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improve filtering behavior
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@kvnjng
kvnjng committed May 21, 2021
1 parent aafc5d2 commit 9007f66
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Showing 3 changed files with 220 additions and 62 deletions.
4 changes: 2 additions & 2 deletions LDlink/LDexpress.py
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Original file line number Diff line number Diff line change
Expand Up @@ -443,8 +443,8 @@ def replace_coords_rsid(db, snp_lst):
}

# find unique thinned genes and tissues
thinned_genes = sorted(list(set(list(map(lambda row: row[5].split("__")[0], combined_matched_snps)))))
thinned_tissues = sorted(list(set(list(map(lambda row: row[7].split("__")[0], combined_matched_snps)))))
thinned_genes = sorted(list(set(list(map(lambda row: row[5], combined_matched_snps)))))
thinned_tissues = sorted(list(set(list(map(lambda row: row[7], combined_matched_snps)))))

# # clean up tmp file(s) generated by each calculation
subprocess.call("rm " + tmp_dir + "pops_" + request + ".txt", shell=True)
Expand Down
258 changes: 208 additions & 50 deletions LDlink/LDlink-5.1.0.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2642,7 +2642,7 @@ function populateSNPlistLDexpress(data) {
//Add the clipped list
$.each(data, function( index, value ){
$("#ldexpress-snp-list").append(
$("<tr>").append(
$("<tr>", { class: 'ldexpress-snps-list-rows', id: 'snp__row__' + value }).append(
$("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
$('<input />', { type: 'checkbox', id: 'filter__snp__' + value, value: 'snp__' + value, 'style': "margin-right: 4px;", class: 'ldexpress-data-filters' }),
$('<label />', { 'for': 'filter__snp__' + value, text: value, 'style': 'white-space: nowrap;' })
Expand All @@ -2658,10 +2658,10 @@ function populateGeneslistLDexpress(data) {
//Add the clipped list
$.each(data, function( index, value ){
$("#ldexpress-genes-list").append(
$("<tr>", { class: 'ldexpress-genes-list-rows', id: 'gene__row__' + value }).append(
$("<tr>", { class: 'ldexpress-genes-list-rows', id: 'gene__row__' + value.split("__")[0] }).append(
$("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
$('<input />', { type: 'checkbox', id: 'filter__gene__' + value, value: 'gene__' + value, 'style': "margin-right: 4px;", class: 'ldexpress-data-filters' }),
$('<label />', { 'for': 'filter_gene__' + value, text: value, 'style': 'white-space: nowrap;' })
$('<input />', { type: 'checkbox', id: 'filter__gene__' + value.split("__")[0], value: 'gene__' + value.split("__")[0], 'style': "margin-right: 4px;", class: 'ldexpress-data-filters' }),
$('<label />', { 'for': 'filter__gene__' + value.split("__")[0], text: value.split("__")[0], 'style': 'white-space: nowrap;' })
])
)
)
Expand All @@ -2674,10 +2674,10 @@ function populateTissueslistLDexpress(data) {
//Add the clipped list
$.each(data, function( index, value ){
$("#ldexpress-tissues-list").append(
$("<tr>").append(
$("<tr>", { class: 'ldexpress-tissues-list-rows', id: 'tissue__row__' + value.split("__")[1] }).append(
$("<td>", { 'style': 'white-space: nowrap; width: 150px;' }).append([
$('<input />', { type: 'checkbox', id: 'filter__tissue__' + value, value: 'tissue__' + value, 'style': 'margin-right: 4px;', class: 'ldexpress-data-filters' }),
$('<label />', { 'for': 'filter__tissue__' + value, text: value, 'style': 'white-space: nowrap;' })
$('<input />', { type: 'checkbox', id: 'filter__tissue__' + value.split("__")[1], value: 'tissue__' + value.split("__")[1], 'style': 'margin-right: 4px;', class: 'ldexpress-data-filters' }),
$('<label />', { 'for': 'filter__tissue__' + value.split("__")[1], text: value.split("__")[0], 'style': 'white-space: nowrap;' })
])
)
)
Expand Down Expand Up @@ -2940,55 +2940,214 @@ function initExpress(data, r2_d) {
selected_genes.push(checked_val);
}
if (category === "tissue") {
selected_tissues.push(checked_val.replace("(", "\\(").replace(")", "\\)"));
var displayTissueName = data.thinned_tissues.filter(function(el) {
return el.split("__")[1] === checked_val;
})
selected_tissues.push(displayTissueName[0].split("__")[0].replace("(", "\\(").replace(")", "\\)"));
}
}
});

