diff options
| author | zsloan | 2018-12-05 11:48:24 -0600 |
|---|---|---|
| committer | zsloan | 2018-12-05 11:48:24 -0600 |
| commit | 4fbeea6d1ed1ac2b81eb431ee837201945abc841 (patch) | |
| tree | c329e8929f1ab1856555787f6909c8eb47483ca7 | |
| parent | dc3bc97b2ae2e751f68ad63359734d569895c711 (diff) | |
| download | genenetwork2-4fbeea6d1ed1ac2b81eb431ee837201945abc841.tar.gz | |
Fixed issue where SNP track for mapping did not appear correctly
Updated style for a variety of tables
Moved transform/blocking tools for trait sample table into its own tab
Added some new customization options to network graph
Started work on implementing third party link-outs
Updated drop-down generation script to order datasets according to CreateTime
18 files changed, 368 insertions, 252 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 55c642a4..4ad921a2 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -248,7 +248,7 @@ def build_datasets(species, group, type_name): ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by - ProbeSetFreeze.OrderList asc""" % (species, group, type_name)) + ProbeSetFreeze.CreateTime desc""" % (species, group, type_name)) dataset_results = Cursor.fetchall() datasets = [] diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/wqflask/external_tools/send_to_bnw.py diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index af75d441..7b328cb5 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -46,9 +46,7 @@ from flask import Flask, g class Heatmap(object): def __init__(self, start_vars, temp_uuid): - trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')] - helper_functions.get_trait_db_obs(self, trait_db_list) self.temp_uuid = temp_uuid diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 09646f57..e63e4af2 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -772,7 +772,8 @@ class DisplayMappingResults(object): fontZoom = 1.5 drawSNPLocationY = yTopOffset + plotHeight - chrName = self.genotype[0].name + #chrName = self.genotype[0].name + chrName = self.ChrList[self.selectedChr][0] stepMb = (endMb-startMb)/plotWidth strainId1, strainId2 = self.diffCol diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index aee3cc2a..3057e340 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -652,9 +652,9 @@ def trim_markers_for_table(markers): else: sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True) - #ZS: So we end up with a list of just 200 markers - if len(sorted_markers) >= 200: - trimmed_sorted_markers = sorted_markers[:200] + #ZS: So we end up with a list of just 2000 markers + if len(sorted_markers) >= 2000: + trimmed_sorted_markers = sorted_markers[:2000] return trimmed_sorted_markers else: return sorted_markers
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css index d81b5021..8d205143 100644 --- a/wqflask/wqflask/static/new/css/marker_regression.css +++ b/wqflask/wqflask/static/new/css/marker_regression.css @@ -35,4 +35,38 @@ rect.pane { /*rect { stroke: WhiteSmoke; fill: Azure; -}*/
\ No newline at end of file +}*/ + +tr .outlier { + background-color: #ffff99; +} + +table.dataTable thead th{ + border-right: 1px solid white; + color: white; + background-color: #369; +} + +table.dataTable thead .sorting_asc { + background-image: url("../packages/DataTables/images/sort_asc_disabled.png"); +} +table.dataTable thead .sorting_desc { + background-image: url("../packages/DataTables/images/sort_desc_disabled.png"); +} + +table.dataTable thead th { + padding: 4px 18px 4px 10px; +} + +table.dataTable tbody td { + padding: 3px 20px 1px 10px; +} + +table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { + border-top: 1px solid #ccc; + border-right: 1px solid #ccc; +} +table.dataTable.cell-border tbody tr th:first-child, +table.dataTable.cell-border tbody tr td:first-child { + border-left: 1px solid #ccc; +}
\ No newline at end of file diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index c03b6103..59901404 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -32,7 +32,7 @@ table.dataTable thead th { } table.dataTable tbody td { - padding: 3px 20px 1px 10px; + padding: 4px 20px 2px 10px; } table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td { diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 72008225..a4ec6ece 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1347,14 +1347,14 @@ "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], [ - "383", - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ "384", "HLCF_0311", "GSE9588 Human Liver Normal (Mar11) Females" + ], + [ + "383", + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" ] ], "Phenotypes": [ @@ -1718,16 +1718,16 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" ], [ - "77", - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ "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" + ], + [ "33", "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" @@ -1824,30 +1824,30 @@ "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" ], [ - "84", - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], - [ "85", "SA_M2_0905_P", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + ], + [ + "84", + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "BHF2": { "Adipose mRNA": [ [ - "196", - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ "197", "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" ], [ + "196", + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male mlratio" + ], + [ "165", "UCLA_BHF2_ADIPOSE_0605", "UCLA BHF2 Adipose (June05) mlratio" @@ -1855,16 +1855,16 @@ ], "Brain mRNA": [ [ - "198", - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ "199", "UCLA_BHF2_BRAIN_FEMALE", "UCLA BHF2 Brain Female mlratio" ], [ + "198", + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], + [ "166", "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" @@ -1879,16 +1879,16 @@ ], "Liver mRNA": [ [ - "200", - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ "201", "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" ], [ + "200", + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], + [ "167", "UCLA_BHF2_LIVER_0605", "UCLA BHF2 Liver (June05) mlratio" @@ -2016,7 +2016,7 @@ [ "779", "EL_BXDCDScWAT_0216", - "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA **" + "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA" ] ], "Adrenal Gland mRNA": [ @@ -2122,9 +2122,9 @@ "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ - "80", - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + "82", + "BR_U_0805_R", + "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], [ "81", @@ -2132,9 +2132,9 @@ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], [ - "82", - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" + "80", + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" ], [ "42", @@ -2238,16 +2238,16 @@ "Eye M430v2 Mutant Tyrp1 (Sep08) RMA" ], [ - "279", - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA" - ], - [ "382", "Eye_M2_0908_WTWT", "Eye M430v2 WT WT (Sep08) RMA" ], [ + "279", + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA" + ], + [ "400", "DBA2J-ONH-1212", "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA" @@ -2531,16 +2531,16 @@ ], "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" @@ -2563,6 +2563,26 @@ ], "Liver Metabolome": [ [ + "838", + "UTHSC-ETHZ-EPFL_LivPMetExtBHFD0817", + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2" + ], + [ + "835", + "UTHSC-ETHZ-EPFL_LivPMetExtACD0817", + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow Diet Cohorts (Mar 2017) log2" + ], + [ + "837", + "UTHSC-ETHZ-EPFL_LivPMetExtBCD0817", + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2" + ], + [ + "836", + "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817", + "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2" + ], + [ "473", "EPFL-LISP_LivPMetCDHFD1213", "EPFL/LISP BXD Liver Polar Metabolites CD+HFD (Jun14)" @@ -2632,19 +2652,29 @@ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" ], [ + "858", + "EPFLMouseLiverHFDRMA0818", + "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], + [ "859", "EPFLMouseLiverCDRMA0818", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" ], [ - "851", - "NIA-AgBXD-Liv_CDHFD-0818", - "NIA Aging BXD CD+HFD Liver Affy Clariom S Gene Level (Aug18) RMA **" + "854", + "NIA-AgBXD-Liv_CDHFD-rna-seq-0818", + "NIA Aging BXD CD+HFD Liver RNA-Seq (Aug18) Log2" + ], + [ + "855", + "NIA-AgBXD-Liv_HFD-rna-seq-0818", + "NIA Aging BXD HFD Liver RNA-Seq (Aug18) Log2" ], [ - "853", - "NIA-AgBXD-Liv_CD-0818", - "NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA **" + "856", + "NIA-AgBXD-Liv_CD-rna-seq-0818", + "NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2" ], [ "818", @@ -2652,16 +2682,6 @@ "UCLA BXD Liver Affy M430 2.0 (Jan16) RMA" ], [ - "858", - "EPFLMouseLiverHFDRMA0818", - "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" - ], - [ - "852", - "NIA-AgBXD-Liv_HFD-0818", - "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **" - ], - [ "430", "EPFLMouseLiverRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" @@ -2672,9 +2692,9 @@ "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], [ - "432", - "EPFLMouseLiverCDRMA0413", - "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" + "849", + "EPFLMouseLiverCDEx0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], [ "848", @@ -2682,16 +2702,16 @@ "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], [ + "432", + "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" ], [ - "849", - "EPFLMouseLiverCDEx0413", - "EPFL/LISP BXD CD 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" @@ -2840,14 +2860,14 @@ "HQF BXD Neocortex ILM6v1.1 (Feb08) 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" + ], + [ + "274", + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens mRNA": [ @@ -3080,14 +3100,14 @@ "VCU BXD VTA Sal M430 2.0 (Jun09) RMA" ], [ - "229", - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA" - ], - [ "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" ] ] }, @@ -3105,17 +3125,7 @@ [ "843", "UTHSC-BXD-Harv_Liv-0118", - "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 **" - ], - [ - "842", - "UTHSC-BXD-Liv-0917", - "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **" - ], - [ - "850", - "UTHSC-BXD-Liv-0818", - "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA **" + "UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2" ] ], "Phenotypes": [ @@ -3522,26 +3532,26 @@ ], "Hippocampus mRNA": [ [ - "211", - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ "212", "Illum_LXS_Hipp_RSE_1008", "Hippocampus Illumina RSE (Oct08) RankInv beta" ], [ - "213", - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ "214", "Illum_LXS_Hipp_NOE_1008", "Hippocampus Illumina NOE (Oct08) RankInv beta" ], [ + "211", + "Illum_LXS_Hipp_RSS_1008", + "Hippocampus Illumina RSS (Oct08) RankInv beta" + ], + [ + "213", + "Illum_LXS_Hipp_NOS_1008", + "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], + [ "219", "Illum_LXS_Hipp_NON_1008", "Hippocampus Illumina NON (Oct08) RankInv beta" @@ -3708,16 +3718,16 @@ "Retina-RGC-Rheaume": { "Retina Single-cell RNA-Seq": [ [ - "866", - "UConn-RGC-RSeq_log2-0918", - "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2" - ], - [ "865", "UConn-RGC-RSeq_r-0918", "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Raw" ], [ + "866", + "UConn-RGC-RSeq_log2-0918", + "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2" + ], + [ "867", "UConn-RGC-RSeq_s-0918", "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Siamak" diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js index 0ecf4743..bc02181f 100644 --- a/wqflask/wqflask/static/new/javascript/network_graph.js +++ b/wqflask/wqflask/static/new/javascript/network_graph.js @@ -1,18 +1,9 @@ -window.onload=function() { - // id of Cytoscape Web container div - //var div_id = "cytoscapeweb"; - - var cy = cytoscape({ - container: $('#cytoscapeweb'), // container to render in - - elements: elements_list, - - style: [ // the stylesheet for the graph +var default_style = [ // the stylesheet for the graph { selector: 'node', style: { 'background-color': '#666', - 'label': 'data(label )', + 'label': 'data(label)', 'font-size': 10 } }, @@ -27,16 +18,28 @@ window.onload=function() { 'font-size': 8 } } - ], - - zoom: 12, - layout: { name: 'circle', + ] + +var default_layout = { name: 'circle', fit: true, // whether to fit the viewport to the graph padding: 30 // the padding on fit //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; }, - }, + } + +window.onload=function() { + // id of Cytoscape Web container div + //var div_id = "cytoscapeweb"; + var cy = cytoscape({ + container: $('#cytoscapeweb'), // container to render in + + elements: elements_list, + style: default_style, + + zoom: 12, + layout: default_layout, + zoomingEnabled: true, userZoomingEnabled: true, panningEnabled: true, @@ -131,22 +134,25 @@ window.onload=function() { create_qtips(cy) - $('#slide').change(function() { + $('#neg_slide').change(function() { eles.restore() + + pos_slide_val = $('#pos_slide').val(); + cy.$("node[max_corr > " + $(this).val() + "][max_corr < " + pos_slide_val + "]").remove(); + cy.$("edge[correlation > " + $(this).val() + "][correlation < " + pos_slide_val + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); - console.log(eles) - - // nodes_to_restore = eles.filter("node[max_corr >= " + $(this).val() + "], edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") - // nodes_to_restore.restore() - - // edges_to_restore = eles.filter("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") - // edges_to_restore.restore() - - //cy.$("node[max_corr >= " + $(this).val() + "]").restore(); - //cy.$("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]").restore(); - - cy.$("node[max_corr < " + $(this).val() + "]").remove(); - cy.$("edge[correlation < " + $(this).val() + "][correlation > -" + $(this).val() + "]").remove(); + }); + $('#pos_slide').change(function() { + eles.restore() + + neg_slide_val = $('#neg_slide').val(); + cy.$("node[max_corr > " + neg_slide_val +"][max_corr < " + $(this).val() + "]").remove(); + cy.