From 02ce39e33fd32b68411ac7b30449507c3f567192 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 16 May 2017 20:00:10 +0000 Subject: Fixed issue that caused mapping to not work for R/qtl Updated dataset menu dropdown info Began adding option to download statistics figures as PNG --- .../marker_regression/marker_regression_gn1.py | 15 +- .../new/javascript/dataset_menu_structure.json | 284 +++++++++++++++++---- .../wqflask/templates/marker_regression_gn1.html | 2 +- wqflask/wqflask/templates/show_trait.html | 1 + .../wqflask/templates/show_trait_statistics.html | 5 +- 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 @@ -1339,15 +1339,15 @@ "HLC_0311", "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": [ [ @@ -1560,6 +1569,11 @@ ] ], "Heart mRNA": [ + [ + "820", + "UCLA_AXB_BXA_Aor_Jan16", + "UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA" + ], [ "421", "IRCM_AXBXA_HRI0213", @@ -1567,6 +1581,11 @@ ] ], "Liver mRNA": [ + [ + "822", + "UCLA_AXB_BXA_Liv_Jan16", + "UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA" + ], [ "352", "GSE16780AB_UCLA_ML0911", @@ -1726,11 +1745,6 @@ ] ], "Striatum mRNA": [ - [ - "85", - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], [ "84", "SA_M2_0905_R", @@ -1740,21 +1754,26 @@ "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", @@ -1762,16 +1781,16 @@ ] ], "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", @@ -1786,16 +1805,16 @@ ] ], "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", @@ -1999,11 +2018,6 @@ "BR_U_1105_P", "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], - [ - "81", - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], [ "80", "BR_U_0805_M", @@ -2014,6 +2028,11 @@ "BR_U_0805_R", "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], + [ + "81", + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], [ "42", "CB_M_0204_P", @@ -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", @@ -2217,6 +2243,26 @@ "UMUTAffyExon_0209_RMA", "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", @@ -2390,15 +2436,25 @@ ] ], "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", @@ -2414,19 +2470,14 @@ "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", @@ -2442,6 +2493,11 @@ "EPFLMouseLiverCDRMA0413", "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", @@ -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": [ @@ -2545,15 +2646,15 @@ "HQFNeoc_0208_RankInv", "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": [ @@ -2760,11 +2861,6 @@ ] ], "Ventral Tegmental Area mRNA": [ - [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA" - ], [ "229", "VCUEtOH_0609_R", @@ -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": [ [ @@ -3544,6 +3681,10 @@ "HSB", "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", @@ -3630,6 +3775,10 @@ "CXB", "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", @@ -4629,6 +4784,10 @@ "Gastrointestinal mRNA", "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", @@ -4821,15 +4990,24 @@ "Genotypes", "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 @@ - {% if mapping_method == "reaper" %} + {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %} {% endif %} 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 @@ + 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 @@
{% if sample_groups|length != 1 %} + Select Group: -

+ +
+
{% endif %}
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