// console.log("selected_snps", selected_snps);
// console.log("selected_genes", selected_genes);
// console.log("selected_tissues", selected_tissues);
// apply filters
var oTable = $('#new-ldexpress').dataTable();
if (selected_snps.length > 0) {
oTable.fnFilter(selected_snps.join("|"), 0, true, false);
} else {
oTable.fnFilter("", 0, true, false);
}
if (selected_genes.length > 0) {
oTable.fnFilter(selected_genes.join("|"), 5, true, false);
} else {
oTable.fnFilter("", 5, true, false);
}
if (selected_tissues.length > 0) {
oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
// show only genes available for tissue
// only register on tissue click
if ($(e.target).attr("id").split("__")[1] === "tissue") {
var newData = Array.from(oTable._('tr', {"filter":"applied"}));
var newGenes = [];
newData.forEach(function(row) {
newGenes.push(row[5].split("__")[0])
});
var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
$('.ldexpress-genes-list-rows').each(function(i, obj) {
if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
$(obj).show();
} else {
$('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
$(obj).hide();
}
});
oTable.fnFilter(selected_snps.join("|"), 0, true, false);
oTable.fnFilter(selected_genes.join("|"), 5, true, false);
oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
var newData = Array.from(oTable._('tr', {"filter":"applied"}));
var newSNPs = [];
var newGenes = [];
var newTissues = [];
newData.forEach(function(row) {
newSNPs.push(row[0]);
newGenes.push(row[5].split("__")[0]);
newTissues.push(row[7].split("__")[1]);
});
newSNPs = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
newGenes = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
newTissues = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// console.log("newSNPs", newSNPs);
// console.log("newGenes", newGenes);
// console.log("newTissues", newTissues);
$('.ldexpress-snps-list-rows').each(function(i, obj) {
if (newSNPs.includes($(obj).attr('id').split('__')[2])) {
$(obj).show();
} else {
$('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
$(obj).hide();
}
} else {
oTable.fnFilter("", 7, true, false);
var newData = Array.from(oTable._('tr', {"filter":"applied"}));
var newGenes = [];
newData.forEach(function(row) {
newGenes.push(row[5].split("__")[0])
});
var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
console.log("newGenesDistinct", newGenesDistinct);
$('.ldexpress-genes-list-rows').each(function(i, obj) {
});
$('.ldexpress-genes-list-rows').each(function(i, obj) {
if (newGenes.includes($(obj).attr('id').split('__')[2])) {
$(obj).show();
});
}
} else {
$('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
$(obj).hide();
}
});
$('.ldexpress-tissues-list-rows').each(function(i, obj) {
if (newTissues.includes($(obj).attr('id').split('__')[2])) {
$(obj).show();
} else {
$('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
$(obj).hide();
}
});


// // refresh all filter options when other snp filters added
// if (selected_snps.length > 0) {
// oTable.fnFilter(selected_snps.join("|"), 0, true, false);
// if ($(e.target).attr("id").split("__")[1] === "snp") {
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newGenes = [];
// var newTissues = [];
// newData.forEach(function(row) {
// newGenes.push(row[5].split("__")[0]);
// newTissues.push(row[7].split("__")[0]);
// });
// var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-genes-list-rows').each(function(i, obj) {
// if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
// $(obj).show();
// } else {
// $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// }
// });
// var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-tissues-list-rows').each(function(i, obj) {
// if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
// $(obj).show();
// } else {
// $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// }
// });
// }
// } else {
// oTable.fnFilter("", 0, true, false);
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newGenes = [];
// var newTissues = [];
// newData.forEach(function(row) {
// newGenes.push(row[5].split("__")[0]);
// newTissues.push(row[7].split("__")[0]);
// });
// var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-genes-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-tissues-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// }
// // refresh all filter options when gene filters added
// if (selected_genes.length > 0) {
// oTable.fnFilter(selected_genes.join("|"), 5, true, false);
// // show only tissues available for gene
// // only register on gene click
// if ($(e.target).attr("id").split("__")[1] === "gene") {
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newTissues = [];
// var newSNPs = [];
// newData.forEach(function(row) {
// newTissues.push(row[7].split("__")[1]);
// newSNPs.push(row[0]);
// });
// var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-tissues-list-rows').each(function(i, obj) {
// if (newTissuesDistinct.includes($(obj).attr('id').split('__')[2])) {
// $(obj).show();
// } else {
// $('#filter__tissue__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// }
// });
// var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// console.log("newSNPsDistinct", newSNPsDistinct);
// $('.ldexpress-snps-list-rows').each(function(i, obj) {
// if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
// console.log("reached 1");
// $(obj).show();
// } else {
// $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// console.log("reached 2");
// }
// });
// }
// } else {
// oTable.fnFilter("", 5, true, false);
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newTissues = [];
// var newSNPs = [];
// newData.forEach(function(row) {
// newTissues.push(row[7].split("__")[0]);
// newSNPs.push(row[0]);
// });
// var newTissuesDistinct = newTissues.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-tissues-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-snps-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// }
// // refresh all filter options when other tissue filters added
// if (selected_tissues.length > 0) {
// oTable.fnFilter(selected_tissues.join("|"), 7, true, false);
// // show only genes available for tissue
// // only register on tissue click
// if ($(e.target).attr("id").split("__")[1] === "tissue") {
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newGenes = [];
// var newSNPs = [];
// newData.forEach(function(row) {
// newGenes.push(row[5].split("__")[0]);
// newSNPs.push(row[0]);
// });
// var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-genes-list-rows').each(function(i, obj) {
// if (newGenesDistinct.includes($(obj).attr('id').split('__')[2])) {
// $(obj).show();
// } else {
// $('#filter__gene__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// }
// });
// var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-snps-list-rows').each(function(i, obj) {
// if (newSNPsDistinct.includes($(obj).attr('id').split('__')[2])) {
// $(obj).show();
// } else {
// $('#filter__snp__' + $(obj).attr('id').split('__')[2]).prop("checked", false);
// $(obj).hide();
// }
// });
// }
// } else {
// oTable.fnFilter("", 7, true, false);
// var newData = Array.from(oTable._('tr', {"filter":"applied"}));
// var newGenes = [];
// var newSNPs = [];
// newData.forEach(function(row) {
// newGenes.push(row[5].split("__")[0]);
// newSNPs.push(row[0]);
// });
// var newGenesDistinct = newGenes.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-genes-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// var newSNPsDistinct = newSNPs.filter((item, i, ar) => ar.indexOf(item) === i).sort();
// $('.ldexpress-snps-list-rows').each(function(i, obj) {
// $(obj).show();
// });
// }
});