$("edge[correlation > " + neg_slide_val +"][correlation < " + $(this).val() + "]").remove(); cy.layout({ name: $('select[name=layout_select]').val(), fit: true, // whether to fit the viewport to the graph @@ -157,7 +163,8 @@ window.onload=function() { $('#reset_graph').click(function() { eles.restore() - $('#slide').val(0) + $('#pos_slide').val(0) + $('#neg_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 @@ -178,13 +185,67 @@ window.onload=function() { $('select[name=layout_select]').change(function() { layout_type = $(this).val() - console.log("LAYOUT:", layout_type) cy.layout({ name: layout_type, fit: true, // whether to fit the viewport to the graph padding: 25 // the padding on fit }); }); + $('select[name=font_size]').change(function() { + font_size = $(this).val() + + new_style = default_style + new_style[0]['style']['font-size'] = parseInt(font_size) + cy.style().fromJson(new_style).update() + }); + $('select[name=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + 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=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + $("a#image_link").click(function(e) { var pngData = cy.png(); diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index 64d5a676..5a2df5e3 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -4,6 +4,7 @@ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -15,7 +16,6 @@ 'You have {}.'.format(numify(collections|count, "collection", "collections"))) }} {% endif %} - <div class="container"> <div class="page-header"> {% if g.user_session.logged_in %} @@ -35,7 +35,7 @@ </div> <br> <div id="collections_list" style="width:50%;"> - <table class="display dataTable nowrap" id='trait_table'> + <table class="table-hover table-striped cell-border" id='trait_table'> <thead> <tr> <th></th> @@ -51,9 +51,9 @@ {% for uc in collections %} <tr class="collection_line"> {% if g.user_session.logged_in %} - <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td> + <td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td> {% else %} - <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td> + <td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td> {% endif %} <td align="right">{{ loop.index }} {% if g.user_session.logged_in %} diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 864299a2..b6ad7be8 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -3,6 +3,7 @@ {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -82,7 +83,7 @@ </form> <br /> <div> - <table class="display dataTable nowrap" id='trait_table' style="float: left;"> + <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <thead> <tr> <th></th> @@ -92,21 +93,21 @@ <th data-export="Description">Description</th> <th data-export="Location">Location</th> <th data-export="Mean">Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th> <th data-export="Max LRS Location">Max LRS Location</th> - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th> </tr> </thead> <tbody> {% for this_trait in trait_obs %} <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> - <TD> + <TD align="center" style="padding: 0px;"> <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"> </TD> <TD data-export="{{ loop.index }}" align="right">{{ loop.index }}</TD> - <TD data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</TD> + <TD title="{{ this_trait.dataset.fullname }}" data-export="{{ this_trait.dataset.fullname }}">{{ this_trait.dataset.fullname }}</TD> <TD data-export="{{ this_trait.name }}"> <a href="{{ url_for('show_trait_page', trait_id = this_trait.name, @@ -159,23 +160,26 @@ console.time("Creating table"); $('#trait_table').dataTable( { "createdRow": function ( row, data, index ) { - $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;'); + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } if ($('td', row).eq(4).text().length > 50) { $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } }, "columns": [ - { "type": "natural", "width": "2%" }, - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "12%" }, - { "type": "natural", "width": "12%" }, + { "type": "natural", "width": 10 }, + { "type": "natural", "width": 50 }, + { "type": "natural" }, + { "type": "natural", "width": 120 }, { "type": "natural" }, - { "type": "natural", "width": "12%" }, - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "12%" }, - { "type": "natural", "width": "8%" } + { "type": "natural", "width": 130 }, + { "type": "natural", "width": 35 }, + { "type": "natural", "width": 35 }, + { "type": "natural", "width": 130 }, + { "type": "natural" } ], "columnDefs": [ { "targets": 0, @@ -194,8 +198,6 @@ "autoWidth": false, "bDeferRender": true, "bSortClasses": false, - "scrollY": "600px", - "scrollCollapse": true, "paging": false, "orderClasses": true } ); diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 0612bfcc..ff5c56f1 