
+ ]
+ ]
+ },
"TIGEM-Retina-RNA-Seq": {
"Phenotypes": [
[
@@ -1561,6 +1570,11 @@
],
"Heart mRNA": [
[
+ "820",
+ "UCLA_AXB_BXA_Aor_Jan16",
+ "UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"421",
"IRCM_AXBXA_HRI0213",
"IRCM AXB/BXA Mouse Heart ILM MouseRef-8 v2.0 (Feb13) RankInv"
@@ -1568,6 +1582,11 @@
],
"Liver mRNA": [
[
+ "822",
+ "UCLA_AXB_BXA_Liv_Jan16",
+ "UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"352",
"GSE16780AB_UCLA_ML0911",
"GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA"
@@ -1727,11 +1746,6 @@
],
"Striatum mRNA": [
[
- "85",
- "SA_M2_0905_P",
- "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
- ],
- [
"84",
"SA_M2_0905_R",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
@@ -1740,22 +1754,27 @@
"83",
"SA_M2_0905_M",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
+ ],
+ [
+ "85",
+ "SA_M2_0905_P",
+ "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
]
]
},
"BHF2": {
"Adipose mRNA": [
[
- "197",
- "UCLA_BHF2_ADIPOSE_FEMALE",
- "UCLA BHF2 Adipose Female mlratio"
- ],
- [
"196",
"UCLA_BHF2_ADIPOSE_MALE",
"UCLA BHF2 Adipose Male mlratio"
],
[
+ "197",
+ "UCLA_BHF2_ADIPOSE_FEMALE",
+ "UCLA BHF2 Adipose Female mlratio"
+ ],
+ [
"165",
"UCLA_BHF2_ADIPOSE_0605",
"UCLA BHF2 Adipose (June05) mlratio"
@@ -1763,16 +1782,16 @@
],
"Brain mRNA": [
[
- "199",
- "UCLA_BHF2_BRAIN_FEMALE",
- "UCLA BHF2 Brain Female mlratio"
- ],
- [
"198",
"UCLA_BHF2_BRAIN_MALE",
"UCLA BHF2 Brain Male mlratio"
],
[
+ "199",
+ "UCLA_BHF2_BRAIN_FEMALE",
+ "UCLA BHF2 Brain Female mlratio"
+ ],
+ [
"166",
"UCLA_BHF2_BRAIN_0605",
"UCLA BHF2 Brain (June05) mlratio"
@@ -1787,16 +1806,16 @@
],
"Liver mRNA": [
[
- "201",
- "UCLA_BHF2_LIVER_FEMALE",
- "UCLA BHF2 Liver Female mlratio"
- ],
- [
"200",
"UCLA_BHF2_LIVER_MALE",
"UCLA BHF2 Liver Male mlratio"
],
[
+ "201",
+ "UCLA_BHF2_LIVER_FEMALE",
+ "UCLA BHF2 Liver Female mlratio"
+ ],
+ [
"167",
"UCLA_BHF2_LIVER_0605",
"UCLA BHF2 Liver (June05) mlratio"
@@ -2000,11 +2019,6 @@
"UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
],
[
- "81",
- "BR_U_0805_P",
- "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
- ],
- [
"80",
"BR_U_0805_M",
"UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
@@ -2015,6 +2029,11 @@
"UTHSC Brain mRNA U74Av2 (Aug05) RMA"
],
[
+ "81",
+ "BR_U_0805_P",
+ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
+ ],
+ [
"42",
"CB_M_0204_P",
"INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2142,6 +2161,13 @@
"BXD Genotypes"
]
],
+ "Heart mRNA": [
+ [
+ "819",
+ "UCLA_BXD_Aor_Jan16",
+ "UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Hematopoietic Cells mRNA": [
[
"149",
@@ -2218,6 +2244,26 @@
"UMUTAffy Hippocampus Exon (Feb09) RMA"
],
[
+ "814",
+ "UTHSC_ILM_BXD_hipp_NOSb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) RankInv"
+ ],
+ [
+ "815",
+ "UTHSC_ILM_BXD_hipp_NOEb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) RankInv"
+ ],
+ [
+ "816",
+ "UTHSC_ILM_BXD_hipp_RSSb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv"
+ ],
+ [
+ "817",
+ "UTHSC_ILM_BXD_hipp_RSEb_0217",
+ "UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) RankInv"
+ ],
+ [
"780",
"UTHSC_ILM_BXD_hipp_NOEb_0216",
"UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) RankInv"
@@ -2391,14 +2437,24 @@
],
"Liver Proteome": [
[
+ "540",
+ "EPFLETHZBXDprotCD0514",
+ "EPFL/ETHZ BXD Liver, Chow Diet (Jun16) Top100 SWATH"
+ ],
+ [
+ "541",
+ "EPFLETHZBXDprotHFD0514",