if(data.details.queryWarnings && data.details.queryWarnings.aaData.length > 0) {
Expand Down Expand Up @@ -3029,7 +3188,6 @@ function initExpressTissues() {
});
ajaxRequest.success(function(data) {
if (displayError(id, data) == false) {
// ldExpressTissues = data;
buildTissueDropdown(id + "-tissue-codes", data);
} else {
buildTissueDropdown("ldexpress-tissue-codes", data);
Expand Down
20 changes: 10 additions & 10 deletions LDlink/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -882,31 +882,31 @@ <h2 class="text-center">LDexpress Tool<sup><a class="help-anchor-link glyphicon
</thead> -->
<tbody id="ldexpress-snp-list" style="display: block; max-height: 350px; overflow-y: auto; overflow-x: auto; max-width: 150px; min-width: 150px;"></tbody>
</table>
<!-- thinned tissues -->
<!-- thinned genes -->
<table class="ldexpress-table-thin table table-striped table-chip" style="position: relative;">
<caption>
<span id="toggle-show-ldexpress-thin-tissues" class="toggle-show-thinned mr-1 glyphicon glyphicon-minus" aria-hidden="true"></span>
Tissues with GTEx QTL
<span id="toggle-show-ldexpress-thin-genes" class="toggle-show-thinned mr-1 glyphicon glyphicon-minus" aria-hidden="true"></span>
Genes with GTEx QTL
</caption>
<!-- <thead>
<tr>
<th>Tissues</th>
<th>Genes</th>
</tr>
</thead> -->
<tbody id="ldexpress-tissues-list" style="display: block; max-height: 350px; overflow-y: auto; overflow-x: auto; max-width: 150px; min-width: 150px;"></tbody>
<tbody id="ldexpress-genes-list" style="display: block; max-height: 350px; overflow-y: auto; overflow-x: auto; max-width: 150px; min-width: 150px;"></tbody>
</table>
<!-- thinned genes -->
<!-- thinned tissues -->
<table class="ldexpress-table-thin table table-striped table-chip" style="position: relative;">
<caption>
<span id="toggle-show-ldexpress-thin-genes" class="toggle-show-thinned mr-1 glyphicon glyphicon-minus" aria-hidden="true"></span>
Genes with GTEx QTL
<span id="toggle-show-ldexpress-thin-tissues" class="toggle-show-thinned mr-1 glyphicon glyphicon-minus" aria-hidden="true"></span>
Tissues with GTEx QTL
</caption>
<!-- <thead>
<tr>
<th>Genes</th>
<th>Tissues</th>
</tr>
</thead> -->
<tbody id="ldexpress-genes-list" style="display: block; max-height: 350px; overflow-y: auto; overflow-x: auto; max-width: 150px; min-width: 150px;"></tbody>
<tbody id="ldexpress-tissues-list" style="display: block; max-height: 350px; overflow-y: auto; overflow-x: auto; max-width: 150px; min-width: 150px;"></tbody>
</table>
<!-- warnings, if any -->
<a id="ldexpress-query-warnings-button" title="View details.">Variants with Warnings</a>
Expand Down

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