100644 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -2,6 +2,7 @@ {% block title %}Search Results{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -28,7 +29,7 @@ </form> <br /> <div style="width: 100%;"> - <table width="100%" id="trait_table" class="display dataTable nowrap" style="float: left;"> + <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;"> <thead> <tr> <th></th> @@ -42,14 +43,14 @@ <th data-export="Description">Description</th> <th data-export="Location">Location</th> <th data-export="Mean">Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th> + <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th> </tr> </thead> <tbody> {% for this_trait in trait_list %} <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}"> - <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td> + <td align="center" style="padding: 0px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td> <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td> <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td> <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td> @@ -78,8 +79,8 @@ <th>Description</th> <th>Location</th> <th>Mean</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th> + <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th> </tr> </tfoot> </table> diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html index c2cbdadd..01b2403e 100644 --- a/wqflask/wqflask/templates/gsearch_pheno.html +++ b/wqflask/wqflask/templates/gsearch_pheno.html @@ -2,6 +2,7 @@ {% block title %}Search Results{% endblock %} {% block css %} <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -28,7 +29,7 @@ </form> <br /> <div> - <table id="trait_table" class="display dataTable nowrap" style="float: left;"> + <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;"> <thead> <tr> <th></th> @@ -39,8 +40,8 @@ <th data-export="Description">Description</th> <th data-export="Authors">Authors</th> <th data-export="Year">Year</th> - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><sup>?</sup></a></th> + <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th> </tr> </thead> <tbody> @@ -55,7 +56,7 @@ <td data-export="{{ this_trait.authors }}">{{ this_trait.authors }}</td> <td data-export="{{ this_trait.pubmed_text }}" data-order="{{ this_trait.pubmed_text }}"><a href="{{ this_trait.pubmed_link }}">{{ this_trait.pubmed_text }}</a></td> <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td> - <td data-export="{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}</td> + <td data-export="{% if this_trait.additive %}{{ this_trait.additive }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive %}{{ '%0.6f' % this_trait.additive }}{% else %}N/A{% endif %}</td> </tr> {% endfor %} </tbody> @@ -110,14 +111,16 @@ console.time("Creating table"); $('#trait_table').DataTable( { "createdRow": function ( row, data, index ) { + $('td', row).eq(0).attr('style', 'padding: 0px;'); + $('td', row).eq(0).attr('align', 'center'); $('td', row).eq(5).attr('title', $('td', row).eq(5).text()); if ($('td', row).eq(5).text().length > 50) { $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 50)); $('td', row).eq(5).text($('td', row).eq(5).text() + '...') } $('td', row).eq(6).attr('title', $('td', row).eq(6).text()); - if ($('td', row).eq(6).text().length > 50) { - $('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 50)); + if ($('td', row).eq(6).text().length > 40) { + $('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 40)); $('td', row).eq(6).text($('td', row).eq(6).text() + '...') } }, @@ -128,11 +131,11 @@ { "type": "natural" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural", "width": "30%"}, - { "type": "natural", "width": "25%"}, { "type": "natural" }, - { "type": "natural", "width": "8%"}, - { "type": "natural" } + { "type": "natural" }, + { "type": "natural" }, + { "type": "natural", "width": "5%"}, + { "type": "natural", "width": "8%" } ], "columnDefs": [ { diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 00d725ea..3138d855 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -181,7 +181,7 @@ </form> {% if selectedChr == -1 %} - <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> + <div class="container" style="padding-left: 30px;"> <h2>Mapping Statistics</h2> <br /> <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> @@ -190,8 +190,8 @@ <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button> <br /> <br /> - <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;"> - <table id="trait_table" class="table table-hover table-striped nowrap"> + <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}480{% else %}450{% endif %}px;"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer"> <thead> <tr> <th></th> @@ -215,7 +215,7 @@ <tbody> {% for marker in trimmed_markers %} <tr> - <td align="center" style="padding-right: 0px;"> + <td align="center" style="padding-right: 0px; padding-left: 0px;"> <input type="checkbox" name="selectCheck" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}"> @@ -257,7 +257,7 @@ <div style="width: 100%;"> <h2>Interval Analyst</h2> <div id="table_container"> - <table id="interval_analyst" class="table-hover table-striped cell-border" style="float: left; width:100%;"> + <table id="interval_analyst" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> <thead> <tr> {% for header in gene_table_header %} @@ -314,37 +314,16 @@ $(document).ready( function () { console.time("Creating table"); $('#trait_table').DataTable( { - {% if mapping_method != "reaper" %} "columns": [ { "type": "natural", "width": "5%" }, { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural" }, { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "15%" } - ], - {% elif dataset.group.genetic_type == "riset" %} - "columns": [ - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "20%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "15%" }, - { "type": "natural", "width": "8%" } - ], - {% else %} - "columns": [ - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "20%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "15%" }, - { "type": "natural", "width": "8%" }, - { "type": "natural", "width": "8%" } + { "type": "natural" }{% if 'additive' in marker %}, + { "type": "natural" }{% endif %}{% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}, + { "type": "natural" }{% endif %} ], - {% endif %} "columnDefs": [ { "targets": 0, "orderable": false diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html index ad5dee9d..57bd5492 100644 --- a/wqflask/wqflask/templates/network_graph.html +++ b/wqflask/wqflask/templates/network_graph.html @@ -47,19 +47,16 @@ </tr> <tr> <td colspan="1"> - <font size="2"><b>0 - - +/- 1</b></font><br> - <input type="range" id="slide" min="0" max="1" value="0" step="0.001" list="corr_range"> - </td> - </tr> - <tr> - <td> - Layouts + <font size="2"><b>-1 + 0 + 1</b></font><br> + <input type="range" id="neg_slide" min="-1" max="0" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%"> + <input type="range" id="pos_slide" min="0" max="1" value="0" step="0.001" list="corr_range" style="display: inline; width: 45%"> </td> </tr> <tr> <td> + Layouts: <select name="layout_select"> <option value="circle">Circle</option> <option value="concentric">Concentric</option> @@ -70,6 +67,39 @@ </select> </td> </tr> + <tr> + <td> + Node Font Size: + <select name="font_size"> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + <option value="10" selected>10</option> + <option value="11">11</option> + <option value="12">12</option> + <option value="13">13</option> + <option value="14">14</option> + <option value="15">15</option> + <option value="16">16</option> + <option value="17">17</option> + <option value="18">18</option> + </select> + </td> + <td> + </tr> + <tr> + <td> + Edge Width: + <select name="edge_width"> + <option value="1" selected>1x</option> + <option value="2">2x</option> + <option value="3">3x</option> + <option value="4">4x</option> + </select> + </td> + <td> + </tr> </tbody> </table> <h3 style="margin-bottom: 5px;"> Download</h3> diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index a325ec9f..eaeb7e6b 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -79,7 +79,7 @@ --> <div id="table_container" style="width: {% if dataset.type == 'ProbeSet' %}1300{% elif dataset.type == 'Publish' %}1300{% elif dataset.type == 'Geno' %}400{% endif %}px;"> - <table class="display dataTable nowrap" id='trait_table' style="float: left;"> + <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;"> <thead> <tr> <th></th> @@ -184,16 +184,21 @@ $('.trait_checkbox:checkbox').on("change", change_buttons); }, "createdRow": function ( row, data, index ) { - $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;'); + $('td', row).eq(0).attr('style', 'padding: 0px;'); + $('td', row).eq(0).attr('align', 'center'); $('td', row).eq(1).attr('align', 'right'); $('td', row).eq(1).attr('data-export', index+1); $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); $('td', row).eq(3).attr('title', $('td', row).eq(3).text()); $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text()); + if ($('td', row).eq(3).text().length > 20) { + $('td', row).eq(3).text($('td', row).eq(3).text().substring(0, 20)); + $('td', row).eq(3).text($('td', row).eq(3).text() + '...') + } $('td', row).eq(4).attr('title', $('td', row).eq(4).text()); $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text()); - if ($('td', row).eq(4).text().length > 