+ "EPFL/ETHZ BXD Liver, High Fat Diet (Jun16) Top100 SWATH"
+ ],
+ [
"704",
"EPFLETHZBXDprotCD_LS1114",
- "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Light SWATH"
+ "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Top10 SWATH"
],
[
"705",
"EPFLETHZBXDprotHF_LS1114",
- "EPFL/ETHZ BXD Liver, High Fat Diet (Oct14) Light SWATH"
+ "EPFL/ETHZ BXD Liver, High Fat Diet Diet (Oct14) Top10 SWATH"
],
[
"703",
@@ -2414,20 +2470,15 @@
"489",
"EPFLBXDprotHFDRPN0214",
"EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM"
- ],
- [
- "540",
- "EPFLETHZBXDprotCD0514",
- "EPFL/ETHZ BXD Liver, Soluble Proteins CD (Jun14) SWATH"
- ],
- [
- "541",
- "EPFLETHZBXDprotHFD0514",
- "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (Jun14) SWATH"
]
],
"Liver mRNA": [
[
+ "818",
+ "UCLA_BXD_Liv_Jan16",
+ "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA"
+ ],
+ [
"430",
"EPFLMouseLiverRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2443,6 +2494,11 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
+ "433",
+ "EPFLMouseLiverBothExRMA0413",
+ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+ ],
+ [
"700",
"UTHSC-VGX_MmBXDHepatocytesRMA1014",
"UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -2466,6 +2522,51 @@
"702",
"SUH_Liv_RMAEx_0611",
"SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA"
+ ],
+ [
+ "256",
+ "GenEx_BXD_liverEt_M5_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes"
+ ],
+ [
+ "257",
+ "GenEx_BXD_liverEt_M5M_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males"
+ ],
+ [
+ "258",
+ "GenEx_BXD_liverEt_M5F_0912",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females"
+ ],
+ [
+ "307",
+ "GenEx_BXD_liverEt_RMA_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes"
+ ],
+ [
+ "308",
+ "GenEx_BXD_liverEt_RMA_M_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males"
+ ],
+ [
+ "309",
+ "GenEx_BXD_liverEt_RMA_F_0211",
+ "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females"
+ ],
+ [
+ "310",
+ "GenEx_BXD_liverSal_RMA_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes"
+ ],
+ [
+ "311",
+ "GenEx_BXD_liverSal_RMA_M_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males"
+ ],
+ [
+ "312",
+ "GenEx_BXD_liverSal_RMA_F_0211",
+ "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females"
]
],
"Lung mRNA": [
@@ -2546,14 +2647,14 @@
"HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
],
[
- "275",
- "DevNeocortex_ILM6.2P14RInv_1110",
- "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
- ],
- [
"274",
"DevNeocortex_ILM6.2P3RInv_1110",
"BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
+ ],
+ [
+ "275",
+ "DevNeocortex_ILM6.2P14RInv_1110",
+ "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
]
],
"Nucleus Accumbens mRNA": [
@@ -2761,11 +2862,6 @@
],
"Ventral Tegmental Area mRNA": [
[
- "230",
- "VCUEtvsSal_0609_R",
- "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
- ],
- [
"229",
"VCUEtOH_0609_R",
"VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
@@ -2774,6 +2870,11 @@
"228",
"VCUSal_0609_R",
"VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
+ ],
+ [
+ "230",
+ "VCUEtvsSal_0609_R",
+ "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
]
]
},
@@ -2920,6 +3021,27 @@
]
]
},
+ "CIE-RMA": {
+ "Midbrain mRNA": [
+ [
+ "830",
+ "INIA_UTHSC_Mid_AffyMTA1_Apr17",
+ "INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) RMA"
+ ],
+ [
+ "834",
+ "INIA_UTHSC_Mid_AffyMTA1_Ex_May17",