60) { - $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60)); + if ($('td', row).eq(4).text().length > 55) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 55)); $('td', row).eq(4).text($('td', row).eq(4).text() + '...') } $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text()); @@ -209,13 +214,13 @@ "columns": [ { "type": "natural", "width": "2%" }, { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "12%" }, - { "type": "natural", "width": "12%" }, + { "type": "natural", "width": "10%" }, + { "type": "natural", "width": "8%" }, { "type": "natural" }, - { "type": "natural", "width": "11%" }, + { "type": "natural", "width": "12%" }, { "type": "natural", "width": "4%" }, { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "11%" }, + { "type": "natural", "width": "12%" }, { "type": "natural", "width": "5%" } ], "columnDefs": [ { @@ -235,10 +240,6 @@ "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollX": true, - "scrollY": "600px", - "scrollCollapse": false, - "scroller": true, "paging": false, "orderClasses": true } ); @@ -254,7 +255,8 @@ $('.trait_checkbox:checkbox').on("change", change_buttons); }, "createdRow": function ( row, data, index ) { - $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;'); + $('td', row).eq(0).attr('style', 'padding: 0px;'); + $('td', row).eq(0).attr('align', 'center'); $('td', row).eq(1).attr('align', 'right'); $('td', row).eq(1).attr('data-export', index+1); $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); @@ -308,9 +310,6 @@ "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "600px", - "scrollCollapse": false, - "scroller": false, "paging": false, "orderClasses": true } ); @@ -325,7 +324,8 @@ $('.trait_checkbox:checkbox').on("change", change_buttons); }, "createdRow": function ( row, data, index ) { - $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;'); + $('td', row).eq(0).attr('style', 'padding: 0px;'); + $('td', row).eq(0).attr('align', 'center'); $('td', row).eq(1).attr('align', 'right'); $('td', row).eq(1).attr('data-export', index+1); $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); @@ -333,10 +333,10 @@ }, "data": json_trait_list, "columns": [ - { "type": "natural", "width": "5%" }, - { "type": "natural", "width": "12%" }, { "type": "natural" }, - { "type": "natural", "width": "30%"} + { "type": "natural" }, + { "type": "natural" }, + { "type": "natural" } ], "columnDefs": [ { "targets": 0, @@ -355,9 +355,6 @@ "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "600px", - "scrollCollapse": true, - "scroller": true, "paging": false, "orderClasses": true } ); diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index ab134663..090602f4 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -110,7 +110,7 @@ <tbody> {% for sample in sample_type.sample_list %} <tr class="{{ sample.class_outlier }} value_se" id="{% if outer_loop.index == 1 %}Primary_{{ sample.this_id }}{% else %}Other_{{ sample.this_id }}{% endif %}"> - <td align="center" style="padding-left: 0px; padding-right: 0px;" class="column_name-"><input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked"> + <td align="center" style="padding-left: 0px; padding-right: 0px; padding-top: 2px; padding-bottom: 0px;" class="column_name-"><input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" style="min-height: 20px;" value="{{ sample.name }}" checked="checked"> </td> <td class="column_name-Index" align="right">{{ loop.index }}</td> <td class="column_name-Sample"> @@ -120,7 +120,7 @@ </td> {# Todo: Add IDs #} - <td class="column_name-Value" align="right"> + <td class="column_name-Value" align="right" style="padding-top: 2px; padding-bottom: 0px;"> <input type="text" data-value="{{ sample.display_value }}" data-qnorm="{{ qnorm_vals[outer_loop.index - 1][loop.index - 1] }}" name="{{ 'value:' + sample.name }}" style="text-align:right;" class="trait_value_input edit_sample_value" @@ -135,7 +135,7 @@ </td> {# Todo: Add IDs #} - <td class="column_name-SE" align="right"> + <td class="column_name-SE" align="right" style="padding-top: 2px; padding-bottom: 0px;"> <input type="text" data-value="{{ sample.display_variance }}" data-qnorm="x" name="{{ 'variance:' + sample.name}}" style="text-align:right;" class="trait_value_input edit_sample_se" diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index 5d14a30e..fdf34c27 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -8,7 +8,7 @@ <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;"> <label for="remove_samples_field">Block samples by index:</label> - <input type="text" id="remove_samples_field"> + <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12"> <select id="block_group" size="1"> <option value="primary"> {{ sample_group_types['samples_primary'] }} |