+ "INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA"
+ ]
+ ],
+ "Phenotypes": [
+ [
+ "None",
+ "CIE-RMAPublish",
+ "CIE-RMA Published Phenotypes"
+ ]
+ ]
+ },
"CMS": {
"Phenotypes": [
[
@@ -3021,6 +3143,13 @@
"CXB Genotypes"
]
],
+ "Heart mRNA": [
+ [
+ "821",
+ "UCLA_CXB_Aor_Jan16",
+ "UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Hippocampus mRNA": [
[
"100",
@@ -3033,6 +3162,13 @@
"Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
]
],
+ "Liver mRNA": [
+ [
+ "823",
+ "UCLA_CXB_Liv_Jan16",
+ "UCLA CXB Liver Affy M430 2.0 (Jan16) RMA"
+ ]
+ ],
"Phenotypes": [
[
"628",
@@ -3048,6 +3184,7 @@
]
]
},
+ "EMSR": {},
"HS": {
"Hippocampus mRNA": [
[
@@ -3545,6 +3682,10 @@
"Brain, Development: Normal Gene Expression (Yale/Sestan)"
],
[
+ "Islets-Gerling",
+ "Pancreatic: Islets (UTHSC/Gerling)"
+ ],
+ [
"TIGEM-Retina-RNA-Seq",
"Retina: Normal Adult Gene Expression, RNA-Seq (TIGEM)"
]
@@ -3616,7 +3757,11 @@
],
[
"CIE-INIA",
- "Chronic Intermittent Ethanol"
+ "Chronic Intermittent Ethanol Phase 1"
+ ],
+ [
+ "CIE-RMA",
+ "Chronic Intermittent Ethanol Phase 2"
],
[
"CMS",
@@ -3631,6 +3776,10 @@
"CXB"
],
[
+ "EMSR",
+ "Ethanol-Medicated Stress Reduction"
+ ],
+ [
"HS",
"Heterogeneous Stock"
],
@@ -4414,6 +4563,12 @@
"Ventrolateral Prefrontal Cortex mRNA"
]
],
+ "Islets-Gerling": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
"TIGEM-Retina-RNA-Seq": [
[
"Phenotypes",
@@ -4630,6 +4785,10 @@
"Gastrointestinal mRNA"
],
[
+ "Heart mRNA",
+ "Heart mRNA"
+ ],
+ [
"Hematopoietic Cells mRNA",
"Hematopoietic Cells mRNA"
],
@@ -4780,6 +4939,16 @@
"LCM Brain Regions mRNA"
]
],
+ "CIE-RMA": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ],
+ [
+ "Midbrain mRNA",
+ "Midbrain mRNA"
+ ]
+ ],
"CMS": [
[
"Phenotypes",
@@ -4822,14 +4991,23 @@
"Genotypes"
],
[
+ "Heart mRNA",
+ "Heart mRNA"
+ ],
+ [
"Hippocampus mRNA",
"Hippocampus mRNA"
],
[
+ "Liver mRNA",
+ "Liver mRNA"
+ ],
+ [
"Spleen mRNA",
"Spleen mRNA"
]
],
+ "EMSR": [],
"HS": [
[
"Phenotypes",
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 4cea51b2..65debd10 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,7 +14,7 @@
<input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
<input type="hidden" name="trait_id" value="{{ this_trait.name }}">
<input type="hidden" name="dataset" value="{{ dataset.name }}">
- {% if mapping_method == "reaper" %}
+ {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %}
<input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
{% endif %}
<input type="hidden" name="method" value="{{ mapping_method }}">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 56b6cc62..5a880647 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -129,6 +129,7 @@
<script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
+ <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script>
<script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 0a0e9990..ac44b656 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -94,12 +94,15 @@
<div class="tab-pane" id="probability_plot">
<div style="padding: 20px" class="form-horizontal">
{% if sample_groups|length != 1 %}
+ Select Group:
<select class="prob_plot_samples_group">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
{% endfor %}
</select>
- <br><br>
+ <button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button>
+ <br>
+ <br>
{% endif %}
<div id="prob_plot_container">
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 12:17:52 +0000